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    Page not found (404)

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    Site built with pkgdown 2.0.7.

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    @@ -28,7 +28,7 @@
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    Pull requests -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

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    License

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    Site built with pkgdown 2.0.7.

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    Custom analyses - -

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    Custom analyses

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    Site built with pkgdown 2.0.7.

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    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png index 65a9b03f..5872498b 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png differ diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline-1.png index 859b59a1..30072f44 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline-1.png differ diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline_more-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline_more-1.png index d0f1d32d..d2ac3e5a 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline_more-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline_more-1.png differ diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_default-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_default-1.png index 2b541c90..d8f30f43 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_default-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_default-1.png differ diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_flex-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_flex-1.png index 34d6d677..48f315df 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_flex-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_flex-1.png differ diff --git a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_stiff-1.png b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_stiff-1.png index d3727620..6e0c5c5a 100644 Binary files a/docs/articles/abfit-baseline-opts_files/figure-html/abfit_stiff-1.png and b/docs/articles/abfit-baseline-opts_files/figure-html/abfit_stiff-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 10698206..b722cf67 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,9 +1,9 @@ -Articles • Spectroscopy Analysis Tools (spant)Articles • Spectroscopy Analysis Tools (spant) - +
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    All vignettes

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html index f1b9d819..7ddfdbe0 100644 --- a/docs/articles/spant-basis-simulation.html +++ b/docs/articles/spant-basis-simulation.html @@ -12,21 +12,19 @@ - + - - - +
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    Basis simulation - -

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    Basis simulation

    -

    Site built with pkgdown 2.0.7.

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    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html index aa3da6d1..87e1f557 100644 --- a/docs/articles/spant-intro.html +++ b/docs/articles/spant-intro.html @@ -12,21 +12,19 @@ - + - - - +
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    Basis simulation
     fit_res$res_tab
 #>   X Y Z Dynamic Coil X.CrCH2          Ala          Asp           Cr
-#> 1 1 1 1       1    1       0 8.228912e-06 3.548337e-05 4.020305e-05
+#> 1 1 1 1       1    1       0 8.133802e-06 3.547064e-05 4.026719e-05
 #>           GABA          Glc          Gln          GSH          Glu          GPC
-#> 1 1.706754e-05 2.442067e-06 3.029726e-06 2.227786e-05 6.499645e-05 1.603288e-05
+#> 1 1.697276e-05 2.446591e-06 3.036118e-06 2.228048e-05 6.503219e-05 1.606706e-05
 #>            Ins          Lac        Lip09       Lip13a Lip13b Lip20         MM09
-#> 1 5.902957e-05 5.818739e-06 2.362972e-05 2.635502e-06      0     0 9.887557e-06
-#>           MM12        MM14         MM17         MM20          NAA         NAAG
-#> 1 6.546986e-06 2.59994e-05 2.245507e-05 9.207418e-05 5.981787e-05 1.556188e-05
-#>   PCh          PCr         sIns Tau         tNAA          tCr         tCho
-#> 1   0 2.101297e-05 6.508636e-06   0 7.537975e-05 6.121601e-05 1.603288e-05
-#>            Glx        tLM09        tLM13        tLM20   X.CrCH2.sd       Ala.sd
-#> 1 6.802617e-05 3.351728e-05 3.518189e-05 9.207418e-05 2.383751e-06 4.353306e-06
+#> 1 5.906155e-05 5.802244e-06 2.387705e-05 2.670583e-06      0     0 9.630767e-06
+#>           MM12         MM14         MM17         MM20          NAA        NAAG
+#> 1 6.511376e-06 2.603852e-05 2.238403e-05 9.203742e-05 6.011109e-05 1.53653e-05
+#>   PCh          PCr         sIns Tau         tNAA         tCr         tCho
+#> 1   0 2.101921e-05 6.504096e-06   0 7.547639e-05 6.12864e-05 1.606706e-05
+#>           Glx        tLM09        tLM13        tLM20   X.CrCH2.sd       Ala.sd
+#> 1 6.80683e-05 3.350782e-05 3.522048e-05 9.203742e-05 2.386862e-06 4.343934e-06
 #>         Asp.sd        Cr.sd      GABA.sd       Glc.sd       Gln.sd       GSH.sd
-#> 1 9.243626e-06 3.715175e-06 4.580082e-06 4.427045e-06 5.089143e-06 2.022836e-06
+#> 1 9.235327e-06 3.689004e-06 4.574399e-06 4.421682e-06 5.083001e-06 2.020427e-06
 #>         Glu.sd       GPC.sd       Ins.sd       Lac.sd     Lip09.sd    Lip13a.sd
-#> 1 5.086888e-06 2.525936e-06 2.091039e-06 5.311855e-06 4.118786e-06 1.328562e-05
+#> 1 5.082976e-06 2.602652e-06 2.093225e-06 5.301706e-06 4.119256e-06 1.328304e-05
 #>      Lip13b.sd     Lip20.sd      MM09.sd      MM12.sd      MM14.sd      MM17.sd
-#> 1 6.477225e-06 7.510915e-06 3.827221e-06 4.597884e-06 7.234429e-06 3.810268e-06
+#> 1 6.474468e-06 7.510908e-06 3.827554e-06 4.594028e-06 7.223426e-06 3.811301e-06
 #>        MM20.sd       NAA.sd      NAAG.sd       PCh.sd       PCr.sd      sIns.sd
-#> 1 8.602464e-06 1.015226e-06 1.215672e-06 2.174697e-06 3.108036e-06 7.233855e-07
-#>         Tau.sd      tNAA.sd       tCr.sd    tCho.sd       Glx.sd     tLM09.sd
-#> 1 3.777984e-06 7.031059e-07 5.881706e-07 2.1135e-07 3.165045e-06 1.006532e-06
-#>       tLM13.sd     tLM20.sd    phase       lw        shift      asym
-#> 1 1.572003e-06 3.018189e-06 11.15087 5.038937 -0.003427612 0.1764497
+#> 1 8.595853e-06 1.017711e-06 1.208984e-06 2.236874e-06 3.084599e-06 7.240069e-07
+#>         Tau.sd      tNAA.sd       tCr.sd      tCho.sd      Glx.sd     tLM09.sd
+#> 1 3.759957e-06 7.031382e-07 5.890482e-07 2.110662e-07 3.16966e-06 1.006794e-06
+#>       tLM13.sd     tLM20.sd    phase       lw       shift      asym
+#> 1 1.573147e-06 3.016809e-06 11.10963 5.023682 -0.00376505 0.1771067
 #>   res.deviance res.niter res.info
-#> 1 7.300317e-05        28        2
+#> 1 7.307671e-05        28        2
 #>                                                        res.message bl_ed_pppm
 #> 1 Relative error between `par' and the solution is at most `ptol'.   2.364083
-#>   max_bl_flex_used     full_res fit_pts ppm_range      SNR      SRR      FQN
-#> 1            FALSE 7.745303e-05     497       3.8 62.79191 51.44068 1.490027
-#>      tNAA_lw     tCr_lw    tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.04565271 0.05199592 0.05438808      -8.904402          -8.947808
+#>   max_bl_flex_used    full_res   spec_resid fit_pts ppm_range      SNR      SRR
+#> 1            FALSE 7.75437e-05 7.307671e-05     497       3.8 62.71686 51.33279
+#>        FQN    tNAA_lw     tCr_lw    tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
+#> 1 1.492722 0.04562445 0.05189506 0.05438237      -8.900349          -8.944159
 #>   auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
-#> 1          -8.980941         -9.003463          -9.016574          -9.023969
+#> 1          -8.977355         -9.000064          -9.013367           -9.02055
 #>   auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
-#> 1          -9.027876          -9.027566          -9.014311          -8.963287
+#> 1          -9.024177          -9.023462          -9.009854          -8.958654
 #>   auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-#> 1         -8.848747          -8.694785          -8.565992          -8.488415
+#> 1         -8.844271          -8.690744           -8.56263          -8.485471
 #>   auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1          -8.449874          -8.432813          -8.425648          -8.42266
+#> 1          -8.447135          -8.430173          -8.423052         -8.420085
 #>   auto_bl_crit_0.532 auto_bl_crit_0.529
-#> 1          -8.421406          -8.420875

    +#> 1 -8.418839 -8.418312

    Note that signal names appended with “.sd” are the CRLB estimates for the uncertainty (standard deviation) in the metabolite quantity estimate. e.g. to calculate the percentage s.d. for tNAA:

     fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9327517
    +#> [1] 0.9316002

    Spectral SNR:

     fit_res$res_tab$SNR
-#> [1] 62.79191
    +#> [1] 62.71686

    Linewidth of the tNAA resonance in PPM:

     fit_res$res_tab$tNAA_lw
-#> [1] 0.04565271
    +#> [1] 0.04562445

    Ratios to total-creatine @@ -264,39 +262,39 @@

    Ratios to total-creatineprint(t(amps)) #> [,1] #> X.CrCH2 0.00000000 -#> Ala 0.13442417 -#> Asp 0.57964197 -#> Cr 0.65674069 -#> GABA 0.27880838 -#> Glc 0.03989262 -#> Gln 0.04949238 -#> GSH 0.36392207 -#> Glu 1.06175561 -#> GPC 0.26190670 -#> Ins 0.96428305 -#> Lac 0.09505257 -#> Lip09 0.38600560 -#> Lip13a 0.04305248 +#> Ala 0.13271789 +#> Asp 0.57876852 +#> Cr 0.65703306 +#> GABA 0.27694176 +#> Glc 0.03992062 +#> Gln 0.04953983 +#> GSH 0.36354693 +#> Glu 1.06111932 +#> GPC 0.26216353 +#> Ins 0.96369742 +#> Lac 0.09467424 +#> Lip09 0.38959787 +#> Lip13a 0.04357545 #> Lip13b 0.00000000 #> Lip20 0.00000000 -#> MM09 0.16151913 -#> MM12 0.10694891 -#> MM14 0.42471563 -#> MM17 0.36681686 -#> MM20 1.50408643 -#> NAA 0.97716047 -#> NAAG 0.25421252 +#> MM09 0.15714362 +#> MM12 0.10624504 +#> MM14 0.42486612 +#> MM17 0.36523650 +#> MM20 1.50175914 +#> NAA 0.98082262 +#> NAAG 0.25071302 #> PCh 0.00000000 -#> PCr 0.34325931 -#> sIns 0.10632244 +#> PCr 0.34296694 +#> sIns 0.10612625 #> Tau 0.00000000 -#> tNAA 1.23137299 +#> tNAA 1.23153565 #> tCr 1.00000000 -#> tCho 0.26190670 -#> Glx 1.11124799 -#> tLM09 0.54752473 -#> tLM13 0.57471702 -#> tLM20 1.50408643

    +#> tCho 0.26216353 +#> Glx 1.11065914 +#> tLM09 0.54674149 +#> tLM13 0.57468661 +#> tLM20 1.50175914

    Water reference scaling, AKA “absolute-quantification” @@ -317,7 +315,7 @@

    Water reference sca TR = 2 fit_res_molal <- scale_amp_molal_pvc(fit_res, mrs_data_wref, p_vols, TE, TR) fit_res_molal$res_tab$tNAA -#> [1] 12.58176

    +#> [1] 12.59789

    An alternative method scales the metabolite values into molar (mM) units (mol / Litre of tissue) based on assumptions outlined in the LCModel manual and references therein (section 10.2). This approach may @@ -326,7 +324,7 @@

    Water reference sca 
     fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
 fit_res_molar$res_tab$tNAA
-#> [1] 6.817594
    +#> [1] 6.826335

    Note, while “absolute” units are attractive, a large number of assumptions about metabolite and water relaxation rates are necessary to arrive at these mM estimates. If you’re not confident at being able to @@ -339,9 +337,7 @@

    Water reference sca + @@ -354,16 +350,16 @@

    Water reference sca

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png index b84cd2d5..3640c474 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png index 15bdc4e5..94a3f545 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png index 11e79ce5..cceccee8 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html index e6efca00..7aeab964 100644 --- a/docs/articles/spant-metabolite-simulation.html +++ b/docs/articles/spant-metabolite-simulation.html @@ -12,21 +12,19 @@ - + - - - +
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    Custom molecules

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html index 28e38762..1db3d7dc 100644 --- a/docs/articles/spant-preprocessing.html +++ b/docs/articles/spant-preprocessing.html @@ -12,21 +12,19 @@ - + - - - +
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    Reading raw data and plotting - -

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    Reading raw data and plotting

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png index 02bdd7ca..d9d919b3 100644 Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png index f8a9f999..9cc14061 100644 Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/authors.html b/docs/authors.html index fd4064a4..0c1de77b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • Spectroscopy Analysis Tools (spant)Authors and Citation • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    -

    Authors

    +

    Authors and Citation

    - +

    • Martin Wilson. Maintainer, author.

    • -

      Yong Wang. Contributor. +

      Yong Wang. Contributor.

    • -

      John Muschelli. Contributor. +

      John Muschelli. Contributor.

    @@ -140,15 +140,15 @@

    Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/index.html b/docs/index.html index 6e715d8e..996301cf 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,16 +12,13 @@ - + - + - +
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    Developers

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index eaf34846..b4f0073c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,9 +1,9 @@ -Changelog • Spectroscopy Analysis Tools (spant)Changelog • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -73,7 +73,19 @@

    Changelog

    -

    spant 2.21.0

    +

    spant 2.23.0

    +
    • abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
      • +
    • Added function to calculate the correlation matrix from a basis_set.
      • +
    • Fix for RDA files where a comma is sometimes used as a decimal point.
      • +
    +
    +

    spant 2.22.02024-07-11

    +
    • Added find_bids_mrs and mrs_data2bids helper functions.
      • +
    • Improved handling of CMRR semi-LASER SVS water reference scans.
      • +
    • Added functions for GLS coil combination.
      • +
    +
    +

    spant 2.21.02024-05-30

    • Fixed compiler warnings for Fortran code.
    • Added glm_spec function.
    • Added add_noise_spec_snr function.
      • @@ -584,15 +596,15 @@

      spant 0.1.02

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 510f032e..e4a8a1ed 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.1 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.1.0 pkgdown_sha: ~ articles: abfit-baseline-opts: abfit-baseline-opts.html @@ -7,8 +7,7 @@ articles: spant-intro: spant-intro.html spant-metabolite-simulation: spant-metabolite-simulation.html spant-preprocessing: spant-preprocessing.html -last_built: 2024-05-29T18:39Z +last_built: 2024-08-27T13:06Z urls: reference: https://martin3141.github.io/spant/reference article: https://martin3141.github.io/spant/articles - diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html index 1372d866..e8bdf2fc 100644 --- a/docs/reference/Arg.mrs_data.html +++ b/docs/reference/Arg.mrs_data.html @@ -1,9 +1,9 @@ -Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant)Apply Arg operator to an MRS dataset. — Arg.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,21 @@

    Apply Arg operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Arg(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Arg operator.

    +

    MRS data following Arg operator.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html index 794d446f..04c05156 100644 --- a/docs/reference/Conj.mrs_data.html +++ b/docs/reference/Conj.mrs_data.html @@ -1,9 +1,9 @@ -Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant)Apply Conj operator to an MRS dataset. — Conj.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,21 @@

    Apply Conj operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Conj(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Conj operator.

    +

    MRS data following Conj operator.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html index 4c9a70eb..b6ad94cb 100644 --- a/docs/reference/Im.mrs_data.html +++ b/docs/reference/Im.mrs_data.html @@ -1,9 +1,9 @@ -Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant)Apply Im operator to an MRS dataset. — Im.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,21 @@

    Apply Im operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Im(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Im operator.

    +

    MRS data following Im operator.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html index a3eeaed6..23333bdd 100644 --- a/docs/reference/Imzap.html +++ b/docs/reference/Imzap.html @@ -1,12 +1,10 @@ -Complex rounding function taken from complexplus package to reduce the number -of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant)Complex rounding function taken from complexplus package to reduce the number of spant dependencies. — Imzap • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Complex rounding function taken from complexplus package to reduce the number -of spant dependencies.

    +

    Complex rounding function taken from complexplus package to reduce the number of spant dependencies.

    Source: R/utils.R
    @@ -88,11 +85,13 @@

    Complex rounding function taken from complexplus package to reduce the numbe

    Arguments

    -
    x
    + + +
    x

    a scalar or vector, real or complex.

    -
    tol
    +
    tol

    a tolerance, 10^-6 by default. Prevents possible numerical problems. Can be set to 0 if desired.

    @@ -110,15 +109,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html index 45b7e781..6337326a 100644 --- a/docs/reference/Mod.mrs_data.html +++ b/docs/reference/Mod.mrs_data.html @@ -1,9 +1,9 @@ -Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant)Apply Mod operator to an MRS dataset. — Mod.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,21 @@

    Apply Mod operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Mod(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Mod operator.

    +

    MRS data following Mod operator.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html index 503ce5c0..0fc69d61 100644 --- a/docs/reference/Ncoils.html +++ b/docs/reference/Ncoils.html @@ -1,9 +1,9 @@ -Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant)Return the total number of coil elements in an MRS dataset. — Ncoils • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of coil elements in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html index 49c3ebb2..5c7494ff 100644 --- a/docs/reference/Ndyns.html +++ b/docs/reference/Ndyns.html @@ -1,9 +1,9 @@ -Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant)Return the total number of dynamic scans in an MRS dataset. — Ndyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of dynamic scans in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html index c63fe64e..b2ede244 100644 --- a/docs/reference/Npts.html +++ b/docs/reference/Npts.html @@ -1,9 +1,9 @@ -Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant)Return the number of data points in an MRS dataset. — Npts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the number of data points in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    number of data points.

    +

    number of data points.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html index e5f2464a..43958e75 100644 --- a/docs/reference/Nspec.html +++ b/docs/reference/Nspec.html @@ -1,9 +1,9 @@ -Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant)Return the total number of spectra in an MRS dataset. — Nspec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of spectra in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html index 3d3ce629..5dd57f2c 100644 --- a/docs/reference/Ntrans.html +++ b/docs/reference/Ntrans.html @@ -1,9 +1,9 @@ -Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant)Return the total number of acquired transients for an MRS dataset. — Ntrans • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of acquired transients for an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html index beb130b8..45cb2564 100644 --- a/docs/reference/Nx.html +++ b/docs/reference/Nx.html @@ -1,9 +1,9 @@ -Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant)Return the total number of x locations in an MRS dataset. — Nx • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of x locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html index 5c23ee37..3684d739 100644 --- a/docs/reference/Ny.html +++ b/docs/reference/Ny.html @@ -1,9 +1,9 @@ -Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant)Return the total number of y locations in an MRS dataset. — Ny • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of y locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html index 2a28bfbb..b69e802d 100644 --- a/docs/reference/Nz.html +++ b/docs/reference/Nz.html @@ -1,9 +1,9 @@ -Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant)Return the total number of z locations in an MRS dataset. — Nz • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Return the total number of z locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html index bbdcd3e7..465d33c6 100644 --- a/docs/reference/Re.mrs_data.html +++ b/docs/reference/Re.mrs_data.html @@ -1,9 +1,9 @@ -Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant)Apply Re operator to an MRS dataset. — Re.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,21 @@

    Apply Re operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Re(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Re operator.

    +

    MRS data following Re operator.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html index d501fc2a..3f64f6f5 100644 --- a/docs/reference/abfit_opts.html +++ b/docs/reference/abfit_opts.html @@ -1,9 +1,9 @@ -Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant)Return a list of options for an ABfit analysis. — abfit_opts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -81,7 +81,8 @@

    Return a list of options for an ABfit analysis.

    abfit_opts(
   init_damping = 5,
   maxiters = 1024,
-  max_shift = 0.078,
+  max_shift_pre = 0.078,
+  max_shift_fine = NULL,
   max_damping = 15,
   max_phase = 360,
   lambda = NULL,
@@ -114,245 +115,270 @@ 
    Return a list of options for an ABfit analysis.
    
   phi1_optim = FALSE,
   phi1_init = 0,
   max_dphi1 = 0.2,
-  max_basis_shift_broad = 0.0078,
-  max_basis_damping_broad = 2,
+  max_basis_shift_broad = NULL,
+  max_basis_damping_broad = NULL,
   ahat_calc_method = "lh_pnnls",
   prefit_phase_search = TRUE,
   freq_reg = NULL,
+  freq_reg_naa = NULL,
   lb_reg = NULL,
   output_all_paras = FALSE,
   output_all_paras_raw = FALSE,
   input_paras_raw = NULL,
   optim_lw_only = FALSE,
   optim_lw_only_limit = 20,
-  lb_init = 0.001
+  lb_init = 0.001,
+  lb_init_approx_fit = FALSE,
+  zf_offset = NULL
 )

    Arguments

    -
    init_damping
    + + +
    init_damping

    initial value of the Gaussian global damping parameter (Hz). Very poorly shimmed or high field data may benefit from a larger value.

    -
    maxiters
    +
    maxiters

    The maximum number of iterations to run for the detailed fit.

    -
    max_shift
    -

    The maximum allowable shift to be applied in the -optimisation phase of fitting (ppm).

    +
    max_shift_pre
    +

    The maximum allowable global shift to be applied in the +approximate (pre-fit) phases of analysis (ppm).

    + +
    max_shift_fine
    +

    The maximum allowable global shift to be applied in the +detailed fit phase of analysis (ppm).

    -
    max_damping
    + +
    max_damping

    maximum permitted value of the global damping parameter (Hz).

    -
    max_phase
    +
    max_phase

    the maximum absolute permitted value of the global zero-order phase term (degrees). Note, the prefit_phase_search option is not constrained by this term.

    -
    lambda
    +
    lambda

    manually set the the baseline smoothness parameter.

    -
    ppm_left
    +
    ppm_left

    downfield frequency limit for the fitting range (ppm).

    -
    ppm_right
    +
    ppm_right

    upfield frequency limit for the fitting range (ppm).

    -
    zp
    +
    zp

    zero pad the data to twice the original length before fitting.

    -
    bl_ed_pppm
    +
    bl_ed_pppm

    manually set the the baseline smoothness parameter (ED per ppm).

    -
    auto_bl_flex
    +
    auto_bl_flex

    automatically determine the level of baseline smoothness.

    -
    bl_comps_pppm
    +
    bl_comps_pppm

    spline basis density (signals per ppm).

    -
    export_sp_fit
    +
    export_sp_fit

    add the fitted spline functions to the fit result.

    -
    max_asym
    +
    max_asym

    maximum allowable value of the asymmetry parameter.

    -
    max_basis_shift
    +
    max_basis_shift

    maximum allowable frequency shift for individual basis signals (ppm).

    -
    max_basis_damping
    +
    max_basis_damping

    maximum allowable Lorentzian damping factor for individual basis signals (Hz).

    -
    maxiters_pre
    +
    maxiters_pre

    maximum iterations for the coarse (pre-)fit.

    -
    algo_pre
    +
    algo_pre

    optimisation method for the coarse (pre-)fit.

    -
    min_bl_ed_pppm
    +
    min_bl_ed_pppm

    minimum value for the candidate baseline flexibility analyses (ED per ppm).

    -
    max_bl_ed_pppm
    +
    max_bl_ed_pppm

    minimum value for the candidate baseline flexibility analyses (ED per ppm).

    -
    auto_bl_flex_n
    +
    auto_bl_flex_n

    number of candidate baseline analyses to perform.

    -
    pre_fit_bl_ed_pppm
    +
    pre_fit_bl_ed_pppm

    level of baseline flexibility to use in the coarse fitting stage of the algorithm (ED per ppm).

    -
    remove_lip_mm_prefit
    +
    remove_lip_mm_prefit

    remove broad signals in the coarse fitting stage of the algorithm.

    -
    pre_align
    +
    pre_align

    perform a pre-alignment step before coarse fitting.

    -
    max_pre_align_shift
    +
    max_pre_align_shift

    maximum allowable shift in the pre-alignment step (ppm).

    -
    pre_align_ref_freqs
    +
    pre_align_ref_freqs

    a vector of prominent spectral frequencies used in the pre-alignment step (ppm).

    -
    noise_region
    +
    noise_region

    spectral region to estimate the noise level (ppm).

    -
    optimal_smooth_criterion
    +
    optimal_smooth_criterion

    method to determine the optimal smoothness.

    -
    aic_smoothing_factor
    -

    modification factor for the AIC calculation.

    +
    aic_smoothing_factor
    +

    modification factor for the AIC calculation. +Larger values result in less flexible baselines.

    -
    anal_jac
    +
    anal_jac

    use a analytical approximation to the jacobian in the detailed fitting stage.

    -
    pre_fit_ppm_left
    +
    pre_fit_ppm_left

    downfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

    -
    pre_fit_ppm_right
    +
    pre_fit_ppm_right

    upfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

    -
    phi1_optim
    +
    phi1_optim

    apply and optimise a frequency dependant phase term.

    -
    phi1_init
    +
    phi1_init

    initial value for the frequency dependant phase term (ms).

    -
    max_dphi1
    +
    max_dphi1

    maximum allowable change from the initial frequency dependant phase term (ms).

    -
    max_basis_shift_broad
    +
    max_basis_shift_broad

    maximum allowable shift for broad signals in the -basis (ppm). Determined based on their name beginning with Lip or MM.

    +basis (ppm). Determined based on their name beginning with Lip or MM. The +default value is set to max_basis_shift.

    -
    max_basis_damping_broad
    +
    max_basis_damping_broad

    maximum allowable Lorentzian damping for broad signals in the basis (Hz). Determined based on their name beginning with Lip -or MM.

    +or MM. The default value is set to max_basis_damping.

    -
    ahat_calc_method
    +
    ahat_calc_method

    method to calculate the metabolite amplitudes. May be one of: "lh_pnnls" or "ls".

    -
    prefit_phase_search
    +

    perform a 1D search for the optimal phase in the prefit stage of the algorithm.

    -
    freq_reg
    +
    freq_reg

    frequency shift parameter.

    -
    lb_reg
    +
    freq_reg_naa
    +

    frequency shift parameter for NAA and NAAG.

    + + +
    lb_reg

    individual line broadening parameter.

    -
    output_all_paras
    +
    output_all_paras

    include more fitting parameters in the fit table, e.g. individual shift and damping factors for each basis set element.

    -
    output_all_paras_raw
    +
    output_all_paras_raw

    include raw fitting parameters in the fit table. For advanced diagnostic use only.

    -
    input_paras_raw
    +
    input_paras_raw

    input raw fitting parameters. For advanced diagnostic use only.

    -
    optim_lw_only
    +
    optim_lw_only

    optimize the global line-broadening term only.

    -
    optim_lw_only_limit
    +
    optim_lw_only_limit

    limits for the line-breading term as a percentage of the starting value when optim_lw_only is TRUE.

    -
    lb_init
    -

    initial Lorentzian line broadening value for the individual -basis signals. Setting to 0 will clash with the minimum allowable value -(eg hard constraint) during the detailed fit.

    +
    lb_init
    +

    initial Lorentzian line broadening value (in Hz) for the +individual basis signals. Setting to 0 will clash with the minimum allowable +value (eg hard constraint) during the detailed fit.

    + + +
    lb_init_approx_fit
    +

    apply lb_init to the basis during the approximate +iterative fit.

    + + +
    zf_offset
    +

    offset in number of data points from the end of the FID to +zero-fill. Default is NULL and will automatically set this to 50 points when +the FID distortion flag is set for the mrs_data.

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -372,15 +398,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html index 1c128a05..dd0b6c95 100644 --- a/docs/reference/abfit_opts_v1_9_0.html +++ b/docs/reference/abfit_opts_v1_9_0.html @@ -1,12 +1,10 @@ -Return a list of options for an ABfit analysis to maintain comparability with -analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant)Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant. — abfit_opts_v1_9_0 • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a list of options for an ABfit analysis to maintain comparability with -analyses performed with version 1.9.0 (and earlier) of spant.

    +

    Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.

    Source: R/abfit.R
    @@ -88,15 +85,15 @@

    Return a list of options for an ABfit analysis to maintain comparability wit

    Arguments

    -
    ...
    + + +
    ...

    arguments passed to abfit_opts.

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html index 4067010c..dc221a42 100644 --- a/docs/reference/acquire.html +++ b/docs/reference/acquire.html @@ -1,9 +1,9 @@ -Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant)Simulate pulse sequence acquisition. — acquire • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Simulate pulse sequence acquisition.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rec_phase
    +
    rec_phase

    receiver phase in degrees.

    -
    tol
    +
    tol

    ignore resonance amplitudes below this threshold.

    -
    detect
    +
    detect

    detection nuclei.

    -
    amp_scale
    +
    amp_scale

    scaling factor for the output amplitudes.

    Value

    - - -

    a list of resonance amplitudes and frequencies.

    +

    a list of resonance amplitudes and frequencies.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html index 5c395587..1f5afc54 100644 --- a/docs/reference/add_noise.html +++ b/docs/reference/add_noise.html @@ -1,9 +1,9 @@ -Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant)Add noise to an mrs_data object. — add_noise • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Add noise to an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to add noise to.

    -
    sd
    +
    sd

    standard deviation of the noise.

    -
    fd
    +
    fd

    generate the noise samples in the frequency-domain (TRUE) or time-domain (FALSE). This is required since the absolute value of the standard deviation of noise samples changes when data is Fourier transformed.

    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    mrs_data object with additive normally distributed noise.

    +

    mrs_data object with additive normally distributed noise.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html index f0072ef4..c685bf8b 100644 --- a/docs/reference/add_noise_spec_snr.html +++ b/docs/reference/add_noise_spec_snr.html @@ -1,9 +1,9 @@ -Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant)Add noise to an mrs_data object to match a given SNR. — add_noise_spec_snr • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,31 +78,41 @@

    Add noise to an mrs_data object to match a given SNR.

    - 
    add_noise_spec_snr(mrs_data, target_snr, sig_region = c(4, 0.5))
    + 
    add_noise_spec_snr(
+  mrs_data,
+  target_snr,
+  sig_region = c(4, 0.5),
+  ref_data = NULL
+)

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to add noise to.

    -
    target_snr
    +
    target_snr

    desired spectral SNR, note this assumes the input data is noise-free, eg simulated data. Note the SNR is estimated from the first scan in the dataset and the same noise level is added to all spectra.

    -
    sig_region
    +
    sig_region

    spectral limits to search for the strongest spectral data point.

    + +
    ref_data
    +

    measure the signal from the first scan in this reference data +and apply the same target noise level to mrs_data.

    +

    Value

    - - -

    mrs_data object with additive normally distributed noise.

    +

    mrs_data object with additive normally distributed noise.

    @@ -117,15 +127,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/align.html b/docs/reference/align.html index f61afc9f..0d500691 100644 --- a/docs/reference/align.html +++ b/docs/reference/align.html @@ -1,9 +1,9 @@ -Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant)Align spectra to a reference frequency using a convolution based method. — align • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -92,46 +92,46 @@

    Align spectra to a reference frequency using a convolution based method.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be aligned.

    -
    ref_freq
    +
    ref_freq

    reference frequency in ppm units. More than one frequency may be specified.

    -
    ref_amp
    +
    ref_amp

    amplitude value for the reference signal. More than one value may be specified to match the number of ref_freq signals.

    -
    zf_factor
    +
    zf_factor

    zero filling factor to increase alignment resolution.

    -
    lb
    +
    lb

    line broadening to apply to the reference signal.

    -
    max_shift
    +
    max_shift

    maximum allowable shift in Hz.

    -
    ret_df
    +
    ret_df

    return frequency shifts in addition to aligned data (logical).

    -
    mean_dyns
    +
    mean_dyns

    align the mean spectrum and apply the same shift to each dynamic.

    Value

    - - -

    aligned data object.

    +

    aligned data object.

    @@ -146,15 +146,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html index 35121da6..9c83a832 100644 --- a/docs/reference/apodise_xy.html +++ b/docs/reference/apodise_xy.html @@ -1,9 +1,9 @@ -Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant)Apodise MRSI data in the x-y direction with a k-space filter. — apodise_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Apodise MRSI data in the x-y direction with a k-space filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    -
    func
    -

    must be "hamming" or "gaussian".

    +
    func
    +

    must be "hamming", "hanning" or "gaussian".

    -
    w
    +
    w

    the reciprocal of the standard deviation for the Gaussian function.

    Value

    - - -

    apodised data.

    +

    apodised data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html index cf58e336..c581b9b1 100644 --- a/docs/reference/append_basis.html +++ b/docs/reference/append_basis.html @@ -1,9 +1,9 @@ -Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant)Combine a pair of basis set objects. — append_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Combine a pair of basis set objects.

    Arguments

    -
    basis_a
    + + +
    basis_a

    first basis.

    -
    basis_b
    +
    basis_b

    second basis.

    Value

    - - -

    combined basis set object.

    +

    combined basis set object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html index 6e2ead5b..7f777f0b 100644 --- a/docs/reference/append_coils.html +++ b/docs/reference/append_coils.html @@ -1,12 +1,10 @@ -Append MRS data across the coil dimension, assumes they matched across the -other dimensions. — append_coils • Spectroscopy Analysis Tools (spant)Append MRS data across the coil dimension, assumes they matched across the other dimensions. — append_coils • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Append MRS data across the coil dimension, assumes they matched across the -other dimensions.

    +

    Append MRS data across the coil dimension, assumes they matched across the other dimensions.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Append MRS data across the coil dimension, assumes they matched across the

    Arguments

    -
    ...
    + + +
    ...

    MRS data objects as arguments, or a list of MRS data objects.

    Value

    - - -

    a single MRS data object with the input objects concatenated together.

    +

    a single MRS data object with the input objects concatenated together.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/append_dyns.html b/docs/reference/append_dyns.html index f857be34..ff5e57cc 100644 --- a/docs/reference/append_dyns.html +++ b/docs/reference/append_dyns.html @@ -1,12 +1,10 @@ -Append MRS data across the dynamic dimension, assumes they matched across the -other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant)Append MRS data across the dynamic dimension, assumes they matched across the other dimensions. — append_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Append MRS data across the dynamic dimension, assumes they matched across the -other dimensions.

    +

    Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Append MRS data across the dynamic dimension, assumes they matched across th

    Arguments

    -
    ...
    + + +
    ...

    MRS data objects as arguments, or a list of MRS data objects.

    Value

    - - -

    a single MRS data object with the input objects concatenated together.

    +

    a single MRS data object with the input objects concatenated together.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/append_regs.html b/docs/reference/append_regs.html index 4c7ee0b5..21e85132 100644 --- a/docs/reference/append_regs.html +++ b/docs/reference/append_regs.html @@ -1,9 +1,9 @@ -Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant)Append multiple regressor data frames into a single data frame. — append_regs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Append multiple regressor data frames into a single data frame.

    Arguments

    -
    ...
    + + +
    ...

    input regressor data frames.

    Value

    - - -

    output regressor data frame.

    +

    output regressor data frame.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html index 0f2f4d55..4cee83da 100644 --- a/docs/reference/apply_axes.html +++ b/docs/reference/apply_axes.html @@ -1,9 +1,9 @@ -Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant)Apply a function over specified array axes. — apply_axes • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,27 @@

    Apply a function over specified array axes.

    Arguments

    -
    x
    + + +
    x

    an array.

    -
    axes
    +
    axes

    a vector of axes to apply fun over.

    -
    fun
    +
    fun

    function to be applied.

    -
    ...
    +
    ...

    optional arguments to fun.

    Value

    - - -

    array.

    +

    array.

    @@ -130,15 +130,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html index 22bc1933..e8b90b38 100644 --- a/docs/reference/apply_mrs.html +++ b/docs/reference/apply_mrs.html @@ -1,9 +1,9 @@ -Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant)Apply a function across given dimensions of a MRS data object. — apply_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,25 @@

    Apply a function across given dimensions of a MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    dims
    +
    dims

    dimensions to apply the function.

    -
    fun
    +
    fun

    name of the function.

    -
    ...
    +
    ...

    arguments to the function.

    -
    data_only
    +
    data_only

    return an array rather than an MRS data object.

    @@ -116,15 +118,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html index cae875cf..000cc7a6 100644 --- a/docs/reference/apply_pulse.html +++ b/docs/reference/apply_pulse.html @@ -1,9 +1,9 @@ -Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant)Simulate an RF pulse on a single spin. — apply_pulse • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,35 +83,35 @@

    Simulate an RF pulse on a single spin.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    spin_n
    +
    spin_n

    spin index.

    -
    angle
    +
    angle

    RF flip angle in degrees.

    -
    nuc
    +
    nuc

    nucleus influenced by the pulse.

    -
    xy
    +
    xy

    x or y pulse.

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -126,15 +126,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html index 26278811..9bc495db 100644 --- a/docs/reference/array2mrs_data.html +++ b/docs/reference/array2mrs_data.html @@ -1,12 +1,10 @@ -Convert a 7 dimensional array in into a mrs_data object. The array dimensions -should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant)Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID. — array2mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert a 7 dimensional array in into a mrs_data object. The array dimensions -should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

    +

    Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

    Source: R/mrs_data_proc.R
    @@ -85,45 +82,50 @@

    Convert a 7 dimensional array in into a mrs_data object. The array dimension 
    array2mrs_data(
   data_array,
-  fs = def_fs(),
-  ft = def_ft(),
-  ref = def_ref(),
-  nuc = def_nuc(),
+  mrs_data = NULL,
+  fs = NULL,
+  ft = NULL,
+  ref = NULL,
+  nuc = NULL,
   fd = FALSE
 )

    Arguments

    -
    data_array
    + + +
    data_array

    7d data array.

    -
    fs
    +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    nucleus that is resonant at the transmitter frequency.

    -
    fd
    +
    fd

    flag to indicate if the matrix is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -138,15 +140,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/auto_phase.html b/docs/reference/auto_phase.html index b2223ce4..3babeb08 100644 --- a/docs/reference/auto_phase.html +++ b/docs/reference/auto_phase.html @@ -1,15 +1,11 @@ -Perform zeroth-order phase correction based on the minimisation of the -squared difference between the real and magnitude components of the -spectrum. — auto_phase • Spectroscopy Analysis Tools (spant)Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum. — auto_phase • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Perform zeroth-order phase correction based on the minimisation of the -squared difference between the real and magnitude components of the -spectrum.

    +

    Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.

    Source: R/mrs_data_proc.R
    @@ -93,27 +87,27 @@

    Perform zeroth-order phase correction based on the minimisation of the

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    xlim
    +
    xlim

    frequency range (default units of PPM) to including in the phase.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    -
    ret_phase
    +
    ret_phase

    return phase values (logical).

    Value

    - - -

    MRS data object and phase values (optional).

    +

    MRS data object and phase values (optional).

    @@ -128,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/back_extrap_ar.html b/docs/reference/back_extrap_ar.html index 14cf25e3..6f09f8cc 100644 --- a/docs/reference/back_extrap_ar.html +++ b/docs/reference/back_extrap_ar.html @@ -1,9 +1,9 @@ -Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant)Back extrapolate time-domain data points using an autoregressive model. — back_extrap_ar • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,38 +90,38 @@

    Back extrapolate time-domain data points using an autoregressive model.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    extrap_pts
    +
    extrap_pts

    number of points to extrapolate.

    -
    pred_pts
    +
    pred_pts

    number of points to base the extrapolation on.

    -
    method
    +
    method

    character string specifying the method to fit the model. Must be one of the strings in the default argument (the first few characters are sufficient). Defaults to "burg".

    -
    rem_add
    +
    rem_add

    remove additional points from the end of the FID to maintain the original length of the dataset. Default to TRUE.

    -
    ...
    +
    ...

    additional arguments to specific methods, see ?ar.

    Value

    - - -

    back extrapolated data.

    +

    back extrapolated data.

    @@ -136,15 +136,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html index 1e334800..ed5a5612 100644 --- a/docs/reference/basis2dyn_mrs_data.html +++ b/docs/reference/basis2dyn_mrs_data.html @@ -1,9 +1,9 @@ -Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant)Convert a basis object to a dynamic mrs_data object. — basis2dyn_mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Convert a basis object to a dynamic mrs_data object.

    Arguments

    -
    basis
    + + +
    basis

    basis set object.

    -
    amps
    +
    amps

    a data frame with each column corresponding to a basis element and each row corresponding to each dynamic scan.

    -
    tr
    +
    tr

    the dataset repetition time in seconds.

    Value

    - - -

    a dynamic mrs_data object.

    +

    a dynamic mrs_data object.

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html index d712d28f..60be6333 100644 --- a/docs/reference/basis2mrs_data.html +++ b/docs/reference/basis2mrs_data.html @@ -1,12 +1,10 @@ -Convert a basis object to an mrs_data object - where basis signals are spread -across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant)Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension. — basis2mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert a basis object to an mrs_data object - where basis signals are spread -across the dynamic dimension.

    +

    Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.

    Source: R/basis_set.R
    @@ -83,33 +80,44 @@

    Convert a basis object to an mrs_data object - where basis signals are sprea

    - 
    basis2mrs_data(basis, sum_elements = FALSE, amps = NULL, shifts = NULL)
    + 
    basis2mrs_data(
+  basis,
+  sum_elements = FALSE,
+  amps = NULL,
+  shifts = NULL,
+  lbs = NULL
+)

    Arguments

    -
    basis
    + + +
    basis

    basis set object.

    -
    sum_elements
    +
    sum_elements

    return the sum of basis elements (logical)

    -
    amps
    +
    amps

    a vector of scaling factors to apply to each basis element.

    -
    shifts
    +
    shifts

    a vector of frequency shifts (in ppm) to apply to each basis element.

    + +
    lbs
    +

    a vector of Lorentzian line broadening terms (in Hz) to apply to +each basis element.

    +

    Value

    - - -

    an mrs_data object with basis signals spread across the dynamic +

    an mrs_data object with basis signals spread across the dynamic dimension or summed.

    @@ -125,15 +133,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bbase.html b/docs/reference/bbase.html index 501b16c4..47cb333b 100644 --- a/docs/reference/bbase.html +++ b/docs/reference/bbase.html @@ -1,11 +1,10 @@ -Generate a spline basis, slightly adapted from : "Splines, knots, and -penalties", Eilers 2010. — bbase • Spectroscopy Analysis Tools (spant) - +
    @@ -30,7 +29,7 @@
    • - +
    -

    Generate a spline basis, slightly adapted from : "Splines, knots, and -penalties", Eilers 2010.

    +

    Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.

    Source: R/abfit.R
    @@ -87,23 +85,23 @@

    Generate a spline basis, slightly adapted from : "Splines, knots, and

    Arguments

    -
    N
    + + +
    N

    number of data points.

    -
    number
    +
    number

    number of spline functions.

    -
    deg
    +
    deg

    spline degree : deg = 1 linear, deg = 2 quadratic, deg = 3 cubic.

    Value

    - - -

    spline basis as a matrix.

    +

    spline basis as a matrix.

    @@ -118,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bc_als.html b/docs/reference/bc_als.html index 1536dc20..0d8cec55 100644 --- a/docs/reference/bc_als.html +++ b/docs/reference/bc_als.html @@ -1,10 +1,10 @@ -Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant)Baseline correction using the ALS method. — bc_als • Spectroscopy Analysis Tools (spant) - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -85,28 +85,28 @@

    Baseline correction using the ALS method.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    lambda
    +
    lambda

    controls the baseline flexibility.

    -
    p
    +
    p

    controls the penalty for negative data points.

    -
    ret_bc_only
    +
    ret_bc_only

    return the baseline corrected data only. When FALSE the baseline estimate and input data will be returned.

    Value

    - - -

    baseline corrected data.

    +

    baseline corrected data.

    @@ -121,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bc_constant.html b/docs/reference/bc_constant.html index 6924596c..98cea610 100644 --- a/docs/reference/bc_constant.html +++ b/docs/reference/bc_constant.html @@ -1,9 +1,9 @@ -Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant)Remove a constant baseline offset based on a reference spectral region. — bc_constant • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Remove a constant baseline offset based on a reference spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range containing a flat baseline region to measure the offset.

    Value

    - - -

    baseline corrected data.

    +

    baseline corrected data.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html index 265fce5e..faa101f5 100644 --- a/docs/reference/bc_gauss.html +++ b/docs/reference/bc_gauss.html @@ -1,9 +1,9 @@ -Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant)Apply and subtract a Gaussian smoother in the spectral domain. — bc_gauss • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Apply and subtract a Gaussian smoother in the spectral domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    Value

    - - -

    smoother subtracted data.

    +

    smoother subtracted data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html index e4f74fea..44803c9a 100644 --- a/docs/reference/bc_poly.html +++ b/docs/reference/bc_poly.html @@ -1,9 +1,9 @@ -Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant)Fit and subtract a polynomial to each spectrum in a dataset. — bc_poly • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Fit and subtract a polynomial to each spectrum in a dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    p_deg
    +
    p_deg

    polynomial degree.

    Value

    - - -

    polynomial subtracted data.

    +

    polynomial subtracted data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html index 09d7fc51..e534e4d9 100644 --- a/docs/reference/bc_spline.html +++ b/docs/reference/bc_spline.html @@ -1,9 +1,9 @@ -Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant)Fit and subtract a smoothing spline to each spectrum in a dataset. — bc_spline • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Fit and subtract a smoothing spline to each spectrum in a dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    spar
    +
    spar

    smoothing parameter typically between 0 and 1.

    -
    nknots
    +
    nknots

    number of spline knots.

    Value

    - - -

    smoothing spline subtracted data.

    +

    smoothing spline subtracted data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html index 331a5c0b..4709cbc7 100644 --- a/docs/reference/beta2lw.html +++ b/docs/reference/beta2lw.html @@ -1,12 +1,10 @@ -Covert a beta value in the time-domain to an equivalent linewidth in Hz: -x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant)Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta). — beta2lw • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Covert a beta value in the time-domain to an equivalent linewidth in Hz: -x * exp(-i * t * t * beta).

    +

    Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Covert a beta value in the time-domain to an equivalent linewidth in Hz:

    Arguments

    -
    beta
    + + +
    beta

    beta damping value.

    Value

    - - -

    linewidth value in Hz.

    +

    linewidth value in Hz.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/bin_spec.html b/docs/reference/bin_spec.html index 3bc4cd33..f1864191 100644 --- a/docs/reference/bin_spec.html +++ b/docs/reference/bin_spec.html @@ -1,9 +1,9 @@ -Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant)Bin equally spaced spectral regions. — bin_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Bin equally spaced spectral regions.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be "binned".

    -
    width
    +
    width

    bin width.

    -
    unit
    +
    unit

    bin width unit, can be "ppm" (default) or "pts".

    Value

    - - -

    binned mrs_data object.

    +

    binned mrs_data object.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_basis_corr_mat.html b/docs/reference/calc_basis_corr_mat.html new file mode 100644 index 00000000..25eed3ef --- /dev/null +++ b/docs/reference/calc_basis_corr_mat.html @@ -0,0 +1,128 @@ + +Estimate the correlation matrix for a basis set. — calc_basis_corr_mat • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Estimate the correlation matrix for a basis set.

    + Source: R/basis_set.R + +
    + +
    +

    Estimate the correlation matrix for a basis set.

    +
    + +
    + 
    calc_basis_corr_mat(basis, xlim = c(4, 0.2), zf = TRUE)
    +
    + +
    +

    Arguments

    + + +
    basis
    +

    basis_set object.

    + + +
    xlim
    +

    spectral range to use in ppm.

    + + +
    zf
    +

    zero-fill the basis set.

    + +
    +
    +

    Value

    +

    correlation matrix.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/calc_basis_crlbs.html b/docs/reference/calc_basis_crlbs.html new file mode 100644 index 00000000..9b8b0c37 --- /dev/null +++ b/docs/reference/calc_basis_crlbs.html @@ -0,0 +1,142 @@ + +Estimate the CRLB for each element in a basis set. — calc_basis_crlbs • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Estimate the CRLB for each element in a basis set.

    + Source: R/basis_set.R + +
    + +
    +

    Estimate the CRLB for each element in a basis set.

    +
    + +
    + 
    calc_basis_crlbs(
+  basis,
+  xlim = c(4, 0.2),
+  zf = TRUE,
+  sd = 1,
+  bl_comp_pppm = NULL
+)
    +
    + +
    +

    Arguments

    + + +
    basis
    +

    basis_set object.

    + + +
    xlim
    +

    spectral range to use in ppm.

    + + +
    zf
    +

    zero-fill the basis set.

    + + +
    sd
    +

    standard deviation of the noise.

    + + +
    bl_comp_pppm
    +

    number spline baseline components to append per-ppm.

    + +
    +
    +

    Value

    +

    a vector of predicted errors.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html index beeab373..ee58c37d 100644 --- a/docs/reference/calc_coil_noise_cor.html +++ b/docs/reference/calc_coil_noise_cor.html @@ -1,9 +1,9 @@ -Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant)Calculate the noise correlation between coil elements. — calc_coil_noise_cor • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the noise correlation between coil elements.

    Arguments

    -
    noise_data
    + + +
    noise_data

    mrs_data object with one FID for each coil element.

    Value

    - - -

    correlation matrix.

    +

    correlation matrix.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html index 2a788fc7..172ef572 100644 --- a/docs/reference/calc_coil_noise_sd.html +++ b/docs/reference/calc_coil_noise_sd.html @@ -1,9 +1,9 @@ -Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant)Calculate the noise standard deviation for each coil element. — calc_coil_noise_sd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the noise standard deviation for each coil element.

    Arguments

    -
    noise_data
    + + +
    noise_data

    mrs_data object with one FID for each coil element.

    Value

    - - -

    array of standard deviations.

    +

    array of standard deviations.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html index 0fc73261..19f82c31 100644 --- a/docs/reference/calc_design_efficiency.html +++ b/docs/reference/calc_design_efficiency.html @@ -1,9 +1,9 @@ -Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant)Calculate the efficiency of a regressor data frame. — calc_design_efficiency • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Calculate the efficiency of a regressor data frame.

    Arguments

    -
    regressor_df
    + + +
    regressor_df

    input regressor data frame.

    -
    contrasts
    +
    contrasts

    a vector of contrast values.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html index 56237859..fa7471d4 100644 --- a/docs/reference/calc_ed_from_lambda.html +++ b/docs/reference/calc_ed_from_lambda.html @@ -1,9 +1,9 @@ -Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant)Calculate the effective dimensions of a spline smoother from lambda. — calc_ed_from_lambda • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Calculate the effective dimensions of a spline smoother from lambda.

    Arguments

    -
    spline_basis
    + + +
    spline_basis

    spline basis.

    -
    deriv_mat
    +
    deriv_mat

    derivative matrix.

    -
    lambda
    +
    lambda

    smoothing parameter.

    Value

    - - -

    the effective dimension value.

    +

    the effective dimension value.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html index 79914d1f..c36f793f 100644 --- a/docs/reference/calc_peak_info_vec.html +++ b/docs/reference/calc_peak_info_vec.html @@ -1,9 +1,9 @@ -Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant)Calculate the FWHM of a peak from a vector of intensity values. — calc_peak_info_vec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Calculate the FWHM of a peak from a vector of intensity values.

    Arguments

    -
    data_pts
    + + +
    data_pts

    input vector.

    -
    interp_f
    +
    interp_f

    interpolation factor to improve the FWHM estimate.

    Value

    - - -

    a vector of: x position of the highest data point, maximum peak +

    a vector of: x position of the highest data point, maximum peak value in the y axis, FWHM in the units of data points.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html index 737d68c7..972d160e 100644 --- a/docs/reference/calc_sd_poly.html +++ b/docs/reference/calc_sd_poly.html @@ -1,12 +1,10 @@ -Perform a polynomial fit, subtract and return the standard deviation of the -residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant)Perform a polynomial fit, subtract and return the standard deviation of the residuals. — calc_sd_poly • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform a polynomial fit, subtract and return the standard deviation of the -residuals.

    +

    Perform a polynomial fit, subtract and return the standard deviation of the residuals.

    Source: R/utils.R
    @@ -88,19 +85,19 @@

    Perform a polynomial fit, subtract and return the standard deviation of the

    Arguments

    -
    y
    + + +
    y

    array.

    -
    degree
    +
    degree

    polynomial degree.

    Value

    - - -

    standard deviation of the fit residuals.

    +

    standard deviation of the fit residuals.

    @@ -115,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_spec_diff.html b/docs/reference/calc_spec_diff.html index 0155242e..acc41148 100644 --- a/docs/reference/calc_spec_diff.html +++ b/docs/reference/calc_spec_diff.html @@ -1,9 +1,9 @@ -Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant)Calculate the sum of squares differences between two mrs_data objects. — calc_spec_diff • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Calculate the sum of squares differences between two mrs_data objects.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    ref
    +
    ref

    reference mrs_data object to calculate differences.

    -
    xlim
    +
    xlim

    spectral limits to perform calculation.

    Value

    - - -

    an array of the sum of squared difference values.

    +

    an array of the sum of squared difference values.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html index 702fc62d..2e88bdf0 100644 --- a/docs/reference/calc_spec_snr.html +++ b/docs/reference/calc_spec_snr.html @@ -1,10 +1,10 @@ -Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant)Calculate the spectral SNR. — calc_spec_snr • Spectroscopy Analysis Tools (spant) - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -92,39 +92,39 @@

    Calculate the spectral SNR.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    sig_region
    +
    sig_region

    a ppm region to define where the maximum signal value should be estimated.

    -
    noise_region
    +
    noise_region

    a ppm region to defined where the noise level should be estimated.

    -
    p_order
    +
    p_order

    polynomial order to fit to the noise region before estimating the standard deviation.

    -
    interp_f
    +
    interp_f

    interpolation factor to improve detection of the highest signal value.

    -
    full_output
    +
    full_output

    output signal, noise and SNR values separately.

    Value

    - - -

    an array of SNR values.

    +

    an array of SNR values.

    Details

    @@ -145,15 +145,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/check_lcm.html b/docs/reference/check_lcm.html index 7f2b5d8e..e05f2d6a 100644 --- a/docs/reference/check_lcm.html +++ b/docs/reference/check_lcm.html @@ -1,9 +1,9 @@ -Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant)Check LCModel can be run — check_lcm • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,15 +94,15 @@

    Check LCModel can be run

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html index 7cdb1d18..5bf9122f 100644 --- a/docs/reference/check_tqn.html +++ b/docs/reference/check_tqn.html @@ -1,9 +1,9 @@ -Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant)Check the TARQUIN binary can be run — check_tqn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,15 +94,15 @@

    Check the TARQUIN binary can be run

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html index 462f90f1..fd748450 100644 --- a/docs/reference/circ_mask.html +++ b/docs/reference/circ_mask.html @@ -1,9 +1,9 @@ -Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant)Create a logical circular mask spanning the full extent of an n x n matrix. — circ_mask • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Create a logical circular mask spanning the full extent of an n x n matrix.<

    Arguments

    -
    d
    + + +
    d

    diameter of the mask.

    -
    n
    +
    n

    number of matrix rows and columns.

    -
    offset
    +
    offset

    offset the mask centre in matrix dimension units.

    Value

    - - -

    logical n x n mask matrix.

    +

    logical n x n mask matrix.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html index 61141857..b9684b59 100644 --- a/docs/reference/coherence_filter.html +++ b/docs/reference/coherence_filter.html @@ -1,9 +1,9 @@ -Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant)Zero all coherence orders other than the one supplied as an argument. — coherence_filter • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Zero all coherence orders other than the one supplied as an argument.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    order
    +
    order

    coherence order to keep (default is 0).

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/collapse_to_dyns.fit_result.html b/docs/reference/collapse_to_dyns.fit_result.html new file mode 100644 index 00000000..63b1d1c8 --- /dev/null +++ b/docs/reference/collapse_to_dyns.fit_result.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html index f4dc6b97..02673454 100644 --- a/docs/reference/collapse_to_dyns.html +++ b/docs/reference/collapse_to_dyns.html @@ -1,9 +1,9 @@ -Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant)Collapse MRS data by concatenating spectra along the dynamic dimension. — collapse_to_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -80,28 +80,28 @@

    Collapse MRS data by concatenating spectra along the dynamic dimension.

    collapse_to_dyns(x, rm_masked = FALSE)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 collapse_to_dyns(x, rm_masked = FALSE)
 
-# S3 method for fit_result
+# S3 method for class 'fit_result'
 collapse_to_dyns(x, rm_masked = FALSE)

    Arguments

    -
    x
    + + +
    x

    data object to be collapsed (mrs_data or fit_result object).

    -
    rm_masked
    +
    rm_masked

    remove masked dynamics from the output.

    Value

    - - -

    collapsed data with spectra or fits concatenated along the dynamic +

    collapsed data with spectra or fits concatenated along the dynamic dimension.

    @@ -117,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/collapse_to_dyns.mrs_data.html b/docs/reference/collapse_to_dyns.mrs_data.html new file mode 100644 index 00000000..63b1d1c8 --- /dev/null +++ b/docs/reference/collapse_to_dyns.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html index 2f1cd561..aa607613 100644 --- a/docs/reference/comb_coils.html +++ b/docs/reference/comb_coils.html @@ -1,11 +1,11 @@ -Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant)Combine coil data based on the first data point of a reference signal. — comb_coils • Spectroscopy Analysis Tools (spant) - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -98,55 +98,55 @@

    Combine coil data based on the first data point of a reference signal.

    Arguments

    -
    metab
    + + +
    metab

    MRS data containing metabolite data.

    -
    ref
    +
    ref

    MRS data containing reference data (optional).

    -
    noise
    +
    noise

    MRS data from a noise scan (optional).

    -
    scale
    +
    scale

    option to rescale coil elements based on the first data point (logical).

    -
    scale_method
    +
    scale_method

    one of "sig_noise_sq", "sig_noise" or "sig".

    -
    sum_coils
    +
    sum_coils

    sum the coil elements as a final step (logical).

    -
    noise_region
    +
    noise_region

    the spectral region (in ppm) to estimate the noise.

    -
    average_ref_dyns
    +
    average_ref_dyns

    take the mean of the reference scans in the dynamic dimension before use.

    -
    ref_pt_index
    +
    ref_pt_index

    time-domain point to use for estimating phase and scaling values.

    -
    ret_metab_only
    +
    ret_metab_only

    return the metabolite data only, even if reference data has been specified.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -161,15 +161,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/comb_coils_mrsi_gls.html b/docs/reference/comb_coils_mrsi_gls.html new file mode 100644 index 00000000..331b2d9a --- /dev/null +++ b/docs/reference/comb_coils_mrsi_gls.html @@ -0,0 +1,131 @@ + +Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_mrsi_gls • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

    + Source: R/mrs_data_proc.R + +
    + +
    +

    Combine MRSI coil data using the GLS method presented by An et al +JMRI 37:1445-1450 (2013).

    +
    + +
    + 
    comb_coils_mrsi_gls(metab, noise_pts = 30, noise_mrs = NULL)
    +
    + +
    +

    Arguments

    + + +
    metab
    +

    MRSI data containing metabolite data.

    + + +
    noise_pts
    +

    number of points from the end of the FIDs to use for noise +covariance estimation.

    + + +
    noise_mrs
    +

    MRS data containing noise information for each coil.

    + +
    +
    +

    Value

    +

    coil combined MRSI data.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/comb_coils_svs_gls.html b/docs/reference/comb_coils_svs_gls.html new file mode 100644 index 00000000..c1e59115 --- /dev/null +++ b/docs/reference/comb_coils_svs_gls.html @@ -0,0 +1,145 @@ + +Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013). — comb_coils_svs_gls • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

    + Source: R/mrs_data_proc.R + +
    + +
    +

    Combine SVS coil data using the GLS method presented by An et al +JMRI 37:1445-1450 (2013).

    +
    + +
    + 
    comb_coils_svs_gls(
+  metab,
+  ref = NULL,
+  noise_pts = 256,
+  noise_mrs = NULL,
+  use_mean_sens = TRUE
+)
    +
    + +
    +

    Arguments

    + + +
    metab
    +

    MRS data containing metabolite data.

    + + +
    ref
    +

    MRS data containing reference data (optional).

    + + +
    noise_pts
    +

    number of points from the end of the FIDs to use for noise +covariance estimation.

    + + +
    noise_mrs
    +

    MRS data containing noise information for each coil.

    + + +
    use_mean_sens
    +

    use the dynamic mean to estimate coil sensitivities.

    + +
    +
    +

    Value

    +

    coil combined MRS data.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/comb_fit_list_fit_tables.html b/docs/reference/comb_fit_list_fit_tables.html index e88c513a..5b0eabf1 100644 --- a/docs/reference/comb_fit_list_fit_tables.html +++ b/docs/reference/comb_fit_list_fit_tables.html @@ -1,9 +1,9 @@ -Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant)Combine all fitting data points from a list of fits into a single data frame. — comb_fit_list_fit_tables • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,39 +90,39 @@

    Combine all fitting data points from a list of fits into a single data frame

    Arguments

    -
    fit_list
    + + +
    fit_list

    list of fit_result objects.

    -
    add_extra
    +
    add_extra

    add variables in the extra data frame to the output (TRUE).

    -
    harmonise_ppm
    +
    harmonise_ppm

    ensure the ppm scale for each fit is identical to the first.

    -
    inc_basis_sigs
    +
    inc_basis_sigs

    include the individual fitting basis signals in the output table, defaults to FALSE.

    -
    inc_indices
    +
    inc_indices

    include indices such as X, Y and coil in the output, defaults to TRUE. These are generally not useful for SVS analysis.

    -
    add_res_id
    +
    add_res_id

    add a res_id column to the output to distinguish between datasets.

    Value

    - - -

    a data frame containing the fit data points.

    +

    a data frame containing the fit data points.

    @@ -137,15 +137,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/comb_fit_list_result_tables.html b/docs/reference/comb_fit_list_result_tables.html index 9a9cd20f..36163985 100644 --- a/docs/reference/comb_fit_list_result_tables.html +++ b/docs/reference/comb_fit_list_result_tables.html @@ -1,9 +1,9 @@ -Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant)Combine the fit result tables from a list of fit results. — comb_fit_list_result_tables • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Combine the fit result tables from a list of fit results.

    Arguments

    -
    fit_list
    + + +
    fit_list

    a list of fit_result objects.

    -
    add_extra
    +
    add_extra

    add variables in the extra data frame to the output (TRUE).

    -
    add_res_id
    +
    add_res_id

    add a res_id column to the output to distinguish between datasets.

    Value

    - - -

    a data frame combine all fit result tables with an additional id +

    a data frame combine all fit result tables with an additional id column to differentiate between data sets. Any variables in the extra data frame may be optionally added to the result.

    @@ -117,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/comb_fit_tables.html b/docs/reference/comb_fit_tables.html index 52315125..8beaa83b 100644 --- a/docs/reference/comb_fit_tables.html +++ b/docs/reference/comb_fit_tables.html @@ -1,9 +1,9 @@ -Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant)Combine all fitting data points into a single data frame. — comb_fit_tables • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Combine all fitting data points into a single data frame.

    Arguments

    -
    fit_res
    + + +
    fit_res

    a single fit_result object.

    -
    inc_basis_sigs
    +
    inc_basis_sigs

    include the individual fitting basis signals in the output table, defaults to FALSE.

    -
    inc_indices
    +
    inc_indices

    include indices such as X, Y and coil in the output, defaults to TRUE. These are generally not useful for SVS analysis.

    Value

    - - -

    a data frame containing the fit data points.

    +

    a data frame containing the fit data points.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/comb_metab_ref.html b/docs/reference/comb_metab_ref.html index 40474562..30c0f794 100644 --- a/docs/reference/comb_metab_ref.html +++ b/docs/reference/comb_metab_ref.html @@ -1,9 +1,9 @@ -Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant)Combine a reference and metabolite mrs_data object. — comb_metab_ref • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Combine a reference and metabolite mrs_data object.

    Arguments

    -
    metab
    + + +
    metab

    metabolite mrs_data object.

    -
    ref
    +
    ref

    reference mrs_data object.

    Value

    - - -

    combined metabolite and reference mrs_data object.

    +

    combined metabolite and reference mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/conv_mrs.html b/docs/reference/conv_mrs.html index 3c349299..f537cc63 100644 --- a/docs/reference/conv_mrs.html +++ b/docs/reference/conv_mrs.html @@ -1,9 +1,9 @@ -Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant)Convolve two MRS data objects. — conv_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Convolve two MRS data objects.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be convolved.

    -
    conv
    +
    conv

    convolution data stored as an mrs_data object.

    Value

    - - -

    convolved data.

    +

    convolved data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_basis.html b/docs/reference/crop_basis.html index 25adfcc2..4f4e70cd 100644 --- a/docs/reference/crop_basis.html +++ b/docs/reference/crop_basis.html @@ -1,9 +1,9 @@ -Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant)Crop basis_set object based on a frequency range. — crop_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Crop basis_set object based on a frequency range.

    Arguments

    -
    basis
    + + +
    basis

    basis_set object to be cropped in the spectral dimension.

    -
    xlim
    +
    xlim

    range of values to crop in the spectral dimension eg xlim = c(4, 0.2).

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_spec.html b/docs/reference/crop_spec.html index bac28c4b..b2bd7c33 100644 --- a/docs/reference/crop_spec.html +++ b/docs/reference/crop_spec.html @@ -1,9 +1,9 @@ -Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant)Crop mrs_data object based on a frequency range. — crop_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Crop mrs_data object based on a frequency range.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    range of values to crop in the spectral dimension eg xlim = c(4, 0.2).

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_td_pts.html b/docs/reference/crop_td_pts.html index c9c4a213..d6ddaba9 100644 --- a/docs/reference/crop_td_pts.html +++ b/docs/reference/crop_td_pts.html @@ -1,9 +1,9 @@ -Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant)Crop mrs_data object data points in the time-domain. — crop_td_pts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Crop mrs_data object data points in the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    start
    +
    start

    starting data point (defaults to 1).

    -
    end
    +
    end

    ending data point (defaults to the last saved point).

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_td_pts_end.html b/docs/reference/crop_td_pts_end.html index 3560fee2..3794f814 100644 --- a/docs/reference/crop_td_pts_end.html +++ b/docs/reference/crop_td_pts_end.html @@ -1,9 +1,9 @@ -Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant)Crop mrs_data object data points at the end of the FID. — crop_td_pts_end • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Crop mrs_data object data points at the end of the FID.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of points to remove from the end of the FID.

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_td_pts_pot.html b/docs/reference/crop_td_pts_pot.html index d6c77479..59fa237d 100644 --- a/docs/reference/crop_td_pts_pot.html +++ b/docs/reference/crop_td_pts_pot.html @@ -1,15 +1,11 @@ -Crop mrs_data object data points in the time-domain rounding down to -the next smallest power of two (pot). Data that already has a pot length will -not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant)Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed. — crop_td_pts_pot • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Crop mrs_data object data points in the time-domain rounding down to -the next smallest power of two (pot). Data that already has a pot length will -not be changed.

    +

    Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.

    Source: R/mrs_data_proc.R
    @@ -93,15 +87,15 @@

    Crop mrs_data object data points in the time-domain rounding do

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -116,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crop_xy.html b/docs/reference/crop_xy.html index 1e9fa735..4fcaad54 100644 --- a/docs/reference/crop_xy.html +++ b/docs/reference/crop_xy.html @@ -1,9 +1,9 @@ -Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant)Crop an MRSI dataset in the x-y direction — crop_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Crop an MRSI dataset in the x-y direction

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_dim
    +
    x_dim

    x dimension output length.

    -
    y_dim
    +
    y_dim

    y dimension output length.

    Value

    - - -

    selected subset of MRS data.

    +

    selected subset of MRS data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/crossprod_3d.html b/docs/reference/crossprod_3d.html index 417852cd..95838415 100644 --- a/docs/reference/crossprod_3d.html +++ b/docs/reference/crossprod_3d.html @@ -1,12 +1,10 @@ -Compute the vector cross product between vectors x and y. Adapted from -http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant)Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function — crossprod_3d • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Compute the vector cross product between vectors x and y. Adapted from -http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

    +

    Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

    Source: R/utils.R
    @@ -88,19 +85,19 @@

    Compute the vector cross product between vectors x and y. Adapted from

    Arguments

    -
    x
    + + +
    x

    vector of length 3.

    -
    y
    +
    y

    vector of length 3.

    Value

    - - -

    vector cross product of x and y.

    +

    vector cross product of x and y.

    @@ -115,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/decimate_mrs_fd.html b/docs/reference/decimate_mrs_fd.html index ff55d43d..f1d2e18b 100644 --- a/docs/reference/decimate_mrs_fd.html +++ b/docs/reference/decimate_mrs_fd.html @@ -1,12 +1,10 @@ -Decimate an MRS signal to half the original sampling frequency by filtering -in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant)Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling. — decimate_mrs_fd • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Decimate an MRS signal to half the original sampling frequency by filtering -in the frequency domain before down sampling.

    +

    Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Decimate an MRS signal to half the original sampling frequency by filtering

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    decimated data at half the original sampling frequency.

    +

    decimated data at half the original sampling frequency.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/decimate_mrs_td.html b/docs/reference/decimate_mrs_td.html index baa4f04a..420dc3b4 100644 --- a/docs/reference/decimate_mrs_td.html +++ b/docs/reference/decimate_mrs_td.html @@ -1,9 +1,9 @@ -Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant)Decimate an MRS signal by filtering in the time domain before downsampling. — decimate_mrs_td • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,27 @@

    Decimate an MRS signal by filtering in the time domain before downsampling.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    q
    +
    q

    integer factor to downsample by (default = 2).

    -
    n
    +
    n

    filter order used in the downsampling.

    -
    ftype
    +
    ftype

    filter type, "iir" or "fir".

    Value

    - - -

    decimated data.

    +

    decimated data.

    @@ -118,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/deconv_mrs.html b/docs/reference/deconv_mrs.html index 1640eb61..5a4d6154 100644 --- a/docs/reference/deconv_mrs.html +++ b/docs/reference/deconv_mrs.html @@ -1,9 +1,9 @@ -Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant)Deconvolve two MRS data objects. — deconv_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Deconvolve two MRS data objects.

    Arguments

    -
    mrs_data_a
    + + +
    mrs_data_a

    MRS data to be deconvolved.

    -
    mrs_data_b
    +
    mrs_data_b

    MRS data to be deconvolved.

    Value

    - - -

    deconvolved data.

    +

    deconvolved data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_N.html b/docs/reference/def_N.html index 1b8c28e2..dcece018 100644 --- a/docs/reference/def_N.html +++ b/docs/reference/def_N.html @@ -1,9 +1,9 @@ -Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant)Return the default number of data points in the spectral dimension. — def_N • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return the default number of data points in the spectral dimension.

    Value

    - - -

    number of data points in the spectral dimension.

    +

    number of data points in the spectral dimension.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_acq_paras.html b/docs/reference/def_acq_paras.html index e5dfddab..6cbdf8cf 100644 --- a/docs/reference/def_acq_paras.html +++ b/docs/reference/def_acq_paras.html @@ -1,12 +1,10 @@ -Return (and optionally modify using the input arguments) a list of the -default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant)Return (and optionally modify using the input arguments) a list of the default acquisition parameters. — def_acq_paras • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return (and optionally modify using the input arguments) a list of the -default acquisition parameters.

    +

    Return (and optionally modify using the input arguments) a list of the default acquisition parameters.

    Source: R/spant.R
    @@ -94,31 +91,31 @@

    Return (and optionally modify using the input arguments) a list of the

    Arguments

    -
    ft
    + + +
    ft

    specify the transmitter frequency in Hz.

    -
    fs
    +
    fs

    specify the sampling frequency in Hz.

    -
    N
    +
    N

    specify the number of data points in the spectral dimension.

    -
    ref
    +
    ref

    specify the reference value for ppm scale.

    -
    nuc
    +
    nuc

    specify the resonant nucleus.

    Value

    - - -

    A list containing the following elements:

    • ft transmitter frequency in Hz.

      • +

      A list containing the following elements:

      • ft transmitter frequency in Hz.

      • fs sampling frequency in Hz.

      • N number of data points in the spectral dimension.

      • ref reference value for ppm scale.

        • @@ -137,15 +134,15 @@

        Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_fs.html b/docs/reference/def_fs.html index 5917ed7e..481def7c 100644 --- a/docs/reference/def_fs.html +++ b/docs/reference/def_fs.html @@ -1,9 +1,9 @@ -Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant)Return the default sampling frequency in Hz. — def_fs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return the default sampling frequency in Hz.

    Value

    - - -

    sampling frequency in Hz.

    +

    sampling frequency in Hz.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_ft.html b/docs/reference/def_ft.html index 715f0c1f..897509ff 100644 --- a/docs/reference/def_ft.html +++ b/docs/reference/def_ft.html @@ -1,9 +1,9 @@ -Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant)Return the default transmitter frequency in Hz. — def_ft • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return the default transmitter frequency in Hz.

    Value

    - - -

    transmitter frequency in Hz.

    +

    transmitter frequency in Hz.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_nuc.html b/docs/reference/def_nuc.html index cfffaa97..cd5fccc6 100644 --- a/docs/reference/def_nuc.html +++ b/docs/reference/def_nuc.html @@ -1,9 +1,9 @@ -Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant)Return the default nucleus. — def_nuc • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return the default nucleus.

    Value

    - - -

    number of data points in the spectral dimension.

    +

    number of data points in the spectral dimension.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/def_ref.html b/docs/reference/def_ref.html index 1aed7ccf..2ba16591 100644 --- a/docs/reference/def_ref.html +++ b/docs/reference/def_ref.html @@ -1,9 +1,9 @@ -Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant)Return the default reference value for ppm scale. — def_ref • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return the default reference value for ppm scale.

    Value

    - - -

    reference value for ppm scale.

    +

    reference value for ppm scale.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dicom_reader.html b/docs/reference/dicom_reader.html index f27d6e7f..4abc211c 100644 --- a/docs/reference/dicom_reader.html +++ b/docs/reference/dicom_reader.html @@ -1,11 +1,11 @@ -A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant)A very simple DICOM reader. — dicom_reader • Spectroscopy Analysis Tools (spant) - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -92,28 +92,28 @@

    A very simple DICOM reader.

    Arguments

    -
    input
    + + +
    input

    either a file path or raw binary object.

    -
    tags
    +
    tags

    a named list of tags to be extracted from the file. eg tags <- list(spec_data = "7FE1,1010", pat_name = "0010,0010")

    -
    endian
    +
    endian

    can be "little" or "big".

    -
    debug
    +
    debug

    print out some debugging information, can be "little" or "big".

    Value

    - - -

    a list with the same structure as the input, but with tag codes +

    a list with the same structure as the input, but with tag codes replaced with the corresponding data in a raw format.

    @@ -129,15 +129,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/diff_mrs.html b/docs/reference/diff_mrs.html index 8d29c377..5944f7c7 100644 --- a/docs/reference/diff_mrs.html +++ b/docs/reference/diff_mrs.html @@ -1,9 +1,9 @@ -Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant)Apply the diff operator to an MRS dataset in the FID/spectral dimension. — diff_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Apply the diff operator to an MRS dataset in the FID/spectral dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    ...
    +
    ...

    additional arguments to the diff function.

    Value

    - - -

    MRS data following diff operator.

    +

    MRS data following diff operator.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/downsample_mrs_fd.html b/docs/reference/downsample_mrs_fd.html index 9974daa5..0a7caf62 100644 --- a/docs/reference/downsample_mrs_fd.html +++ b/docs/reference/downsample_mrs_fd.html @@ -1,9 +1,9 @@ -Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant)Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter. — downsample_mrs_fd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    downsampled data.

    +

    downsampled data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/downsample_mrs_td.html b/docs/reference/downsample_mrs_td.html index 1a131574..f4ffbec5 100644 --- a/docs/reference/downsample_mrs_td.html +++ b/docs/reference/downsample_mrs_td.html @@ -1,15 +1,11 @@ -Downsample an MRS signal by a factor of 2 by removing every other data point -in the time-domain. Note, signals outside the new sampling frequency will be -aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant)Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased. — downsample_mrs_td • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Downsample an MRS signal by a factor of 2 by removing every other data point -in the time-domain. Note, signals outside the new sampling frequency will be -aliased.

    +

    Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.

    Source: R/mrs_data_proc.R
    @@ -93,15 +87,15 @@

    Downsample an MRS signal by a factor of 2 by removing every other data point

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    downsampled data.

    +

    downsampled data.

    @@ -116,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/dyn_acq_times.html b/docs/reference/dyn_acq_times.html index f9f2ba22..3470c96a 100644 --- a/docs/reference/dyn_acq_times.html +++ b/docs/reference/dyn_acq_times.html @@ -1,12 +1,10 @@ -Return a time scale vector of acquisition times for a dynamic MRS scan. The -first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant)Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0. — dyn_acq_times • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a time scale vector of acquisition times for a dynamic MRS scan. The -first temporal scan is assigned a value of 0.

    +

    Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.

    Source: R/mrs_data_proc.R
    @@ -83,20 +80,33 @@

    Return a time scale vector of acquisition times for a dynamic MRS scan. The

    - 
    dyn_acq_times(mrs_data)
    + 
    dyn_acq_times(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    + +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    +

    Value

    - - -

    time scale vector in units of seconds.

    +

    time scale vector in units of seconds.

    @@ -111,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ecc.html b/docs/reference/ecc.html index c49aabe9..9c078a92 100644 --- a/docs/reference/ecc.html +++ b/docs/reference/ecc.html @@ -1,9 +1,9 @@ -Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant)Eddy current correction. — ecc • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Eddy current correction.

    Arguments

    -
    metab
    + + +
    metab

    MRS data to be corrected.

    -
    ref
    +
    ref

    reference dataset.

    -
    rev
    +
    rev

    reverse the correction.

    Value

    - - -

    corrected data in the time domain.

    +

    corrected data in the time domain.

    Details

    @@ -120,15 +120,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/elliptical_mask.html b/docs/reference/elliptical_mask.html index 9736c7c1..49dbd46b 100644 --- a/docs/reference/elliptical_mask.html +++ b/docs/reference/elliptical_mask.html @@ -1,9 +1,9 @@ -Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant)Create an elliptical mask stored as a matrix of logical values. — elliptical_mask • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,39 +83,39 @@

    Create an elliptical mask stored as a matrix of logical values.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of ellipse in the x direction in units of pixels.

    -
    y0
    +
    y0

    centre of ellipse in the y direction in units of pixels.

    -
    xr
    +
    xr

    radius in the x direction in units of pixels.

    -
    yr
    +
    yr

    radius in the y direction in units of pixels.

    -
    angle
    +
    angle

    angle of rotation in degrees.

    Value

    - - -

    logical mask matrix with dimensions fov_yN x fov_xN.

    +

    logical mask matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +130,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/est_noise_sd.html b/docs/reference/est_noise_sd.html index d0bcbc47..776be5c7 100644 --- a/docs/reference/est_noise_sd.html +++ b/docs/reference/est_noise_sd.html @@ -1,12 +1,10 @@ -Estimate the standard deviation of the noise from a segment of an mrs_data -object. — est_noise_sd • Spectroscopy Analysis Tools (spant)Estimate the standard deviation of the noise from a segment of an mrs_data object. — est_noise_sd • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Estimate the standard deviation of the noise from a segment of an mrs_data -object.

    +

    Estimate the standard deviation of the noise from a segment of an mrs_data object.

    Source: R/mrs_data_proc.R
    @@ -88,29 +85,29 @@

    Estimate the standard deviation of the noise from a segment of an mrs_data

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    n
    +
    n

    number of data points (taken from the end of array) to use in the estimation.

    -
    offset
    +
    offset

    number of final points to exclude from the calculation.

    -
    p_order
    +
    p_order

    polynomial order to fit to the data before estimating the standard deviation.

    Value

    - - -

    standard deviation array.

    +

    standard deviation array.

    @@ -125,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fd2td.html b/docs/reference/fd2td.html index 08902bdc..baafb2e8 100644 --- a/docs/reference/fd2td.html +++ b/docs/reference/fd2td.html @@ -1,9 +1,9 @@ -Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant)Transform frequency-domain data to the time-domain. — fd2td • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Transform frequency-domain data to the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data in frequency-domain representation.

    Value

    - - -

    MRS data in time-domain representation.

    +

    MRS data in time-domain representation.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fd_conv_filt.html b/docs/reference/fd_conv_filt.html index d419e680..df2faf57 100644 --- a/docs/reference/fd_conv_filt.html +++ b/docs/reference/fd_conv_filt.html @@ -1,9 +1,9 @@ -Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant)Frequency-domain convolution based filter. — fd_conv_filt • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Frequency-domain convolution based filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    K
    +
    K

    window width in data points.

    -
    ext
    +
    ext

    point separation for linear extrapolation.

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fd_gauss_smo.html b/docs/reference/fd_gauss_smo.html index 43fbb24b..4e50baf1 100644 --- a/docs/reference/fd_gauss_smo.html +++ b/docs/reference/fd_gauss_smo.html @@ -1,9 +1,9 @@ -Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant)Apply a Gaussian smoother in the spectral domain. — fd_gauss_smo • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Apply a Gaussian smoother in the spectral domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    Value

    - - -

    spectrally smoothed data.

    +

    spectrally smoothed data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/find_bids_mrs.html b/docs/reference/find_bids_mrs.html index 81ef7726..7f8cfeb1 100644 --- a/docs/reference/find_bids_mrs.html +++ b/docs/reference/find_bids_mrs.html @@ -1,9 +1,9 @@ -Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant)Search for MRS data files in a BIDS filesystem structure. — find_bids_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,20 +78,24 @@

    Search for MRS data files in a BIDS filesystem structure.

    - 
    find_bids_mrs(path)
    + 
    find_bids_mrs(path, output_full_path = FALSE)

    Arguments

    -
    path
    + + +
    path

    path to the directory containing the BIDS structure.

    + +
    output_full_path
    +

    output the full normalised data paths.

    +

    Value

    - - -

    data frame containing full paths and information on each MRS file.

    +

    data frame containing full paths and information on each MRS file.

    @@ -106,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/find_mrs_files.html b/docs/reference/find_mrs_files.html index aa88618b..062198d6 100644 --- a/docs/reference/find_mrs_files.html +++ b/docs/reference/find_mrs_files.html @@ -1,9 +1,9 @@ -Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant)Find valid MRS data files recursively from a directory path. — find_mrs_files • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Find valid MRS data files recursively from a directory path.

    Arguments

    -
    dir
    + + +
    dir

    a directory path.

    Value

    - - -

    a vector of valid MRS data files.

    +

    a vector of valid MRS data files.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_amps.html b/docs/reference/fit_amps.html index 2190b708..0732a3d5 100644 --- a/docs/reference/fit_amps.html +++ b/docs/reference/fit_amps.html @@ -1,9 +1,9 @@ -Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant)Extract the fit amplitudes from an object of class fit_result. — fit_amps • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -88,28 +88,28 @@

    Extract the fit amplitudes from an object of class fit_result.<

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    inc_index
    +
    inc_index

    include columns for the voxel index.

    -
    sort_names
    +
    sort_names

    sort the basis set names alphabetically.

    -
    append_common_1h_comb
    +
    append_common_1h_comb

    append commonly used 1H metabolite combinations eg tNAA = NAA + NAAG.

    Value

    - - -

    a dataframe of amplitudes.

    +

    a dataframe of amplitudes.

    @@ -124,15 +124,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_diags.html b/docs/reference/fit_diags.html index 9f940ff1..9cd37e08 100644 --- a/docs/reference/fit_diags.html +++ b/docs/reference/fit_diags.html @@ -1,9 +1,9 @@ -Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant)Calculate diagnostic information for object of class fit_result. — fit_diags • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Calculate diagnostic information for object of class fit_result

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    amps
    +
    amps

    known metabolite amplitudes.

    Value

    - - -

    a dataframe of diagnostic information.

    +

    a dataframe of diagnostic information.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_mrs.html b/docs/reference/fit_mrs.html index 9eb523df..7141294c 100644 --- a/docs/reference/fit_mrs.html +++ b/docs/reference/fit_mrs.html @@ -1,11 +1,11 @@ -Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant)Perform a fit based analysis of MRS data. — fit_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -89,6 +89,7 @@

    Perform a fit based analysis of MRS data.

    w_ref = NULL, opts = NULL, parallel = FALSE, + cl = NULL, time = TRUE, progress = "text", extra = NULL @@ -97,53 +98,58 @@

    Perform a fit based analysis of MRS data.

    Arguments

    -
    metab
    + + +
    metab

    metabolite data.

    -
    basis
    +
    basis

    basis class object or character vector to basis file in LCModel .basis format.

    -
    method
    +
    method

    'ABFIT' (default), 'VARPRO', 'VARPRO_3P', 'TARQUIN' or 'LCMODEL'.

    -
    w_ref
    +
    w_ref

    water reference data for concentration scaling (optional).

    -
    opts
    +
    opts

    options to pass to the analysis method.

    -
    parallel
    +
    parallel

    perform analyses in parallel (TRUE or FALSE).

    -
    time
    +
    cl
    +

    a parallel socket cluster required to run analyses in parallel. +Eg, cl <- parallel::makeCluster(4).

    + + +
    time

    measure the time taken for the analysis to complete (TRUE or FALSE).

    -
    progress
    +
    progress

    option is passed to plyr::alply function to display a progress bar during fitting. Default value is "text", set to "none" to disable.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    Value

    - - -

    MRS analysis object.

    +

    MRS analysis object.

    Details

    @@ -169,10 +175,10 @@

    Examples

    fname <- system.file("extdata", "philips_spar_sdat_WS.SDAT", package =
 "spant")
 svs <- read_mrs(fname)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 basis <- sim_basis_1h_brain_press(svs)
 fit_result <- fit_mrs(svs, basis)
-}
+} # }
    @@ -187,15 +193,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_res2csv.html b/docs/reference/fit_res2csv.html index 2b428397..cd7ac9e4 100644 --- a/docs/reference/fit_res2csv.html +++ b/docs/reference/fit_res2csv.html @@ -1,9 +1,9 @@ -Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant)Write fit results table to a csv file. — fit_res2csv • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Write fit results table to a csv file.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit result object.

    -
    fname
    +
    fname

    filename of csv file.

    -
    unscaled
    +
    unscaled

    output the unscaled result table (default = FALSE).

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_t1_ti_array.html b/docs/reference/fit_t1_ti_array.html index 5360fbc3..50c1808d 100644 --- a/docs/reference/fit_t1_ti_array.html +++ b/docs/reference/fit_t1_ti_array.html @@ -1,9 +1,9 @@ -Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant)Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes. — fit_t1_ti_array • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,37 +90,37 @@

    Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes.

    Arguments

    -
    ti_vec
    + + +
    ti_vec

    vector of TI values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T1 value.

    -
    upper
    +
    upper

    maximum allowable T1 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +136,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_t1_tr_array.html b/docs/reference/fit_t1_tr_array.html index 42d6961a..65cf05a9 100644 --- a/docs/reference/fit_t1_tr_array.html +++ b/docs/reference/fit_t1_tr_array.html @@ -1,9 +1,9 @@ -Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant)Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes. — fit_t1_tr_array • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,37 +90,37 @@

    Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes.

    Arguments

    -
    tr_vec
    + + +
    tr_vec

    vector of TR values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T1 value.

    -
    upper
    +
    upper

    maximum allowable T1 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +136,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fit_t2_te_array.html b/docs/reference/fit_t2_te_array.html index abfc708c..32b9de8d 100644 --- a/docs/reference/fit_t2_te_array.html +++ b/docs/reference/fit_t2_te_array.html @@ -1,9 +1,9 @@ -Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant)Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes. — fit_t2_te_array • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,37 +90,37 @@

    Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes.

    Arguments

    -
    te_vec
    + + +
    te_vec

    vector of TE values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T2 value.

    -
    upper
    +
    upper

    maximum allowable T2 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +136,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fp_phase.html b/docs/reference/fp_phase.html index 55b65a21..7d606275 100644 --- a/docs/reference/fp_phase.html +++ b/docs/reference/fp_phase.html @@ -1,9 +1,9 @@ -Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant)Return the phase of the first data point in the time-domain. — fp_phase • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the phase of the first data point in the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    phase values in degrees.

    +

    phase values in degrees.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fp_phase_correct.html b/docs/reference/fp_phase_correct.html index 8f847ebf..17bde14d 100644 --- a/docs/reference/fp_phase_correct.html +++ b/docs/reference/fp_phase_correct.html @@ -1,12 +1,10 @@ -Perform a zeroth order phase correction based on the phase of the first data -point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant)Perform a zeroth order phase correction based on the phase of the first data point in the time-domain. — fp_phase_correct • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform a zeroth order phase correction based on the phase of the first data -point in the time-domain.

    +

    Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.

    Source: R/mrs_data_proc.R
    @@ -88,19 +85,19 @@

    Perform a zeroth order phase correction based on the phase of the first data

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ret_phase
    +
    ret_phase

    return phase values (logical).

    Value

    - - -

    corrected data or a list with corrected data and optional phase +

    corrected data or a list with corrected data and optional phase values.

    @@ -116,15 +113,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fp_scale.html b/docs/reference/fp_scale.html index 6709ad74..dbcb90a2 100644 --- a/docs/reference/fp_scale.html +++ b/docs/reference/fp_scale.html @@ -1,9 +1,9 @@ -Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant)Scale the first time-domain data point in an mrs_data object. — fp_scale • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Scale the first time-domain data point in an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    scale
    +
    scale

    scaling value, defaults to 0.5.

    Value

    - - -

    scaled mrs_data object.

    +

    scaled mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fs.html b/docs/reference/fs.html index 9e576eef..794e0485 100644 --- a/docs/reference/fs.html +++ b/docs/reference/fs.html @@ -1,9 +1,9 @@ -Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant)Return the sampling frequency in Hz of an MRS dataset. — fs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the sampling frequency in Hz of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    sampling frequency in Hz.

    +

    sampling frequency in Hz.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ft_dyns.html b/docs/reference/ft_dyns.html index de5e96a4..2046b890 100644 --- a/docs/reference/ft_dyns.html +++ b/docs/reference/ft_dyns.html @@ -1,9 +1,9 @@ -Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant)Apply the Fourier transform over the dynamic dimension. — ft_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,28 +83,28 @@

    Apply the Fourier transform over the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data where the dynamic dimension is in the time-domain.

    -
    ft_shift
    +
    ft_shift

    apply FT shift to the output, default is FALSE.

    -
    ret_mod
    +
    ret_mod

    return the modulus out the transform, default is FALSE.

    -
    fd
    +
    fd

    transform the chemical shift axis to the frequency domain first, default is TRUE.

    Value

    - - -

    transformed MRS data.

    +

    transformed MRS data.

    @@ -119,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ft_shift.html b/docs/reference/ft_shift.html index 7b55740b..aff9f333 100644 --- a/docs/reference/ft_shift.html +++ b/docs/reference/ft_shift.html @@ -1,9 +1,9 @@ -Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant)Perform a fft and ffshift on a vector. — ft_shift • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Perform a fft and ffshift on a vector.

    Arguments

    -
    vec_in
    + + +
    vec_in

    vector input.

    Value

    - - -

    output vector.

    +

    output vector.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ft_shift_mat.html b/docs/reference/ft_shift_mat.html index 7009d0b9..5bce583d 100644 --- a/docs/reference/ft_shift_mat.html +++ b/docs/reference/ft_shift_mat.html @@ -1,12 +1,10 @@ -Perform a fft and fftshift on a matrix with each column replaced by its -shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant)Perform a fft and fftshift on a matrix with each column replaced by its shifted fft. — ft_shift_mat • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform a fft and fftshift on a matrix with each column replaced by its -shifted fft.

    +

    Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Perform a fft and fftshift on a matrix with each column replaced by its

    Arguments

    -
    mat_in
    + + +
    mat_in

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gausswin_2d.html b/docs/reference/gausswin_2d.html index a92a644c..b289f230 100644 --- a/docs/reference/gausswin_2d.html +++ b/docs/reference/gausswin_2d.html @@ -1,9 +1,9 @@ -Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant)Create a two dimensional Gaussian window function stored as a matrix. — gausswin_2d • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,39 +83,39 @@

    Create a two dimensional Gaussian window function stored as a matrix.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of window function in the x direction in units of pixels. Note, only integer values are applied.

    -
    y0
    +
    y0

    centre of window function in the y direction in units of pixels. Note, only integer values are applied.

    -
    xw
    +
    xw

    the reciprocal of the standard deviation of the Gaussian window in x direction.

    -
    yw
    +
    yw

    the reciprocal of the standard deviation of the Gaussian window in y direction.

    Value

    - - -

    matrix with dimensions fov_yN x fov_xN.

    +

    matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +130,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_F.html b/docs/reference/gen_F.html index 0eee85ab..f6f8a5fb 100644 --- a/docs/reference/gen_F.html +++ b/docs/reference/gen_F.html @@ -1,9 +1,9 @@ -Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant)Generate the F product operator. — gen_F • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Generate the F product operator.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    op
    +
    op

    operator, one of "x", "y", "z", "p", "m".

    -
    detect
    +
    detect

    detection nuclei.

    Value

    - - -

    F product operator matrix.

    +

    F product operator matrix.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_F_xy.html b/docs/reference/gen_F_xy.html index 67c141e0..e2abf9ee 100644 --- a/docs/reference/gen_F_xy.html +++ b/docs/reference/gen_F_xy.html @@ -1,9 +1,9 @@ -Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant)Generate the Fxy product operator with a specified phase. — gen_F_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Generate the Fxy product operator with a specified phase.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    phase
    +
    phase

    phase angle in degrees.

    -
    detect
    +
    detect

    detection nuclei.

    Value

    - - -

    product operator matrix.

    +

    product operator matrix.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_I.html b/docs/reference/gen_I.html index 546e31e0..2b42a987 100644 --- a/docs/reference/gen_I.html +++ b/docs/reference/gen_I.html @@ -1,9 +1,9 @@ -Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant)Generate the I product operator for a single spin. — gen_I • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Generate the I product operator for a single spin.

    Arguments

    -
    n
    + + +
    n

    spin index number for the required operator.

    -
    spin_num
    +
    spin_num

    vector of spin numbers in the system.

    -
    op
    +
    op

    operator, one of "x", "y", "z", "p", "m".

    Value

    - - -

    I product operator matrix.

    +

    I product operator matrix.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_baseline_reg.html b/docs/reference/gen_baseline_reg.html index 499cd905..9ec30635 100644 --- a/docs/reference/gen_baseline_reg.html +++ b/docs/reference/gen_baseline_reg.html @@ -1,9 +1,9 @@ -Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant)Generate baseline regressor. — gen_baseline_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,20 +78,33 @@

    Generate baseline regressor.

    - 
    gen_baseline_reg(mrs_data)
    + 
    gen_baseline_reg(mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object for timing information.

    + +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    +

    Value

    - - -

    a single baseline regressor with value of 1.

    +

    a single baseline regressor with value of 1.

    @@ -106,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_bold_reg.html b/docs/reference/gen_bold_reg.html index 56bf47b9..890dcbac 100644 --- a/docs/reference/gen_bold_reg.html +++ b/docs/reference/gen_bold_reg.html @@ -1,9 +1,9 @@ -Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant)Generate BOLD regressors. — gen_bold_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,6 +83,9 @@

    Generate BOLD regressors.

    duration = NULL, trial_type = NULL, mrs_data = NULL, + tr = NULL, + Ndyns = NULL, + Ntrans = NULL, match_tr = TRUE, dt = 0.1, normalise = FALSE @@ -91,40 +94,53 @@

    Generate BOLD regressors.

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    -
    match_tr
    +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    match_tr

    match the output to the input mrs_data.

    -
    dt
    +
    dt

    timing resolution for internal calculations.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    BOLD regressor data frame.

    +

    BOLD regressor data frame.

    @@ -139,15 +155,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_conv_reg.html b/docs/reference/gen_conv_reg.html index e94d6114..0a94adae 100644 --- a/docs/reference/gen_conv_reg.html +++ b/docs/reference/gen_conv_reg.html @@ -1,12 +1,10 @@ -Generate regressors by convolving a specified response function with a -stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant)Generate regressors by convolving a specified response function with a stimulus. — gen_conv_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Generate regressors by convolving a specified response function with a -stimulus.

    +

    Generate regressors by convolving a specified response function with a stimulus.

    Source: R/fmrs.R
    @@ -88,6 +85,9 @@

    Generate regressors by convolving a specified response function with a duration = NULL, trial_type = NULL, mrs_data = NULL, + tr = NULL, + Ndyns = NULL, + Ntrans = NULL, resp_fn, match_tr = TRUE, normalise = FALSE @@ -96,40 +96,53 @@

    Generate regressors by convolving a specified response function with a

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    -
    resp_fn
    +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    resp_fn

    a data frame specifying the response function to be convolved.

    -
    match_tr
    +
    match_tr

    match the output to the input mrs_data.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    BOLD regressor data frame.

    +

    BOLD regressor data frame.

    @@ -144,15 +157,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_group_reg.html b/docs/reference/gen_group_reg.html new file mode 100644 index 00000000..f0a94a5e --- /dev/null +++ b/docs/reference/gen_group_reg.html @@ -0,0 +1,120 @@ + +Expand a regressor matrix for a group analysis. — gen_group_reg • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Expand a regressor matrix for a group analysis.

    + Source: R/fmrs.R + +
    + +
    +

    Expand a regressor matrix for a group analysis.

    +
    + +
    + 
    gen_group_reg(regressor_df, n)
    +
    + +
    +

    Arguments

    + + +
    regressor_df
    +

    input regressor data frame.

    + + +
    n
    +

    number of datasets n the group.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/gen_impulse_reg.html b/docs/reference/gen_impulse_reg.html index a900c805..a21ddc01 100644 --- a/docs/reference/gen_impulse_reg.html +++ b/docs/reference/gen_impulse_reg.html @@ -1,9 +1,9 @@ -Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant)Generate impulse regressors. — gen_impulse_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,28 +78,48 @@

    Generate impulse regressors.

    - 
    gen_impulse_reg(onset, trial_type = NULL, mrs_data = NULL)
    + 
    gen_impulse_reg(
+  onset,
+  trial_type = NULL,
+  mrs_data = NULL,
+  tr = NULL,
+  Ndyns = NULL,
+  Ntrans = NULL
+)

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    + +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    +

    Value

    - - -

    impulse regressors data frame.

    +

    impulse regressors data frame.

    @@ -114,15 +134,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_poly_reg.html b/docs/reference/gen_poly_reg.html index 44c2aee5..091f3928 100644 --- a/docs/reference/gen_poly_reg.html +++ b/docs/reference/gen_poly_reg.html @@ -1,9 +1,9 @@ -Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant)Generate polynomial regressors. — gen_poly_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,24 +78,37 @@

    Generate polynomial regressors.

    - 
    gen_poly_reg(mrs_data, degree)
    + 
    gen_poly_reg(degree, mrs_data = NULL, tr = NULL, Ndyns = NULL, Ntrans = NULL)

    Arguments

    -
    mrs_data
    -

    mrs_data object for timing information.

    -
    degree
    +
    degree

    the degree of the polynomial.

    + +
    mrs_data
    +

    mrs_data object for timing information.

    + + +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    +

    Value

    - - -

    polynomial regressors.

    +

    polynomial regressors.

    @@ -110,15 +123,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gen_trap_reg.html b/docs/reference/gen_trap_reg.html index 6c3d083a..c63d78da 100644 --- a/docs/reference/gen_trap_reg.html +++ b/docs/reference/gen_trap_reg.html @@ -1,9 +1,9 @@ -Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant)Generate trapezoidal regressors. — gen_trap_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,6 +83,9 @@

    Generate trapezoidal regressors.

    duration, trial_type = NULL, mrs_data = NULL, + tr = NULL, + Ndyns = NULL, + Ntrans = NULL, rise_t = 0, fall_t = 0, exp_fall = FALSE, @@ -96,61 +99,74 @@

    Generate trapezoidal regressors.

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    -
    rise_t
    +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +

    number of dynamic scans stored, potentially less than Ntrans +if block averaging has been performed.

    + + +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    rise_t

    time to reach a plateau from baseline in seconds.

    -
    fall_t
    +
    fall_t

    time to fall from plateau level back to baseline in seconds.

    -
    exp_fall
    +
    exp_fall

    model an exponential fall instead of linear.

    -
    exp_fall_power
    +
    exp_fall_power

    exponential fall power.

    -
    smo_sigma
    +
    smo_sigma

    standard deviation of Gaussian smoothing kernel in seconds. Set to NULL to disable (default behavior).

    -
    match_tr
    +
    match_tr

    match the output to the input mrs_data.

    -
    dt
    +
    dt

    timing resolution for internal calculations.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    trapezoidal regressor data frame.

    +

    trapezoidal regressor data frame.

    @@ -165,15 +181,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_brain_basis_names.html b/docs/reference/get_1h_brain_basis_names.html index a8496ee7..21e35d12 100644 --- a/docs/reference/get_1h_brain_basis_names.html +++ b/docs/reference/get_1h_brain_basis_names.html @@ -1,12 +1,10 @@ -Return a character vector of common 1H molecules found in healthy human -brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant)Return a character vector of common 1H molecules found in healthy human brain. — get_1h_brain_basis_names • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a character vector of common 1H molecules found in healthy human -brain.

    +

    Return a character vector of common 1H molecules found in healthy human brain.

    Source: R/qm_simulation.R
    @@ -88,25 +85,25 @@

    Return a character vector of common 1H molecules found in healthy human

    Arguments

    -
    add
    + + +
    add

    optional character vector of additional molecular names. Eg c("asc", "gly", "peth").

    -
    remove
    +
    remove

    optional character vector of molecular names to remove from the set. Eg c("m_cr_ch2").

    -
    inc_lip_mm
    +
    inc_lip_mm

    include Lipid and MM basis signals.

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -121,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras.html b/docs/reference/get_1h_brain_basis_paras.html index 90abfc02..c19295cd 100644 --- a/docs/reference/get_1h_brain_basis_paras.html +++ b/docs/reference/get_1h_brain_basis_paras.html @@ -1,12 +1,10 @@ -Return a list of mol_parameter objects suitable for 1H brain MRS -analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant)Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    Source: R/qm_simulation.R
    @@ -88,24 +85,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -120,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v1.html b/docs/reference/get_1h_brain_basis_paras_v1.html index d957fd50..4ee05707 100644 --- a/docs/reference/get_1h_brain_basis_paras_v1.html +++ b/docs/reference/get_1h_brain_basis_paras_v1.html @@ -1,12 +1,10 @@ -Return a list of mol_parameter objects suitable for 1H brain MRS -analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant)Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v1 • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    Source: R/qm_simulation.R
    @@ -88,24 +85,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -120,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v2.html b/docs/reference/get_1h_brain_basis_paras_v2.html index 646ddaae..e8e8412a 100644 --- a/docs/reference/get_1h_brain_basis_paras_v2.html +++ b/docs/reference/get_1h_brain_basis_paras_v2.html @@ -1,12 +1,10 @@ -Return a list of mol_parameter objects suitable for 1H brain MRS -analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant)Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v2 • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    Source: R/qm_simulation.R
    @@ -88,24 +85,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -120,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v3.html b/docs/reference/get_1h_brain_basis_paras_v3.html index f43240a2..d72bc3ba 100644 --- a/docs/reference/get_1h_brain_basis_paras_v3.html +++ b/docs/reference/get_1h_brain_basis_paras_v3.html @@ -1,12 +1,10 @@ -Return a list of mol_parameter objects suitable for 1H brain MRS -analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant)Return a list of mol_parameter objects suitable for 1H brain MRS analyses. — get_1h_brain_basis_paras_v3 • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    Source: R/qm_simulation.R
    @@ -88,24 +85,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -120,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_braino_basis_names.html b/docs/reference/get_1h_braino_basis_names.html index c7cb2fcc..a8d4bf8d 100644 --- a/docs/reference/get_1h_braino_basis_names.html +++ b/docs/reference/get_1h_braino_basis_names.html @@ -1,9 +1,9 @@ -Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant)Return a character vector of molecules included in the GE BRAINO phantom. — get_1h_braino_basis_names • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,9 +83,7 @@

    Return a character vector of molecules included in the GE BRAINO phantom.

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -100,15 +98,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_1h_spectre_basis_names.html b/docs/reference/get_1h_spectre_basis_names.html index 14f088ac..3b94f74d 100644 --- a/docs/reference/get_1h_spectre_basis_names.html +++ b/docs/reference/get_1h_spectre_basis_names.html @@ -1,12 +1,10 @@ -Return a character vector of molecules included in the Gold Star Phantoms -SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant)Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom. — get_1h_spectre_basis_names • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a character vector of molecules included in the Gold Star Phantoms -SPECTRE phantom.

    +

    Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.

    Source: R/qm_simulation.R
    @@ -88,9 +85,7 @@

    Return a character vector of molecules included in the Gold Star Phantoms

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -105,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_2d_psf.html b/docs/reference/get_2d_psf.html index b6656923..c625d78d 100644 --- a/docs/reference/get_2d_psf.html +++ b/docs/reference/get_2d_psf.html @@ -1,9 +1,9 @@ -Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant)Get the point spread function (PSF) for a 2D phase encoded MRSI scan. — get_2d_psf • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -89,32 +89,32 @@

    Get the point spread function (PSF) for a 2D phase encoded MRSI scan.

    Arguments

    -
    FOV
    + + +
    FOV

    field of view in mm.

    -
    mat_size
    +
    mat_size

    acquisition matrix size (not interpolated).

    -
    sampling
    +
    sampling

    can be either "circ" for circular or "rect" for rectangular.

    -
    hamming
    +
    hamming

    should Hamming k-space weighting be applied (default FALSE).

    -
    ensure_odd
    +
    ensure_odd

    add 1mm to the FOV when required to ensure the output pdf has odd dimensions. Required when using get_mrsi2d_seg.

    Value

    - - -

    A matrix of the PSF with 1mm resolution.

    +

    A matrix of the PSF with 1mm resolution.

    @@ -129,15 +129,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_acq_paras.html b/docs/reference/get_acq_paras.html index 5bb919aa..cb2396c2 100644 --- a/docs/reference/get_acq_paras.html +++ b/docs/reference/get_acq_paras.html @@ -1,9 +1,9 @@ -Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant)Return acquisition parameters from a MRS data object. — get_acq_paras • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return acquisition parameters from a MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    list of acquisition parameters.

    +

    list of acquisition parameters.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_basis_subset.html b/docs/reference/get_basis_subset.html index b7c1b5ed..74bf51e7 100644 --- a/docs/reference/get_basis_subset.html +++ b/docs/reference/get_basis_subset.html @@ -1,9 +1,9 @@ -Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant)Return a subset of the input basis. — get_basis_subset • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Return a subset of the input basis.

    Arguments

    -
    basis
    + + +
    basis

    input basis.

    -
    names
    +
    names

    basis set elements to keep in the returned object.

    -
    invert
    +
    invert

    set to true to return all basis elements except those given in the names argument.

    Value

    - - -

    a subset of the input basis.

    +

    a subset of the input basis.

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_dyns.html b/docs/reference/get_dyns.html index d4376131..abcbb517 100644 --- a/docs/reference/get_dyns.html +++ b/docs/reference/get_dyns.html @@ -1,9 +1,9 @@ -Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant)Extract a subset of dynamic scans. — get_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Extract a subset of dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be returned.

    Value

    - - -

    MRS data containing the subset of requested dynamics.

    +

    MRS data containing the subset of requested dynamics.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_even_dyns.html b/docs/reference/get_even_dyns.html index 85fac0a6..62fe1965 100644 --- a/docs/reference/get_even_dyns.html +++ b/docs/reference/get_even_dyns.html @@ -1,9 +1,9 @@ -Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant)Return even numbered dynamic scans starting from 1 (2,4,6...). — get_even_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return even numbered dynamic scans starting from 1 (2,4,6...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data containing even numbered scans.

    +

    dynamic MRS data containing even numbered scans.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_fh_dyns.html b/docs/reference/get_fh_dyns.html index 80d45928..c8e309dc 100644 --- a/docs/reference/get_fh_dyns.html +++ b/docs/reference/get_fh_dyns.html @@ -1,9 +1,9 @@ -Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant)Return the first half of a dynamic series. — get_fh_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the first half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    first half of the dynamic series.

    +

    first half of the dynamic series.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_fit_map.html b/docs/reference/get_fit_map.html index 9584babd..cceefb27 100644 --- a/docs/reference/get_fit_map.html +++ b/docs/reference/get_fit_map.html @@ -1,9 +1,9 @@ -Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant)Get a data array from a fit result. — get_fit_map • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Get a data array from a fit result.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    name
    +
    name

    name of the quantity to plot, eg "tNAA".

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_fp.html b/docs/reference/get_fp.html index cce9f222..0e2fcf09 100644 --- a/docs/reference/get_fp.html +++ b/docs/reference/get_fp.html @@ -1,9 +1,9 @@ -Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant)Return the first time-domain data point. — get_fp • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the first time-domain data point.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    first time-domain data point.

    +

    first time-domain data point.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_guassian_pulse.html b/docs/reference/get_guassian_pulse.html index 739ef620..f4432ddc 100644 --- a/docs/reference/get_guassian_pulse.html +++ b/docs/reference/get_guassian_pulse.html @@ -1,9 +1,9 @@ -Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant)Generate a gaussian pulse shape. — get_guassian_pulse • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Generate a gaussian pulse shape.

    Arguments

    -
    angle
    + + +
    angle

    pulse angle in degrees.

    -
    n
    +
    n

    number of points to generate.

    -
    trunc
    +
    trunc

    percentage truncation factor.

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_head_dyns.html b/docs/reference/get_head_dyns.html index 075c37b7..4bfd0672 100644 --- a/docs/reference/get_head_dyns.html +++ b/docs/reference/get_head_dyns.html @@ -1,9 +1,9 @@ -Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant)Return the first scans of a dynamic series. — get_head_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Return the first scans of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    n
    +
    n

    the number of dynamic scans to return.

    Value

    - - -

    first scans of a dynamic series.

    +

    first scans of a dynamic series.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_lcm_cmd.html b/docs/reference/get_lcm_cmd.html index 84ae0186..738108cf 100644 --- a/docs/reference/get_lcm_cmd.html +++ b/docs/reference/get_lcm_cmd.html @@ -1,9 +1,9 @@ -Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant)Print the command to run the LCModel command-line program. — get_lcm_cmd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,15 +94,15 @@

    Print the command to run the LCModel command-line program.

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_metab.html b/docs/reference/get_metab.html index 8c345609..03fb42ac 100644 --- a/docs/reference/get_metab.html +++ b/docs/reference/get_metab.html @@ -1,9 +1,9 @@ -Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant)Extract the metabolite component from an mrs_data object. — get_metab • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Extract the metabolite component from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    metabolite component.

    +

    metabolite component.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mol_names.html b/docs/reference/get_mol_names.html index ac6a75b5..86eb838a 100644 --- a/docs/reference/get_mol_names.html +++ b/docs/reference/get_mol_names.html @@ -1,12 +1,10 @@ -Return a character array of names that may be used with the -get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant)Return a character array of names that may be used with the get_mol_paras function. — get_mol_names • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return a character array of names that may be used with the -get_mol_paras function.

    +

    Return a character array of names that may be used with the get_mol_paras function.

    Source: R/mol_parameters.R
    @@ -88,9 +85,7 @@

    Return a character array of names that may be used with the

    Value

    - - -

    a character array of names.

    +

    a character array of names.

    @@ -105,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mol_paras.html b/docs/reference/get_mol_paras.html index 81f5a5c0..c501cb39 100644 --- a/docs/reference/get_mol_paras.html +++ b/docs/reference/get_mol_paras.html @@ -1,9 +1,9 @@ -Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant)Get a mol_parameters object for a named molecule. — get_mol_paras • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Get a mol_parameters object for a named molecule.

    Arguments

    -
    name
    + + +
    name

    the name of the molecule.

    -
    ...
    +
    ...

    arguments to pass to molecule definition function.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mrs_affine.html b/docs/reference/get_mrs_affine.html index ae0672bd..aae8e6c7 100644 --- a/docs/reference/get_mrs_affine.html +++ b/docs/reference/get_mrs_affine.html @@ -1,9 +1,9 @@ -Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant)Generate an affine for nifti generation. — get_mrs_affine • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,27 @@

    Generate an affine for nifti generation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    input data.

    -
    x_pos
    +
    x_pos

    x_position coordinate.

    -
    y_pos
    +
    y_pos

    y_position coordinate.

    -
    z_pos
    +
    z_pos

    z_position coordinate.

    Value

    - - -

    affine matrix.

    +

    affine matrix.

    @@ -118,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mrsi2d_seg.html b/docs/reference/get_mrsi2d_seg.html index c8d981cd..032b7ddf 100644 --- a/docs/reference/get_mrsi2d_seg.html +++ b/docs/reference/get_mrsi2d_seg.html @@ -1,10 +1,10 @@ -Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant)Calculate the partial volume estimates for each voxel in a 2D MRSI dataset. — get_mrsi2d_seg • Spectroscopy Analysis Tools (spant) - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -85,25 +85,25 @@

    Calculate the partial volume estimates for each voxel in a 2D MRSI dataset.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data with multiple voxels in the x-y dimension.

    -
    mri_seg
    +
    mri_seg

    MRI data with values corresponding to the segmentation class. Must be 1mm isotropic resolution.

    -
    ker
    +
    ker

    MRSI PSF kernel in the x-y direction compatible with the mmand package, eg: mmand::shapeKernel(c(10, 10), type = "box").

    Value

    - - -

    a data frame of partial volume estimates and individual segmentation +

    a data frame of partial volume estimates and individual segmentation maps.

    @@ -119,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mrsi_voi.html b/docs/reference/get_mrsi_voi.html index 429cac99..62144145 100644 --- a/docs/reference/get_mrsi_voi.html +++ b/docs/reference/get_mrsi_voi.html @@ -1,9 +1,9 @@ -Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant)Generate a MRSI VOI from an mrs_data object. — get_mrsi_voi • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,28 +83,28 @@

    Generate a MRSI VOI from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    map
    +
    map

    optional voi intensity map.

    -
    ker
    +
    ker

    kernel to rescale the map data to the target_mri. Default value is mmand::boxKernel(), use mmand::mnKernel() for a smoothed map.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -119,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mrsi_voxel.html b/docs/reference/get_mrsi_voxel.html index c4255416..52b5074d 100644 --- a/docs/reference/get_mrsi_voxel.html +++ b/docs/reference/get_mrsi_voxel.html @@ -1,9 +1,9 @@ -Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant)Generate a MRSI voxel from an mrs_data object. — get_mrsi_voxel • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Generate a MRSI voxel from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    x_pos
    +
    x_pos

    x voxel coordinate.

    -
    y_pos
    +
    y_pos

    y voxel coordinate.

    -
    z_pos
    +
    z_pos

    z voxel coordinate.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_mrsi_voxel_xy_psf.html b/docs/reference/get_mrsi_voxel_xy_psf.html index 04c90780..c37cd545 100644 --- a/docs/reference/get_mrsi_voxel_xy_psf.html +++ b/docs/reference/get_mrsi_voxel_xy_psf.html @@ -1,9 +1,9 @@ -Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant)Generate a MRSI voxel PSF from an mrs_data object. — get_mrsi_voxel_xy_psf • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Generate a MRSI voxel PSF from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    x_pos
    +
    x_pos

    x voxel coordinate.

    -
    y_pos
    +
    y_pos

    y voxel coordinate.

    -
    z_pos
    +
    z_pos

    z voxel coordinate.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_odd_dyns.html b/docs/reference/get_odd_dyns.html index d016c241..ccf08461 100644 --- a/docs/reference/get_odd_dyns.html +++ b/docs/reference/get_odd_dyns.html @@ -1,9 +1,9 @@ -Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant)Return odd numbered dynamic scans starting from 1 (1,3,5...). — get_odd_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return odd numbered dynamic scans starting from 1 (1,3,5...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data containing odd numbered scans.

    +

    dynamic MRS data containing odd numbered scans.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_ref.html b/docs/reference/get_ref.html index d8234a92..64409895 100644 --- a/docs/reference/get_ref.html +++ b/docs/reference/get_ref.html @@ -1,9 +1,9 @@ -Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant)Extract the reference component from an mrs_data object. — get_ref • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Extract the reference component from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    reference component.

    +

    reference component.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_seg_ind.html b/docs/reference/get_seg_ind.html index e97e51ac..ad344549 100644 --- a/docs/reference/get_seg_ind.html +++ b/docs/reference/get_seg_ind.html @@ -1,9 +1,9 @@ -Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant)Get the indices of data points lying between two values (end > x > start). — get_seg_ind • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Get the indices of data points lying between two values (end > x > sta

    Arguments

    -
    scale
    + + +
    scale

    full list of values.

    -
    start
    +
    start

    smallest value in the subset.

    -
    end
    +
    end

    largest value in the subset.

    Value

    - - -

    set of indices.

    +

    set of indices.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_sh_dyns.html b/docs/reference/get_sh_dyns.html index 932c4247..3370bdd8 100644 --- a/docs/reference/get_sh_dyns.html +++ b/docs/reference/get_sh_dyns.html @@ -1,9 +1,9 @@ -Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant)Return the second half of a dynamic series. — get_sh_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the second half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    second half of the dynamic series.

    +

    second half of the dynamic series.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_slice.html b/docs/reference/get_slice.html index e8b9fa7e..d804fa88 100644 --- a/docs/reference/get_slice.html +++ b/docs/reference/get_slice.html @@ -1,9 +1,9 @@ -Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant)Return a single slice from a larger MRSI dataset. — get_slice • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Return a single slice from a larger MRSI dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    -
    z_pos
    +
    z_pos

    the z index to extract.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_spin_num.html b/docs/reference/get_spin_num.html index 021d4e60..ee0105f7 100644 --- a/docs/reference/get_spin_num.html +++ b/docs/reference/get_spin_num.html @@ -1,9 +1,9 @@ -Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant)Return the spin number for a given nucleus. — get_spin_num • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the spin number for a given nucleus.

    Arguments

    -
    nucleus
    + + +
    nucleus

    nucleus name, eg "1H".

    Value

    - - -

    spin number.

    +

    spin number.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_subset.html b/docs/reference/get_subset.html index 34df3128..a58693f3 100644 --- a/docs/reference/get_subset.html +++ b/docs/reference/get_subset.html @@ -1,9 +1,9 @@ -Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant)Extract a subset of MRS data. — get_subset • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -92,44 +92,44 @@

    Extract a subset of MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_set
    +
    x_set

    x indices to include in the output (default all).

    -
    y_set
    +
    y_set

    y indices to include in the output (default all).

    -
    z_set
    +
    z_set

    z indices to include in the output (default all).

    -
    dyn_set
    +
    dyn_set

    dynamic indices to include in the output (default all).

    -
    coil_set
    +
    coil_set

    coil indices to include in the output (default all).

    -
    fd_set
    +
    fd_set

    frequency domain data indices to include in the output (default all).

    -
    td_set
    +
    td_set

    time-domain indices to include in the output (default all).

    Value

    - - -

    selected subset of MRS data.

    +

    selected subset of MRS data.

    @@ -144,15 +144,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_svs_voi.html b/docs/reference/get_svs_voi.html index 54de4821..b079c5f3 100644 --- a/docs/reference/get_svs_voi.html +++ b/docs/reference/get_svs_voi.html @@ -1,9 +1,9 @@ -Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant)Generate a SVS acquisition volume from an mrs_data object. — get_svs_voi • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Generate a SVS acquisition volume from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_tail_dyns.html b/docs/reference/get_tail_dyns.html index cace1556..38836a73 100644 --- a/docs/reference/get_tail_dyns.html +++ b/docs/reference/get_tail_dyns.html @@ -1,9 +1,9 @@ -Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant)Return the last scans of a dynamic series. — get_tail_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Return the last scans of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    n
    +
    n

    the number of dynamic scans to return.

    Value

    - - -

    last scans of a dynamic series.

    +

    last scans of a dynamic series.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_td_amp.html b/docs/reference/get_td_amp.html index ad9f3f71..1d563918 100644 --- a/docs/reference/get_td_amp.html +++ b/docs/reference/get_td_amp.html @@ -1,12 +1,10 @@ -Return an array of amplitudes derived from fitting the initial points in the -time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant)Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0. — get_td_amp • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Return an array of amplitudes derived from fitting the initial points in the -time domain and extrapolating back to t=0.

    +

    Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.

    Source: R/mrs_data_proc.R
    @@ -88,28 +85,28 @@

    Return an array of amplitudes derived from fitting the initial points in the

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    nstart
    +
    nstart

    first data point to fit.

    -
    nend
    +
    nend

    last data point to fit.

    -
    method
    +
    method

    method for measuring the amplitude, one of "poly", spline" or exp".

    Value

    - - -

    array of amplitudes.

    +

    array of amplitudes.

    @@ -124,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_tqn_cmd.html b/docs/reference/get_tqn_cmd.html index 923b8751..826330fa 100644 --- a/docs/reference/get_tqn_cmd.html +++ b/docs/reference/get_tqn_cmd.html @@ -1,9 +1,9 @@ -Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant)Print the command to run the TARQUIN command-line program. — get_tqn_cmd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,15 +94,15 @@

    Print the command to run the TARQUIN command-line program.

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_uncoupled_mol.html b/docs/reference/get_uncoupled_mol.html index 0747cc21..dc78ea7a 100644 --- a/docs/reference/get_uncoupled_mol.html +++ b/docs/reference/get_uncoupled_mol.html @@ -1,12 +1,10 @@ -Generate a mol_parameters object for a simple spin system with one -resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant)Generate a mol_parameters object for a simple spin system with one resonance. — get_uncoupled_mol • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Generate a mol_parameters object for a simple spin system with one -resonance.

    +

    Generate a mol_parameters object for a simple spin system with one resonance.

    Source: R/mol_parameters.R
    @@ -96,40 +93,40 @@

    Generate a mol_parameters object for a simple spin system with

    Arguments

    -
    name
    + + +
    name

    abbreviated name of the molecule.

    -
    chem_shift
    +
    chem_shift

    chemical shift of the resonance (PPM).

    -
    nucleus
    +
    nucleus

    nucleus (1H, 31P...).

    -
    scale_factor
    +
    scale_factor

    multiplicative scaling factor. Note, this value can be made complex to adjust the phase of the resonance.

    -
    lw
    +
    lw

    linewidth in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    -
    full_name
    +
    full_name

    long name of the molecule (optional).

    Value

    - - -

    mol_parameters object.

    +

    mol_parameters object.

    @@ -144,15 +141,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_voi_cog.html b/docs/reference/get_voi_cog.html index 9c556ad1..aeaaf06b 100644 --- a/docs/reference/get_voi_cog.html +++ b/docs/reference/get_voi_cog.html @@ -1,9 +1,9 @@ -Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant)Calculate the centre of gravity for an image containing 0 and 1's. — get_voi_cog • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the centre of gravity for an image containing 0 and 1's.

    Arguments

    -
    voi
    + + +
    voi

    nifti object.

    Value

    - - -

    triplet of x,y,z coordinates.

    +

    triplet of x,y,z coordinates.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_voi_seg.html b/docs/reference/get_voi_seg.html index 9f0f7f44..b749d90c 100644 --- a/docs/reference/get_voi_seg.html +++ b/docs/reference/get_voi_seg.html @@ -1,9 +1,9 @@ -Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant)Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Return the white matter, gray matter and CSF composition of a volume.

    Arguments

    -
    voi
    + + +
    voi

    volume data as a nifti object.

    -
    mri_seg
    +
    mri_seg

    segmented brain volume as a nifti object.

    Value

    - - -

    a vector of partial volumes expressed as percentages.

    +

    a vector of partial volumes expressed as percentages.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_voi_seg_psf.html b/docs/reference/get_voi_seg_psf.html index 2e632a30..26f01fa1 100644 --- a/docs/reference/get_voi_seg_psf.html +++ b/docs/reference/get_voi_seg_psf.html @@ -1,9 +1,9 @@ -Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant)Return the white matter, gray matter and CSF composition of a volume. — get_voi_seg_psf • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Return the white matter, gray matter and CSF composition of a volume.

    Arguments

    -
    psf
    + + +
    psf

    volume data as a nifti object.

    -
    mri_seg
    +
    mri_seg

    segmented brain volume as a nifti object.

    Value

    - - -

    a vector of partial volumes expressed as percentages.

    +

    a vector of partial volumes expressed as percentages.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/get_voxel.html b/docs/reference/get_voxel.html index cb474e6c..79d26897 100644 --- a/docs/reference/get_voxel.html +++ b/docs/reference/get_voxel.html @@ -1,9 +1,9 @@ -Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant)Return a single voxel from a larger mrs dataset. — get_voxel • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,35 +83,35 @@

    Return a single voxel from a larger mrs dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    x_pos
    +
    x_pos

    the x index to plot.

    -
    y_pos
    +
    y_pos

    the y index to plot.

    -
    z_pos
    +
    z_pos

    the z index to plot.

    -
    dyn
    +
    dyn

    the dynamic index to plot.

    -
    coil
    +
    coil

    the coil element number to plot.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -126,15 +126,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/glm_spec.html b/docs/reference/glm_spec.html index 20459117..bb9bb336 100644 --- a/docs/reference/glm_spec.html +++ b/docs/reference/glm_spec.html @@ -1,9 +1,9 @@ -Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant)Perform a GLM analysis of dynamic MRS data in the spectral domain. — glm_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,25 +78,29 @@

    Perform a GLM analysis of dynamic MRS data in the spectral domain.

    - 
    glm_spec(mrs_data, regressor_df)
    + 
    glm_spec(mrs_data, regressor_df, full_output = FALSE)

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    single-voxel dynamics MRS data.

    -
    regressor_df
    +
    regressor_df

    a data frame containing temporal regressors to be applied to each spectral datapoint.

    + +
    full_output
    +

    append mrs_data and regressor_df to the output list.

    +

    Value

    - - -

    list of statistical results.

    +

    list of statistical results.

    @@ -111,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/glm_spec_fmrs_fl.html b/docs/reference/glm_spec_fmrs_fl.html new file mode 100644 index 00000000..13bbf1da --- /dev/null +++ b/docs/reference/glm_spec_fmrs_fl.html @@ -0,0 +1,151 @@ + +Perform first-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_fl • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Perform first-level spectral GLM analysis of an fMRS dataset.

    + Source: R/fmrs.R + +
    + +
    +

    Perform first-level spectral GLM analysis of an fMRS dataset.

    +
    + +
    + 
    glm_spec_fmrs_fl(
+  regressor_df,
+  analysis_dir = "spant_analysis",
+  exclude_labels = NULL,
+  labels = NULL,
+  xlim = c(4, 0.2),
+  vline = c(1.35, 1.28, 2.35, 2.29),
+  return_results = FALSE
+)
    +
    + +
    +

    Arguments

    + + +
    regressor_df
    +

    a data frame containing temporal regressors to be applied +to each spectral datapoint.

    + + +
    analysis_dir
    +

    directory containing preprocessed data generated by +the preproc_svs_dataset function.

    + + +
    exclude_labels
    +

    vector of labels of scans to exclude, eg poor quality +data.

    + + +
    labels
    +

    labels to describe each data set.

    + + +
    xlim
    +

    spectral range to include in the analysis.

    + + +
    vline
    +

    vertical lines to add to the plot.

    + + +
    return_results
    +

    function will return key outputs, defaults to FALSE.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/glm_spec_fmrs_group.html b/docs/reference/glm_spec_fmrs_group.html new file mode 100644 index 00000000..12ca453b --- /dev/null +++ b/docs/reference/glm_spec_fmrs_group.html @@ -0,0 +1,136 @@ + +Perform group-level spectral GLM analysis of an fMRS dataset. — glm_spec_fmrs_group • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Perform group-level spectral GLM analysis of an fMRS dataset.

    + Source: R/fmrs.R + +
    + +
    +

    Perform group-level spectral GLM analysis of an fMRS dataset.

    +
    + +
    + 
    glm_spec_fmrs_group(
+  regressor_df,
+  analysis_dir = "spant_analysis",
+  exclude_labels = NULL,
+  labels = NULL
+)
    +
    + +
    +

    Arguments

    + + +
    regressor_df
    +

    a data frame containing temporal regressors to be applied +to each spectral datapoint.

    + + +
    analysis_dir
    +

    directory containing preprocessed data generated by +the preproc_svs_dataset function.

    + + +
    exclude_labels
    +

    vector of labels of scans to exclude, eg poor quality +data.

    + + +
    labels
    +

    labels to describe each data set.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/glm_spec_group_linhyp.html b/docs/reference/glm_spec_group_linhyp.html new file mode 100644 index 00000000..bfea8f75 --- /dev/null +++ b/docs/reference/glm_spec_group_linhyp.html @@ -0,0 +1,121 @@ + +Test a group-level spectral GLM linear hypothesis. — glm_spec_group_linhyp • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Test a group-level spectral GLM linear hypothesis.

    + Source: R/fmrs.R + +
    + +
    +

    Test a group-level spectral GLM linear hypothesis.

    +
    + +
    + 
    glm_spec_group_linhyp(hmat, analysis_dir = "spant_analysis")
    +
    + +
    +

    Arguments

    + + +
    hmat
    +

    linear hypothesis matrix.

    + + +
    analysis_dir
    +

    directory containing preprocessed data generated by +the preproc_svs_dataset function.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/grid_shift_xy.html b/docs/reference/grid_shift_xy.html index 592fa3ec..87366325 100644 --- a/docs/reference/grid_shift_xy.html +++ b/docs/reference/grid_shift_xy.html @@ -1,9 +1,9 @@ -Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant)Grid shift MRSI data in the x/y dimension. — grid_shift_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Grid shift MRSI data in the x/y dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data in the spatial domain.

    -
    x_shift
    +
    x_shift

    shift to apply in the x-direction in units of voxels.

    -
    y_shift
    +
    y_shift

    shift to apply in the y-direction in units of voxels.

    Value

    - - -

    shifted data.

    +

    shifted data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gridplot.html b/docs/reference/gridplot.html index ca385d91..7b12b0c1 100644 --- a/docs/reference/gridplot.html +++ b/docs/reference/gridplot.html @@ -1,9 +1,9 @@ -Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant)Arrange spectral plots in a grid. — gridplot • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Arrange spectral plots in a grid.

    Arguments

    -
    x
    + + +
    x

    object for plotting.

    -
    ...
    +
    ...

    arguments to be passed to methods.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/gridplot.mrs_data.html b/docs/reference/gridplot.mrs_data.html index 1f4d09b5..d98a337d 100644 --- a/docs/reference/gridplot.mrs_data.html +++ b/docs/reference/gridplot.mrs_data.html @@ -1,9 +1,9 @@ -Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant)Arrange spectral plots in a grid. — gridplot.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,7 +78,7 @@

    Arrange spectral plots in a grid.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 gridplot(
   x,
   rows = NA,
@@ -93,36 +93,38 @@ 
    Arrange spectral plots in a grid.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    rows
    
+
    rows
    
 
    number of grid rows.
    
 
 
-
    cols
    
+
    cols
    
 
    number of grid columns.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    oma
    
+
    oma
    
 
    outer margin area.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -139,15 +141,15 @@ 
    Arguments
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/hsvd.html b/docs/reference/hsvd.html index 25734f49..7a762164 100644 --- a/docs/reference/hsvd.html +++ b/docs/reference/hsvd.html @@ -1,12 +1,12 @@ -HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant)HSVD of an mrs_data object. — hsvd • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -89,27 +89,27 @@

    HSVD of an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object to be decomposed.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor.

    Value

    - - -

    basis matrix and signal table.

    +

    basis matrix and signal table.

    @@ -124,15 +124,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hsvd_filt.html b/docs/reference/hsvd_filt.html index d18dfc49..c2237b7f 100644 --- a/docs/reference/hsvd_filt.html +++ b/docs/reference/hsvd_filt.html @@ -1,12 +1,12 @@ -HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant)HSVD based signal filter. — hsvd_filt • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -97,41 +97,41 @@

    HSVD based signal filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    xlim
    +
    xlim

    frequency range to filter, default units are Hz which can be changed to ppm using the "scale" argument.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor.

    -
    scale
    +
    scale

    either "hz" or "ppm" to set the frequency units of xlim.

    -
    return_model
    +
    return_model

    by default the filtered spectrum is returned. Set return_model to TRUE to return the HSVD model of the data.

    Value

    - - -

    filtered data or model depending on the return_model argument.

    +

    filtered data or model depending on the return_model argument.

    @@ -146,15 +146,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hsvd_vec.html b/docs/reference/hsvd_vec.html index acd13582..e9cc1dd8 100644 --- a/docs/reference/hsvd_vec.html +++ b/docs/reference/hsvd_vec.html @@ -1,12 +1,12 @@ -HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant)HSVD of a complex vector. — hsvd_vec • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -89,32 +89,32 @@

    HSVD of a complex vector.

    Arguments

    -
    y
    + + +
    y

    time domain signal to be filtered as a vector.

    -
    fs
    +
    fs

    sampling frequency of y.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor. Default value of 0 ensures resultant model is damped.

    Value

    - - -

    basis matrix and signal table.

    +

    basis matrix and signal table.

    @@ -129,15 +129,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hz.html b/docs/reference/hz.html index 3d72fdc4..698584fd 100644 --- a/docs/reference/hz.html +++ b/docs/reference/hz.html @@ -1,9 +1,9 @@ -Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant)Return the frequency scale of an MRS dataset in Hz. — hz • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Return the frequency scale of an MRS dataset in Hz.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    Value

    - - -

    frequency scale.

    +

    frequency scale.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ift_shift.html b/docs/reference/ift_shift.html index 9fba4a24..30570990 100644 --- a/docs/reference/ift_shift.html +++ b/docs/reference/ift_shift.html @@ -1,9 +1,9 @@ -Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant)Perform an iffshift and ifft on a vector. — ift_shift • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Perform an iffshift and ifft on a vector.

    Arguments

    -
    vec_in
    + + +
    vec_in

    vector input.

    Value

    - - -

    output vector.

    +

    output vector.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ift_shift_mat.html b/docs/reference/ift_shift_mat.html index 1a7c85ca..c809b6f6 100644 --- a/docs/reference/ift_shift_mat.html +++ b/docs/reference/ift_shift_mat.html @@ -1,12 +1,10 @@ -Perform an ifft and ifftshift on a matrix with each column replaced by its -shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant)Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft. — ift_shift_mat • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform an ifft and ifftshift on a matrix with each column replaced by its -shifted ifft.

    +

    Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Perform an ifft and ifftshift on a matrix with each column replaced by its

    Arguments

    -
    mat_in
    + + +
    mat_in

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/image.mrs_data.html b/docs/reference/image.mrs_data.html index 562be8ff..d6dad1d1 100644 --- a/docs/reference/image.mrs_data.html +++ b/docs/reference/image.mrs_data.html @@ -1,9 +1,9 @@ -Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant)Image plot method for objects of class mrs_data. — image.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,7 +78,7 @@

    Image plot method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 image(
   x,
   xlim = NULL,
@@ -92,8 +92,12 @@ 
    Image plot method for objects of class mrs_data.
    
   coil = 1,
   restore_def_par = TRUE,
   y_ticks = NULL,
-  vline = NULL,
   hline = NULL,
+  hline_lty = 2,
+  hline_col = "white",
+  vline = NULL,
+  vline_lty = 2,
+  vline_col = "white",
   legend = FALSE,
   ...
 )
    
@@ -101,73 +105,91 @@ 
    Image plot method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    col
    
+
    col
    
 
    Colour map to use, defaults to viridis.
    
 
 
-
    plot_dim
    
+
    plot_dim
    
 
    the dimension to display on the y-axis, can be one of: "dyn",
 "time_sec", x", "y", "z", "coil" or NULL. If NULL (the default) all spectra
 are collapsed into the dynamic dimension and displayed.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    y_ticks
    
+
    y_ticks
    
 
    a vector of indices specifying where to place additional red
 tick marks.
    
 
 
-
    vline
    
-
    draw a vertical line at the value of vline.
    
+
    hline
    
+
    add a horizontal line at the specified value.
    
+
 
+
    hline_lty
    
+
    linetype for the horizontal line.
    
 
-
    hline
    
-
    draw a horizontal line at the value of hline.
    
 
+
    hline_col
    
+
    colour for the horizontal line.
    
 
-
    legend
    
+
+
    vline
    
+
    add a vertical line at the specified value.
    
+
+
+
    vline_lty
    
+
    linetype for the vertical line.
    
+
+
+
    vline_col
    
+
    colour for the vertical line.
    
+
+
+
    legend
    
 
    add a colour bar to the plot using the imagePlot function
 from the fields package.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -184,15 +206,15 @@ 
    Arguments
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/img2kspace_xy.html b/docs/reference/img2kspace_xy.html index db04668f..1425b832 100644 --- a/docs/reference/img2kspace_xy.html +++ b/docs/reference/img2kspace_xy.html @@ -1,9 +1,9 @@ -Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant)Transform 2D MRSI data to k-space in the x-y direction. — img2kspace_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Transform 2D MRSI data to k-space in the x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data.

    Value

    - - -

    k-space data.

    +

    k-space data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 1ef7cafd..a0278cc7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • Spectroscopy Analysis Tools (spant)Package index • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,8 +90,7 @@

    All functions

    Imzap()

    -

    Complex rounding function taken from complexplus package to reduce the number -of spant dependencies.

    +

    Complex rounding function taken from complexplus package to reduce the number of spant dependencies.

    Mod(<mrs_data>)

    @@ -139,8 +138,7 @@

    All functions

    abfit_opts_v1_9_0()

    -

    Return a list of options for an ABfit analysis to maintain comparability with -analyses performed with version 1.9.0 (and earlier) of spant.

    +

    Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.

    acquire()

    @@ -168,13 +166,11 @@

    All functions

    append_coils()

    -

    Append MRS data across the coil dimension, assumes they matched across the -other dimensions.

    +

    Append MRS data across the coil dimension, assumes they matched across the other dimensions.

    append_dyns()

    -

    Append MRS data across the dynamic dimension, assumes they matched across the -other dimensions.

    +

    Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.

    append_regs()

    @@ -194,14 +190,11 @@

    All functions

    array2mrs_data()

    -

    Convert a 7 dimensional array in into a mrs_data object. The array dimensions -should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

    +

    Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

    auto_phase()

    -

    Perform zeroth-order phase correction based on the minimisation of the -squared difference between the real and magnitude components of the -spectrum.

    +

    Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.

    back_extrap_ar()

    @@ -213,13 +206,11 @@

    All functions

    basis2mrs_data()

    -

    Convert a basis object to an mrs_data object - where basis signals are spread -across the dynamic dimension.

    +

    Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.

    bbase()

    -

    Generate a spline basis, slightly adapted from : "Splines, knots, and -penalties", Eilers 2010.

    +

    Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.

    bc_als()

    @@ -243,12 +234,19 @@

    All functions

    beta2lw()

    -

    Covert a beta value in the time-domain to an equivalent linewidth in Hz: -x * exp(-i * t * t * beta).

    +

    Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).

    bin_spec()

    Bin equally spaced spectral regions.

    + +

    calc_basis_corr_mat()

    + +

    Estimate the correlation matrix for a basis set.

    + +

    calc_basis_crlbs()

    + +

    Estimate the CRLB for each element in a basis set.

    calc_coil_noise_cor()

    @@ -272,8 +270,7 @@

    All functions

    calc_sd_poly()

    -

    Perform a polynomial fit, subtract and return the standard deviation of the -residuals.

    +

    Perform a polynomial fit, subtract and return the standard deviation of the residuals.

    calc_spec_diff()

    @@ -306,6 +303,14 @@

    All functions comb_coils()

    Combine coil data based on the first data point of a reference signal.

    + +

    comb_coils_mrsi_gls()

    + +

    Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

    + +

    comb_coils_svs_gls()

    + +

    Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

    comb_fit_list_fit_tables()

    @@ -345,9 +350,7 @@

    All functions

    crop_td_pts_pot()

    -

    Crop mrs_data object data points in the time-domain rounding down to -the next smallest power of two (pot). Data that already has a pot length will -not be changed.

    +

    Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.

    crop_xy()

    @@ -355,13 +358,11 @@

    All functions

    crossprod_3d()

    -

    Compute the vector cross product between vectors x and y. Adapted from -http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

    +

    Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

    decimate_mrs_fd()

    -

    Decimate an MRS signal to half the original sampling frequency by filtering -in the frequency domain before down sampling.

    +

    Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.

    decimate_mrs_td()

    @@ -377,8 +378,7 @@

    All functions

    def_acq_paras()

    -

    Return (and optionally modify using the input arguments) a list of the -default acquisition parameters.

    +

    Return (and optionally modify using the input arguments) a list of the default acquisition parameters.

    def_fs()

    @@ -410,14 +410,11 @@

    All functions

    downsample_mrs_td()

    -

    Downsample an MRS signal by a factor of 2 by removing every other data point -in the time-domain. Note, signals outside the new sampling frequency will be -aliased.

    +

    Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.

    dyn_acq_times()

    -

    Return a time scale vector of acquisition times for a dynamic MRS scan. The -first temporal scan is assigned a value of 0.

    +

    Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.

    ecc()

    @@ -429,8 +426,7 @@

    All functions

    est_noise_sd()

    -

    Estimate the standard deviation of the noise from a segment of an mrs_data -object.

    +

    Estimate the standard deviation of the noise from a segment of an mrs_data object.

    fd2td()

    @@ -486,8 +482,7 @@

    All functions

    fp_phase_correct()

    -

    Perform a zeroth order phase correction based on the phase of the first data -point in the time-domain.

    +

    Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.

    fp_scale()

    @@ -507,8 +502,7 @@

    All functions

    ft_shift_mat()

    -

    Perform a fft and fftshift on a matrix with each column replaced by its -shifted fft.

    +

    Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

    gausswin_2d()

    @@ -536,8 +530,11 @@

    All functions

    gen_conv_reg()

    -

    Generate regressors by convolving a specified response function with a -stimulus.

    +

    Generate regressors by convolving a specified response function with a stimulus.

    + +

    gen_group_reg()

    + +

    Expand a regressor matrix for a group analysis.

    gen_impulse_reg()

    @@ -553,28 +550,23 @@

    All functions

    get_1h_brain_basis_names()

    -

    Return a character vector of common 1H molecules found in healthy human -brain.

    +

    Return a character vector of common 1H molecules found in healthy human brain.

    get_1h_brain_basis_paras()

    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    get_1h_brain_basis_paras_v1()

    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    get_1h_brain_basis_paras_v2()

    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    get_1h_brain_basis_paras_v3()

    -

    Return a list of mol_parameter objects suitable for 1H brain MRS -analyses.

    +

    Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

    get_1h_braino_basis_names()

    @@ -582,8 +574,7 @@

    All functions

    get_1h_spectre_basis_names()

    -

    Return a character vector of molecules included in the Gold Star Phantoms -SPECTRE phantom.

    +

    Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.

    get_2d_psf()

    @@ -635,8 +626,7 @@

    All functions

    get_mol_names()

    -

    Return a character array of names that may be used with the -get_mol_paras function.

    +

    Return a character array of names that may be used with the get_mol_paras function.

    get_mol_paras()

    @@ -700,8 +690,7 @@

    All functions

    get_td_amp()

    -

    Return an array of amplitudes derived from fitting the initial points in the -time domain and extrapolating back to t=0.

    +

    Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.

    get_tqn_cmd()

    @@ -709,8 +698,7 @@

    All functions

    get_uncoupled_mol()

    -

    Generate a mol_parameters object for a simple spin system with one -resonance.

    +

    Generate a mol_parameters object for a simple spin system with one resonance.

    get_voi_cog()

    @@ -731,6 +719,18 @@

    All functions glm_spec()

    Perform a GLM analysis of dynamic MRS data in the spectral domain.

    + +

    glm_spec_fmrs_fl()

    + +

    Perform first-level spectral GLM analysis of an fMRS dataset.

    + +

    glm_spec_fmrs_group()

    + +

    Perform group-level spectral GLM analysis of an fMRS dataset.

    + +

    glm_spec_group_linhyp()

    + +

    Test a group-level spectral GLM linear hypothesis.

    grid_shift_xy()

    @@ -766,8 +766,7 @@

    All functions

    ift_shift_mat()

    -

    Perform an ifft and ifftshift on a matrix with each column replaced by its -shifted ifft.

    +

    Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.

    image(<mrs_data>)

    @@ -799,8 +798,7 @@

    All functions

    is_fd()

    -

    Check if the chemical shift dimension of an MRS data object is in the -frequency domain.

    +

    Check if the chemical shift dimension of an MRS data object is in the frequency domain.

    kspace2img_xy()

    @@ -820,18 +818,15 @@

    All functions

    lw2alpha()

    -

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: -x * exp(-t * alpha).

    +

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).

    lw2beta()

    -

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: -x * exp(-t * t * beta).

    +

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

    make_basis_from_raw()

    -

    Make a basis-set object from a directory containing LCModel formatted RAW -files.

    +

    Make a basis-set object from a directory containing LCModel formatted RAW files.

    mask_dyns()

    @@ -851,8 +846,7 @@

    All functions

    mask_xy_ellipse()

    -

    Mask the voxels outside an elliptical region spanning the MRSI dataset in the -x-y plane.

    +

    Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.

    mask_xy_mat()

    @@ -860,13 +854,11 @@

    All functions

    mat2mrs_data()

    -

    Convert a matrix (with spectral points in the column dimension and dynamics -in the row dimensions) into a mrs_data object.

    +

    Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.

    matexp()

    -

    Matrix exponential function taken from complexplus package to reduce the -number of spant dependencies.

    +

    Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.

    max_mrs()

    @@ -914,31 +906,31 @@

    All functions

    mrs_data2basis()

    -

    Convert an mrs_data object to basis object - where basis signals are spread -across the dynamic dimension in the MRS data.

    +

    Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.

    + +

    mrs_data2bids()

    + +

    Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.

    mrs_data2mat()

    -

    Convert mrs_data object to a matrix, with spectral points in the column -dimension and dynamics in the row dimension.

    +

    Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

    -

    mrs_data2vec()

    +

    mrs_data2spec_mat()

    -

    Convert mrs_data object to a vector.

    +

    Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

    -

    mrs_data_list2bids()

    +

    mrs_data2vec()

    -

    Create a BIDS directory and file structure from a list of mrs_data objects.

    +

    Convert mrs_data object to a vector.

    mvfftshift()

    -

    Perform a fftshift on a matrix, with each column replaced by its shifted -result.

    +

    Perform a fftshift on a matrix, with each column replaced by its shifted result.

    mvifftshift()

    -

    Perform an ifftshift on a matrix, with each column replaced by its shifted -result.

    +

    Perform an ifftshift on a matrix, with each column replaced by its shifted result.

    n2coord()

    @@ -946,9 +938,7 @@

    All functions

    nifti_flip_lr()

    -

    Flip the x data dimension order of a nifti image. This corresponds to -flipping MRI data in the left-right direction, assuming the data in save in -neurological format (can check with fslorient program).

    +

    Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).

    one_page_pdf()

    @@ -964,8 +954,7 @@

    All functions

    peak_info()

    -

    Search for the highest peak in a spectral region and return the frequency, -height and FWHM.

    +

    Search for the highest peak in a spectral region and return the frequency, height and FWHM.

    pg_extrap_xy()

    @@ -974,6 +963,10 @@

    All functions phase()

    Apply phasing parameters to MRS data.

    + +

    phase_ref_1h_brain()

    + +

    Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.

    plot(<fit_result>)

    @@ -1005,8 +998,7 @@

    All functions

    plot_slice_map_inter()

    -

    Plot an interactive slice map from a data array where voxels can be selected -to display a corresponding spectrum.

    +

    Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.

    plot_spec_sd()

    @@ -1026,8 +1018,15 @@

    All functions

    precomp()

    -

    Save function results to file and load on subsequent calls to avoid repeat -computation.

    +

    Save function results to file and load on subsequent calls to avoid repeat computation.

    + +

    preproc_svs()

    + +

    Preprocess and perform quality assessment of a single SVS data set.

    + +

    preproc_svs_dataset()

    + +

    Preprocess and perform quality assessment of one or more SVS data sets.

    print(<fit_result>)

    @@ -1055,15 +1054,11 @@

    All functions

    read_ima_coil_dir()

    -

    Read a directory containing Siemens MRS IMA files and combine along the coil -dimension. Note that the coil ID is inferred from the sorted file name and -should be checked when consistency is required between two directories.

    +

    Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.

    read_ima_dyn_dir()

    -

    Read a directory containing Siemens MRS IMA files and combine along the -dynamic dimension. Note that the coil ID is inferred from the sorted file -name and should be checked when consistency is required.

    +

    Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.

    read_lcm_coord()

    @@ -1103,13 +1098,11 @@

    All functions

    recon_imag()

    -

    Reconstruct complex time-domain data from the real part of frequency-domain -data.

    +

    Reconstruct complex time-domain data from the real part of frequency-domain data.

    recon_imag_vec()

    -

    Reconstruct complex time-domain data from the real part of frequency-domain -data.

    +

    Reconstruct complex time-domain data from the real part of frequency-domain data.

    recon_twix_2d_mrsi()

    @@ -1141,8 +1134,7 @@

    All functions

    resample_voi()

    -

    Resample a VOI to match a target image space using nearest-neighbour -interpolation.

    +

    Resample a VOI to match a target image space using nearest-neighbour interpolation.

    reslice_to_mrs()

    @@ -1158,23 +1150,19 @@

    All functions

    scale_amp_molal()

    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

    scale_amp_molal_pvc()

    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

    scale_amp_molar()

    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / Litre of tissue).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).

    scale_amp_molar2molal_pvc()

    -

    Convert default LCM/TARQUIN concentration scaling to molal units with partial -volume correction.

    +

    Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.

    scale_amp_ratio()

    @@ -1222,8 +1210,7 @@

    All functions

    seq_mega_press_ideal()

    -

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped -editing pulse.

    +

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.

    seq_press_2d_shaped()

    @@ -1251,13 +1238,11 @@

    All functions

    seq_steam_ideal_cof()

    -

    STEAM sequence with ideal pulses and coherence order filtering to simulate -gradient crushers.

    +

    STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.

    seq_steam_ideal_young()

    -

    STEAM sequence with ideal pulses using the z-rotation gradient simulation -method described by Young et al JMR 140, 146-152 (1999).

    +

    STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).

    set_Ntrans()

    @@ -1293,8 +1278,7 @@

    All functions

    set_td_pts()

    -

    Set the number of time-domain data points, truncating or zero-filling as -appropriate.

    +

    Set the number of time-domain data points, truncating or zero-filling as appropriate.

    set_tqn_cmd()

    @@ -1318,18 +1302,15 @@

    All functions

    sim_basis_1h_brain()

    -

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.

    +

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

    sim_basis_1h_brain_press()

    -

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.

    +

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

    sim_basis_mm_lip_lcm()

    -

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS -analysis.

    +

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.

    sim_basis_tqn()

    @@ -1353,8 +1334,7 @@

    All functions

    sim_th_excit_profile()

    -

    Simulate an ideal pulse excitation profile by smoothing a top-hat function -with a Gaussian.

    +

    Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.

    sim_zero()

    @@ -1374,17 +1354,19 @@

    All functions

    spant_abfit_benchmark()

    -

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic -timing and performance metrics will be printed.

    +

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.

    spant_mpress_drift

    Example MEGA-PRESS data with significant B0 drift.

    + +

    spant_sim_fmrs_dataset()

    + +

    Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.

    spant_simulation_benchmark()

    -

    Simulate a typical metabolite basis set for benchmarking. Timing metrics will -be printed on completion.

    +

    Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.

    spec_decomp()

    @@ -1400,8 +1382,7 @@

    All functions

    spm_pve2categorical()

    -

    Convert SPM style segmentation files to a single categorical image where -the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.

    +

    Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.

    ssp()

    @@ -1413,8 +1394,7 @@

    All functions

    stackplot(<fit_result>)

    -

    Plot the fitting results of an object of class fit_result with -individual basis set components shown.

    +

    Plot the fitting results of an object of class fit_result with individual basis set components shown.

    stackplot(<mrs_data>)

    @@ -1459,6 +1439,10 @@

    All functions svs_1h_brain_batch_analysis()

    Batch interface to the standard SVS 1H brain analysis pipeline.

    + +

    t_test_spec()

    + +

    Perform a t-test on spectral data points.

    td2fd()

    @@ -1518,8 +1502,7 @@

    All functions

    zero_fade_spec()

    -

    Fade a spectrum to zero by frequency domain multiplication with a tanh -function. Note this operation distorts data points at the end of the FID.

    +

    Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.

    zero_higher_orders()

    @@ -1549,15 +1532,15 @@

    All functions
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html index c7060fe7..2c66337a 100644 --- a/docs/reference/int_spec.html +++ b/docs/reference/int_spec.html @@ -1,9 +1,9 @@ -Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant)Integrate a spectral region. — int_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,27 @@

    Integrate a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    Value

    - - -

    an array of integral values.

    +

    an array of integral values.

    @@ -118,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html index effe5543..6a38a395 100644 --- a/docs/reference/interleave_dyns.html +++ b/docs/reference/interleave_dyns.html @@ -1,9 +1,9 @@ -Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant)Interleave the first and second half of a dynamic series. — interleave_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Interleave the first and second half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    interleaved data.

    +

    interleaved data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html index 9f9d4fff..20f533df 100644 --- a/docs/reference/inv_even_dyns.html +++ b/docs/reference/inv_even_dyns.html @@ -1,9 +1,9 @@ -Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant)Invert even numbered dynamic scans starting from 1 (2,4,6...). — inv_even_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Invert even numbered dynamic scans starting from 1 (2,4,6...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data with inverted even numbered scans.

    +

    dynamic MRS data with inverted even numbered scans.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html index 26212e2b..ec78cbfe 100644 --- a/docs/reference/inv_odd_dyns.html +++ b/docs/reference/inv_odd_dyns.html @@ -1,9 +1,9 @@ -Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant)Invert odd numbered dynamic scans starting from 1 (1,3,5...). — inv_odd_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Invert odd numbered dynamic scans starting from 1 (1,3,5...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data with inverted odd numbered scans.

    +

    dynamic MRS data with inverted odd numbered scans.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html index f196ffd0..b9557e0c 100644 --- a/docs/reference/is.def.html +++ b/docs/reference/is.def.html @@ -1,9 +1,9 @@ -Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant)Check if an object is defined, which is the same as being not NULL. — is.def • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Check if an object is defined, which is the same as being not NULL.

    Arguments

    -
    x
    + + +
    x

    object to test for being NULL.

    Value

    - - -

    logical value.

    +

    logical value.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html index 3b0ca165..fe0262b7 100644 --- a/docs/reference/is_fd.html +++ b/docs/reference/is_fd.html @@ -1,12 +1,10 @@ -Check if the chemical shift dimension of an MRS data object is in the -frequency domain. — is_fd • Spectroscopy Analysis Tools (spant)Check if the chemical shift dimension of an MRS data object is in the frequency domain. — is_fd • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Check if the chemical shift dimension of an MRS data object is in the -frequency domain.

    +

    Check if the chemical shift dimension of an MRS data object is in the frequency domain.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Check if the chemical shift dimension of an MRS data object is in the

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    logical value.

    +

    logical value.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/kspace2img_xy.html b/docs/reference/kspace2img_xy.html index 6f275f22..45106df6 100644 --- a/docs/reference/kspace2img_xy.html +++ b/docs/reference/kspace2img_xy.html @@ -1,9 +1,9 @@ -Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant)Transform 2D MRSI data from k-space to image space in the x-y direction. — kspace2img_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Transform 2D MRSI data from k-space to image space in the x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data.

    Value

    - - -

    MRSI data in image space.

    +

    MRSI data in image space.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html index 3d781d80..ae4ce248 100644 --- a/docs/reference/l2_reg.html +++ b/docs/reference/l2_reg.html @@ -1,10 +1,10 @@ -Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant)Perform l2 regularisation artefact suppression. — l2_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -94,47 +94,47 @@

    Perform l2 regularisation artefact suppression.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    input data for artefact suppression.

    -
    thresh
    +
    thresh

    threshold parameter to extract lipid signals from mrs_data based on the spectral integration of the thresh_xlim region in magnitude mode.

    -
    b
    +
    b

    regularisation parameter.

    -
    A
    +
    A

    set of spectra containing the artefact basis signals. The thresh parameter is ignored when A is specified.

    -
    xlim
    +
    xlim

    spectral limits in ppm to restrict the reconstruction range. Defaults to the full spectral width.

    -
    thresh_xlim
    +
    thresh_xlim

    spectral limits in ppm to integrate for the threshold map.

    -
    A_append
    +
    A_append

    additional spectra to append to the A basis.

    -
    ret_norms
    +
    ret_norms

    return the residual norm and solution norms.

    Value

    - - -

    l2 reconstructed mrs_data object.

    +

    l2 reconstructed mrs_data object.

    @@ -149,15 +149,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/lb.basis_set.html b/docs/reference/lb.basis_set.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.basis_set.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lb.html b/docs/reference/lb.html index 9f2322f8..f6fdfeec 100644 --- a/docs/reference/lb.html +++ b/docs/reference/lb.html @@ -1,9 +1,9 @@ -Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant)Apply line-broadening (apodisation) to MRS data or basis object. — lb • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -80,35 +80,35 @@

    Apply line-broadening (apodisation) to MRS data or basis object.

    lb(x, lb, lg = 1)
 
-# S3 method for list
+# S3 method for class 'list'
 lb(x, lb, lg = 1)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 lb(x, lb, lg = 1)
 
-# S3 method for basis_set
+# S3 method for class 'basis_set'
 lb(x, lb, lg = 1)

    Arguments

    -
    x
    + + +
    x

    input mrs_data or basis_set object.

    -
    lb
    +
    lb

    amount of line-broadening in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    Value

    - - -

    line-broadened data.

    +

    line-broadened data.

    @@ -123,15 +123,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/lb.list.html b/docs/reference/lb.list.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.list.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lb.mrs_data.html b/docs/reference/lb.mrs_data.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html index 5419b1ec..f6ca52d8 100644 --- a/docs/reference/lofdc.html +++ b/docs/reference/lofdc.html @@ -1,9 +1,9 @@ -Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant)Correct linear frequency drift. — lofdc • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,39 +91,39 @@

    Correct linear frequency drift.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    max_hz_s
    +
    max_hz_s

    the maximum drift rate to search over.

    -
    tr
    +
    tr

    mrs_data repetition time.

    -
    ret_corr_only
    +
    ret_corr_only

    return the corrected mrs_data object only.

    -
    outlier_thresh
    +
    outlier_thresh

    threshold to remove outliers.

    -
    xlim
    +
    xlim

    spectral width (in ppm) to evaluate outliers.

    -
    order
    +
    order

    correction order.

    Value

    - - -

    drift corrected mrs_data object.

    +

    drift corrected mrs_data object.

    @@ -138,15 +138,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html index b83db682..3029ec94 100644 --- a/docs/reference/lw2alpha.html +++ b/docs/reference/lw2alpha.html @@ -1,12 +1,10 @@ -Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: -x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant)Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha). — lw2alpha • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: -x * exp(-t * alpha).

    +

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:

    Arguments

    -
    lw
    + + +
    lw

    linewidth in Hz.

    Value

    - - -

    beta damping value.

    +

    beta damping value.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/lw2beta.html b/docs/reference/lw2beta.html index 7ddef7cd..b2af49a6 100644 --- a/docs/reference/lw2beta.html +++ b/docs/reference/lw2beta.html @@ -1,12 +1,10 @@ -Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: -x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant)Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta). — lw2beta • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: -x * exp(-t * t * beta).

    +

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:

    Arguments

    -
    lw
    + + +
    lw

    linewidth in Hz.

    Value

    - - -

    beta damping value.

    +

    beta damping value.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/make_basis_from_raw.html b/docs/reference/make_basis_from_raw.html index ab4f50ff..f666df90 100644 --- a/docs/reference/make_basis_from_raw.html +++ b/docs/reference/make_basis_from_raw.html @@ -1,12 +1,10 @@ -Make a basis-set object from a directory containing LCModel formatted RAW -files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant)Make a basis-set object from a directory containing LCModel formatted RAW files. — make_basis_from_raw • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Make a basis-set object from a directory containing LCModel formatted RAW -files.

    +

    Make a basis-set object from a directory containing LCModel formatted RAW files.

    Source: R/basis_set.R
    @@ -88,28 +85,28 @@

    Make a basis-set object from a directory containing LCModel formatted RAW

    Arguments

    -
    dir_path
    + + +
    dir_path

    path to the directory containing LCModel RAW files. One file per signal.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    Value

    - - -

    a basis-set object.

    +

    a basis-set object.

    @@ -124,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_dyns.html b/docs/reference/mask_dyns.html index b9d294c3..2a8c3b7d 100644 --- a/docs/reference/mask_dyns.html +++ b/docs/reference/mask_dyns.html @@ -1,9 +1,9 @@ -Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant)Mask an MRS dataset in the dynamic dimension. — mask_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Mask an MRS dataset in the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    mask
    +
    mask

    vector of boolean values specifying the dynamics to mask, where a value of TRUE indicates the spectrum should be removed.

    Value

    - - -

    masked dataset.

    +

    masked dataset.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html index 97baaa3f..3bac3dfa 100644 --- a/docs/reference/mask_fit_res.html +++ b/docs/reference/mask_fit_res.html @@ -1,9 +1,9 @@ -Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant)Mask fit result spectra depending on a vector of bool values. — mask_fit_res • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Mask fit result spectra depending on a vector of bool values.

    Arguments

    -
    fit_result
    + + +
    fit_result

    fit result object to be masked.

    -
    mask_vec
    +
    mask_vec

    a Boolean vector with the same number of rows as there are rows in the results table.

    -
    amps_only
    +
    amps_only

    only mask the amplitude and associated error estimate columns.

    Value

    - - -

    a masked fit result object.

    +

    a masked fit result object.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html index 11bb577c..e81fcea7 100644 --- a/docs/reference/mask_xy.html +++ b/docs/reference/mask_xy.html @@ -1,9 +1,9 @@ -Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant)Mask an MRSI dataset in the x-y direction — mask_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Mask an MRSI dataset in the x-y direction

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_dim
    +
    x_dim

    x dimension output length.

    -
    y_dim
    +
    y_dim

    y dimension output length.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html index 09b16cd2..7795c76a 100644 --- a/docs/reference/mask_xy_corners.html +++ b/docs/reference/mask_xy_corners.html @@ -1,9 +1,9 @@ -Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant)Mask the four corners of an MRSI dataset in the x-y plane. — mask_xy_corners • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Mask the four corners of an MRSI dataset in the x-y plane.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html index 1d8b02e4..d67b1b27 100644 --- a/docs/reference/mask_xy_ellipse.html +++ b/docs/reference/mask_xy_ellipse.html @@ -1,12 +1,10 @@ -Mask the voxels outside an elliptical region spanning the MRSI dataset in the -x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant)Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane. — mask_xy_ellipse • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Mask the voxels outside an elliptical region spanning the MRSI dataset in the -x-y plane.

    +

    Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Mask the voxels outside an elliptical region spanning the MRSI dataset in th

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mask_xy_mat.html b/docs/reference/mask_xy_mat.html index 5d42de91..27ed888b 100644 --- a/docs/reference/mask_xy_mat.html +++ b/docs/reference/mask_xy_mat.html @@ -1,9 +1,9 @@ -Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant)Mask a 2D MRSI dataset in the x-y dimension. — mask_xy_mat • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Mask a 2D MRSI dataset in the x-y dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    mask
    +
    mask

    matrix of boolean values specifying the voxels to mask, where a value of TRUE indicates the voxel should be removed.

    -
    value
    +
    value

    the value to set masked data to (usually NA or 0).

    Value

    - - -

    masked dataset.

    +

    masked dataset.

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html index 2e2895f3..c0e66081 100644 --- a/docs/reference/mat2mrs_data.html +++ b/docs/reference/mat2mrs_data.html @@ -1,12 +1,10 @@ -Convert a matrix (with spectral points in the column dimension and dynamics -in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant)Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object. — mat2mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert a matrix (with spectral points in the column dimension and dynamics -in the row dimensions) into a mrs_data object.

    +

    Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.

    Source: R/mrs_data_proc.R
    @@ -85,45 +82,50 @@

    Convert a matrix (with spectral points in the column dimension and dynamics 
    mat2mrs_data(
   mat,
-  fs = def_fs(),
-  ft = def_ft(),
-  ref = def_ref(),
-  nuc = def_nuc(),
+  mrs_data = NULL,
+  fs = NULL,
+  ft = NULL,
+  ref = NULL,
+  nuc = NULL,
   fd = FALSE
 )

    Arguments

    -
    mat
    + + +
    mat

    data matrix.

    -
    fs
    +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    -
    fd
    +
    fd

    flag to indicate if the matrix is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -138,15 +140,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/matexp.html b/docs/reference/matexp.html index df7af6e8..ac3c8b8a 100644 --- a/docs/reference/matexp.html +++ b/docs/reference/matexp.html @@ -1,12 +1,10 @@ -Matrix exponential function taken from complexplus package to reduce the -number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant)Matrix exponential function taken from complexplus package to reduce the number of spant dependencies. — matexp • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Matrix exponential function taken from complexplus package to reduce the -number of spant dependencies.

    +

    Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Matrix exponential function taken from complexplus package to reduce the

    Arguments

    -
    x
    + + +
    x

    a square complex matrix.

    Value

    - - -

    the matrix exponential of x.

    +

    the matrix exponential of x.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/max_mrs.html b/docs/reference/max_mrs.html index 50f078e3..f67dbfc9 100644 --- a/docs/reference/max_mrs.html +++ b/docs/reference/max_mrs.html @@ -1,9 +1,9 @@ -Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant)Apply the max operator to an MRS dataset. — max_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Apply the max operator to an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    MRS data following max operator.

    +

    MRS data following max operator.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html index e4474764..2ccd5472 100644 --- a/docs/reference/max_mrs_interp.html +++ b/docs/reference/max_mrs_interp.html @@ -1,9 +1,9 @@ -Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant)Apply the max operator to an interpolated MRS dataset. — max_mrs_interp • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Apply the max operator to an interpolated MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    interp_f
    +
    interp_f

    interpolation factor.

    Value

    - - -

    Array of maximum values (real only).

    +

    Array of maximum values (real only).

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html index b8eb3463..d5c6ecf2 100644 --- a/docs/reference/mean.list.html +++ b/docs/reference/mean.list.html @@ -1,9 +1,9 @@ -Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant)Calculate the mean spectrum from an mrs_data object. — mean.list • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,25 +78,25 @@

    Calculate the mean spectrum from an mrs_data object.

    - 
    # S3 method for list
+    
    # S3 method for class 'list'
 mean(x, ...)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    ...
    +
    ...

    other arguments to pass to the colMeans function.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html index 5531a28d..769e716f 100644 --- a/docs/reference/mean.mrs_data.html +++ b/docs/reference/mean.mrs_data.html @@ -1,9 +1,9 @@ -Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant)Calculate the mean spectrum from an mrs_data object. — mean.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,25 +78,25 @@

    Calculate the mean spectrum from an mrs_data object.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 mean(x, ...)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    ...
    +
    ...

    other arguments to pass to the colMeans function.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html index 10467098..d7650743 100644 --- a/docs/reference/mean_dyn_blocks.html +++ b/docs/reference/mean_dyn_blocks.html @@ -1,9 +1,9 @@ -Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant)Calculate the mean of adjacent dynamic scans. — mean_dyn_blocks • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Calculate the mean of adjacent dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    block_size
    +
    block_size

    number of adjacent dynamics scans to average over.

    Value

    - - -

    dynamic data averaged in blocks.

    +

    dynamic data averaged in blocks.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html index 63e909ea..293d211a 100644 --- a/docs/reference/mean_dyn_pairs.html +++ b/docs/reference/mean_dyn_pairs.html @@ -1,9 +1,9 @@ -Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant)Calculate the pairwise means across a dynamic data set. — mean_dyn_pairs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the pairwise means across a dynamic data set.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    mean dynamic data of adjacent dynamic pairs.

    +

    mean dynamic data of adjacent dynamic pairs.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html index 73fdbfa7..ca77f047 100644 --- a/docs/reference/mean_dyns.html +++ b/docs/reference/mean_dyns.html @@ -1,9 +1,9 @@ -Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant)Calculate the mean dynamic data. — mean_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Calculate the mean dynamic data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be averaged.

    Value

    - - -

    mean dynamic data.

    +

    mean dynamic data.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html index 808b6c50..03e34d0e 100644 --- a/docs/reference/mean_mrs_list.html +++ b/docs/reference/mean_mrs_list.html @@ -1,9 +1,9 @@ -Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant)Return the mean of a list of mrs_data objects. — mean_mrs_list • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the mean of a list of mrs_data objects.

    Arguments

    -
    mrs_list
    + + +
    mrs_list

    list of mrs_data objects.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html index 8fc92eaa..3f194d97 100644 --- a/docs/reference/mean_vec_blocks.html +++ b/docs/reference/mean_vec_blocks.html @@ -1,9 +1,9 @@ -Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant)Calculate the mean of adjacent blocks in a vector. — mean_vec_blocks • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Calculate the mean of adjacent blocks in a vector.

    Arguments

    -
    x
    + + +
    x

    input vector.

    -
    block_size
    +
    block_size

    number of adjacent elements to average over.

    Value

    - - -

    vector data averaged in blocks.

    +

    vector data averaged in blocks.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html index 1039d4b5..68cb730e 100644 --- a/docs/reference/median_dyns.html +++ b/docs/reference/median_dyns.html @@ -1,9 +1,9 @@ -Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant)Calculate the median dynamic data. — median_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the median dynamic data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    median dynamic data.

    +

    median dynamic data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html index 76ad0a40..921171a1 100644 --- a/docs/reference/mod_td.html +++ b/docs/reference/mod_td.html @@ -1,9 +1,9 @@ -Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant)Apply the Modulus operator to the time-domain MRS signal. — mod_td • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Apply the Modulus operator to the time-domain MRS signal.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data input.

    Value

    - - -

    time-domain modulus of input.

    +

    time-domain modulus of input.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html index 62f7d749..87923716 100644 --- a/docs/reference/mrs_data2basis.html +++ b/docs/reference/mrs_data2basis.html @@ -1,12 +1,10 @@ -Convert an mrs_data object to basis object - where basis signals are spread -across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant)Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data. — mrs_data2basis • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert an mrs_data object to basis object - where basis signals are spread -across the dynamic dimension in the MRS data.

    +

    Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.

    Source: R/basis_set.R
    @@ -88,19 +85,19 @@

    Convert an mrs_data object to basis object - where basis signals are spread

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object with basis signals spread across the dynamic dimension.

    -
    names
    +
    names

    list of names corresponding to basis signals.

    Value

    - - -

    basis set object.

    +

    basis set object.

    @@ -115,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mrs_data2bids.html b/docs/reference/mrs_data2bids.html new file mode 100644 index 00000000..76935284 --- /dev/null +++ b/docs/reference/mrs_data2bids.html @@ -0,0 +1,191 @@ + +Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects. — mrs_data2bids • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.

    + Source: R/fmrs.R + +
    + +
    +

    Create a BIDS file structure from a vector of MRS data paths or list of +mrs_data objects.

    +
    + +
    + 
    mrs_data2bids(
+  mrs_data,
+  output_dir,
+  suffix = NULL,
+  sub = NULL,
+  ses = NULL,
+  task = NULL,
+  acq = NULL,
+  nuc = NULL,
+  voi = NULL,
+  rec = NULL,
+  run = NULL,
+  echo = NULL,
+  inv = NULL,
+  skip_existing = TRUE
+)
    +
    + +
    +

    Arguments

    + + +
    mrs_data
    +

    vector of MRS data paths or list of mrs_data objects.

    + + +
    output_dir
    +

    the base directory to create the BIDS structure.

    + + +
    suffix
    +

    optional vector of file suffixes. Default behaviour is to +automatically determine these from the input data, however it is recommended +that they are specified to allow more efficient skipping of existing data.

    + + +
    sub
    +

    optional vector of subject labels. If not specified, these will be +automatically generated as a series of increasing zero-padded integer values +corresponding to the mrs_data input indices.

    + + +
    ses
    +

    optional vector of session labels.

    + + +
    task
    +

    optional vector of task labels.

    + + +
    acq
    +

    optional vector of acquisition labels.

    + + +
    nuc
    +

    optional vector of nucleus labels.

    + + +
    voi
    +

    optional vector of volume of interest labels.

    + + +
    rec
    +

    optional vector of reconstruction labels.

    + + +
    run
    +

    optional vector of run indices.

    + + +
    echo
    +

    optional vector of echo time indices.

    + + +
    inv
    +

    optional vector of inversion indices.

    + + +
    skip_existing
    +

    skip any data files that have already been converted. +Defaults to TRUE, set to FALSE to force an overwrite of any existing data +files.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html index cf5ff28c..c533a9d4 100644 --- a/docs/reference/mrs_data2mat.html +++ b/docs/reference/mrs_data2mat.html @@ -1,12 +1,10 @@ -Convert mrs_data object to a matrix, with spectral points in the column -dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant)Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2mat • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert mrs_data object to a matrix, with spectral points in the column -dimension and dynamics in the row dimension.

    +

    Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

    Source: R/mrs_data_proc.R
    @@ -88,20 +85,20 @@

    Convert mrs_data object to a matrix, with spectral points in the column

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object or list of MRS data objects.

    -
    collapse
    +
    collapse

    collapse all other dimensions along the dynamic dimension, eg a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.

    Value

    - - -

    MRS data matrix.

    +

    MRS data matrix.

    @@ -116,15 +113,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mrs_data2spec_mat.html b/docs/reference/mrs_data2spec_mat.html new file mode 100644 index 00000000..9254c96f --- /dev/null +++ b/docs/reference/mrs_data2spec_mat.html @@ -0,0 +1,127 @@ + +Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension. — mrs_data2spec_mat • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

    + Source: R/mrs_data_proc.R + +
    + +
    +

    Convert mrs_data object to a matrix, with spectral points in the column +dimension and dynamics in the row dimension.

    +
    + +
    + 
    mrs_data2spec_mat(mrs_data, collapse = TRUE)
    +
    + +
    +

    Arguments

    + + +
    mrs_data
    +

    MRS data object or list of MRS data objects.

    + + +
    collapse
    +

    collapse all other dimensions along the dynamic dimension, eg +a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.

    + +
    +
    +

    Value

    +

    MRS data matrix.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html index fb172d68..b67ce6f5 100644 --- a/docs/reference/mrs_data2vec.html +++ b/docs/reference/mrs_data2vec.html @@ -1,9 +1,9 @@ -Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant)Convert mrs_data object to a vector. — mrs_data2vec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,35 +83,35 @@

    Convert mrs_data object to a vector.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    dyn
    +
    dyn

    dynamic index.

    -
    x_pos
    +
    x_pos

    x index.

    -
    y_pos
    +
    y_pos

    y index.

    -
    z_pos
    +
    z_pos

    z index.

    -
    coil
    +
    coil

    coil element index.

    Value

    - - -

    MRS data vector.

    +

    MRS data vector.

    @@ -126,15 +126,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html index 92b0841b..1e8eb342 100644 --- a/docs/reference/mvfftshift.html +++ b/docs/reference/mvfftshift.html @@ -1,12 +1,10 @@ -Perform a fftshift on a matrix, with each column replaced by its shifted -result. — mvfftshift • Spectroscopy Analysis Tools (spant)Perform a fftshift on a matrix, with each column replaced by its shifted result. — mvfftshift • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform a fftshift on a matrix, with each column replaced by its shifted -result.

    +

    Perform a fftshift on a matrix, with each column replaced by its shifted result.

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Perform a fftshift on a matrix, with each column replaced by its shifted

    Arguments

    -
    x
    + + +
    x

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/mvifftshift.html b/docs/reference/mvifftshift.html index 4ece8b1a..4a1db094 100644 --- a/docs/reference/mvifftshift.html +++ b/docs/reference/mvifftshift.html @@ -1,12 +1,10 @@ -Perform an ifftshift on a matrix, with each column replaced by its shifted -result. — mvifftshift • Spectroscopy Analysis Tools (spant)Perform an ifftshift on a matrix, with each column replaced by its shifted result. — mvifftshift • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Perform an ifftshift on a matrix, with each column replaced by its shifted -result.

    +

    Perform an ifftshift on a matrix, with each column replaced by its shifted result.

    Source: R/utils.R
    @@ -88,15 +85,15 @@

    Perform an ifftshift on a matrix, with each column replaced by its shifted

    Arguments

    -
    x
    + + +
    x

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/n2coord.html b/docs/reference/n2coord.html index 327342e8..ca4c691a 100644 --- a/docs/reference/n2coord.html +++ b/docs/reference/n2coord.html @@ -1,9 +1,9 @@ -Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant)Print fit coordinates from a single index. — n2coord • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Print fit coordinates from a single index.

    Arguments

    -
    n
    + + +
    n

    fit index.

    -
    fit_res
    +
    fit_res

    fit_result object.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html index 730abe3c..69f739ff 100644 --- a/docs/reference/nifti_flip_lr.html +++ b/docs/reference/nifti_flip_lr.html @@ -1,15 +1,11 @@ -Flip the x data dimension order of a nifti image. This corresponds to -flipping MRI data in the left-right direction, assuming the data in save in -neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant)Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program). — nifti_flip_lr • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Flip the x data dimension order of a nifti image. This corresponds to -flipping MRI data in the left-right direction, assuming the data in save in -neurological format (can check with fslorient program).

    +

    Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).

    Source: R/image_reg.R
    @@ -93,15 +87,15 @@

    Flip the x data dimension order of a nifti image. This corresponds to

    Arguments

    -
    x
    + + +
    x

    nifti object to be processed.

    Value

    - - -

    nifti object with reversed x data direction.

    +

    nifti object with reversed x data direction.

    @@ -116,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/one_page_pdf.html b/docs/reference/one_page_pdf.html index f7587ea2..24b76d0e 100644 --- a/docs/reference/one_page_pdf.html +++ b/docs/reference/one_page_pdf.html @@ -1,9 +1,9 @@ -Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant)Export a one-page pdf of a single fit result — one_page_pdf • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Export a one-page pdf of a single fit result

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    pdf_out_path
    +
    pdf_out_path

    path to the exported pdf file.

    -
    title
    +
    title

    ouptut title.

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html index 13ade97d..e170a85b 100644 --- a/docs/reference/ortho3.html +++ b/docs/reference/ortho3.html @@ -1,9 +1,9 @@ -Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant)Display an orthographic projection plot of a nifti object. — ortho3 • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -99,63 +99,65 @@

    Display an orthographic projection plot of a nifti object.

    Arguments

    -
    underlay
    + + +
    underlay

    underlay image to be shown in grayscale.

    -
    overlay
    +
    overlay

    optional overlay image.

    -
    xyz
    +
    xyz

    x, y, z slice coordinates to display.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    zlim_ol
    +
    zlim_ol

    overlay intensity limits.

    -
    alpha
    +
    alpha

    transparency of overlay.

    -
    col_ol
    +
    col_ol

    colour palette of overlay.

    -
    orient_lab
    +
    orient_lab

    display orientation labels (default TRUE).

    -
    rescale
    +
    rescale

    rescale factor for the underlay and overlay images.

    -
    crosshairs
    +
    crosshairs

    display the crosshairs (default TRUE).

    -
    ch_lwd
    +
    ch_lwd

    crosshair linewidth.

    -
    colourbar
    +
    colourbar

    display a colourbar for the overlay (default TRUE).

    -
    bg
    +
    bg

    plot background colour.

    -
    mar
    +
    mar

    plot margins.

    -
    smallplot
    +
    smallplot

    smallplot option for positioning the colourbar.

    @@ -172,15 +174,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html index 090cc5e5..3222df89 100644 --- a/docs/reference/ortho3_inter.html +++ b/docs/reference/ortho3_inter.html @@ -1,9 +1,9 @@ -Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant)Display an interactive orthographic projection plot of a nifti object. — ortho3_inter • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,31 +91,33 @@

    Display an interactive orthographic projection plot of a nifti object.

    Arguments

    -
    underlay
    + + +
    underlay

    underlay image to be shown in grayscale.

    -
    overlay
    +
    overlay

    optional overlay image.

    -
    xyz
    +
    xyz

    x, y, z slice coordinates to display.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    zlim_ol
    +
    zlim_ol

    overlay intensity limits.

    -
    alpha
    +
    alpha

    transparency of overlay.

    -
    ...
    +
    ...

    other options to be passed to the ortho3 function.

    @@ -132,15 +134,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html index 09058bd8..6229d501 100644 --- a/docs/reference/peak_info.html +++ b/docs/reference/peak_info.html @@ -1,12 +1,10 @@ -Search for the highest peak in a spectral region and return the frequency, -height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant)Search for the highest peak in a spectral region and return the frequency, height and FWHM. — peak_info • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Search for the highest peak in a spectral region and return the frequency, -height and FWHM.

    +

    Search for the highest peak in a spectral region and return the frequency, height and FWHM.

    Source: R/mrs_data_proc.R
    @@ -94,33 +91,33 @@

    Search for the highest peak in a spectral region and return the frequency,

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    xlim
    +
    xlim

    frequency range (default units of PPM) to search for the highest peak.

    -
    interp_f
    +
    interp_f

    interpolation factor, defaults to 4x.

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "real", "imag" or "mod".

    Value

    - - -

    list of arrays containing the highest peak frequency, height and FWHM +

    list of arrays containing the highest peak frequency, height and FWHM in units of PPM and Hz.

    @@ -136,15 +133,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/pg_extrap_xy.html b/docs/reference/pg_extrap_xy.html index 61dc81d3..12fd386f 100644 --- a/docs/reference/pg_extrap_xy.html +++ b/docs/reference/pg_extrap_xy.html @@ -1,12 +1,12 @@ -Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant)Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation. — pg_extrap_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -95,37 +95,37 @@

    Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    img_mask
    +
    img_mask

    a boolean matrix of voxels with strong signals to be extrapolated. Must be twice the dimensions of the input data.

    -
    kspace_mask
    +
    kspace_mask

    a boolean matrix of kspace points that have been sampled. Typically a circle for MRSI, but defaults to the full rectangular area of k-space covered by the input data. Must match the x-y dimensions of the input data.

    -
    intensity_thresh
    +
    intensity_thresh

    used to define img_mask based on the strength of the signal in each voxel. Defaults to intensities greater than 15% of the maximum. Ignored if img_mask is specified as argument.

    -
    iters
    +
    iters

    number of iterations to perform.

    Value

    - - -

    extrapolated mrs_data object.

    +

    extrapolated mrs_data object.

    @@ -140,15 +140,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/phase.html b/docs/reference/phase.html index 84174c81..cea6e788 100644 --- a/docs/reference/phase.html +++ b/docs/reference/phase.html @@ -1,9 +1,9 @@ -Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant)Apply phasing parameters to MRS data. — phase • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Apply phasing parameters to MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    zero_order
    +
    zero_order

    zero'th order phase term in degrees.

    -
    first_order
    +
    first_order

    first order (frequency dependent) phase term in ms.

    Value

    - - -

    MRS data with applied phase parameters.

    +

    MRS data with applied phase parameters.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html new file mode 100644 index 00000000..e8641a4d --- /dev/null +++ b/docs/reference/phase_ref_1h_brain.html @@ -0,0 +1,131 @@ + +Corrected zero order phase and chemical shift offset in 1H MRS data from the brain. — phase_ref_1h_brain • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.

    + Source: R/rats.R + +
    + +
    +

    Corrected zero order phase and chemical shift offset in 1H MRS data from the +brain.

    +
    + +
    + 
    phase_ref_1h_brain(mrs_data, mean_ref = FALSE, ret_corr_only = TRUE)
    +
    + +
    +

    Arguments

    + + +
    mrs_data
    +

    MRS data to be corrected.

    + + +
    mean_ref
    +

    apply the phase and offset of the mean spectrum to all +others. Default is FALSE.

    + + +
    ret_corr_only
    +

    return the corrected data only.

    + +
    +
    +

    Value

    +

    corrected MRS data.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html index e54d3bc1..ca4dc494 100644 --- a/docs/reference/plot.fit_result.html +++ b/docs/reference/plot.fit_result.html @@ -1,9 +1,9 @@ -Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant)Plot the fitting results of an object of class fit_result. — plot.fit_result • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,7 +78,7 @@

    Plot the fitting results of an object of class fit_result.

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 plot(
   x,
   dyn = 1,
@@ -106,91 +106,93 @@ 
    Plot the fitting results of an object of class fit_result.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    fit_result object.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    data_only
    
+
    data_only
    
 
    display only the processed data (logical).
    
 
 
-
    label
    
+
    label
    
 
    character string to add to the top left of the plot window.
    
 
 
-
    plot_sigs
    
+
    plot_sigs
    
 
    a character vector of signal names to add to the plot.
    
 
 
-
    n
    
+
    n
    
 
    single index element to plot (overrides other indices when given).
    
 
 
-
    sub_bl
    
+
    sub_bl
    
 
    subtract the baseline from the data and fit (logical).
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    ylim
    
+
    ylim
    
 
    range of values to display on the y-axis, eg ylim = c(0,10).
    
 
 
-
    y_scale
    
+
    y_scale
    
 
    option to display the y-axis values (logical).
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    invert_fit
    
+
    invert_fit
    
 
    show the fit result "upside-down"/
    
 
 
-
    ...
    
+
    ...
    
 
    further arguments to plot method.
    
 
 
    
@@ -207,15 +209,15 @@ 
    Arguments
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html index fabcc35b..277fb9c8 100644 --- a/docs/reference/plot.mrs_data.html +++ b/docs/reference/plot.mrs_data.html @@ -1,9 +1,9 @@ -Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant)Plotting method for objects of class mrs_data. — plot.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,7 +78,7 @@

    Plotting method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 plot(
   x,
   dyn = 1,
@@ -121,156 +121,158 @@ 
    Plotting method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    fd
    
+
    fd
    
 
    display data in the frequency-domain (default), or time-domain
 (logical).
    
 
 
-
    x_units
    
+
    x_units
    
 
    the units to use for the x-axis, can be one of: "ppm", "hz",
 "points" or "seconds".
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    y_scale
    
+
    y_scale
    
 
    option to display the y-axis values (logical).
    
 
 
-
    x_ax
    
+
    x_ax
    
 
    option to display the x-axis values (logical).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    lwd
    
+
    lwd
    
 
    plot linewidth.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    label
    
+
    label
    
 
    character string to add to the top left of the plot window.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    xaxis_lab
    
+
    xaxis_lab
    
 
    x-axis label.
    
 
 
-
    yaxis_lab
    
+
    yaxis_lab
    
 
    y-axis label.
    
 
 
-
    xat
    
+
    xat
    
 
    x-axis tick label values.
    
 
 
-
    xlabs
    
+
    xlabs
    
 
    x-axis tick labels.
    
 
 
-
    yat
    
+
    yat
    
 
    y-axis tick label values.
    
 
 
-
    ylabs
    
+
    ylabs
    
 
    y-axis tick labels.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    col
    
+
    col
    
 
    set the line colour, eg col = rgb(0.5, 0.5, 0.5).
    
 
 
-
    alpha
    
+
    alpha
    
 
    set the line transparency, eg alpha = 0.5 is 50% transparency.
 Overrides any transparency levels set by col.
    
 
 
-
    bl_lty
    
+
    bl_lty
    
 
    linetype for the y = 0 baseline trace. A default value NULL
 results in no baseline being plotted.
    
 
 
-
    hline
    
+
    hline
    
 
    add a horizontal line at the specified value.
    
 
 
-
    hline_lty
    
+
    hline_lty
    
 
    linetype for the horizontal line.
    
 
 
-
    hline_col
    
+
    hline_col
    
 
    colour for the horizontal line.
    
 
 
-
    vline
    
+
    vline
    
 
    add a vertical line at the specified value.
    
 
 
-
    vline_lty
    
+
    vline_lty
    
 
    linetype for the vertical line.
    
 
 
-
    vline_col
    
+
    vline_col
    
 
    colour for the vertical line.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -287,15 +289,15 @@ 
    Arguments
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html index 4f8309b4..67ce0131 100644 --- a/docs/reference/plot_bc.html +++ b/docs/reference/plot_bc.html @@ -1,9 +1,9 @@ -Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant)Convenience function to plot a baseline estimate with the original data. — plot_bc • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Convenience function to plot a baseline estimate with the original data.

    Arguments

    -
    orig_data
    + + +
    orig_data

    the original data.

    -
    bc_data
    +
    bc_data

    the baseline corrected data.

    -
    ...
    +
    ...

    other arguments to pass to the stackplot function.

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html index ae1acbe7..8f3ea0ff 100644 --- a/docs/reference/plot_reg.html +++ b/docs/reference/plot_reg.html @@ -1,9 +1,9 @@ -Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant)Plot regressors as an image. — plot_reg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Plot regressors as an image.

    Arguments

    -
    regressor_df
    + + +
    regressor_df

    input regressor data frame.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html index fbc7b560..b9ae7a84 100644 --- a/docs/reference/plot_slice_fit.html +++ b/docs/reference/plot_slice_fit.html @@ -1,9 +1,9 @@ -Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant)Plot a 2D slice from an MRSI fit result object. — plot_slice_fit • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,29 +90,31 @@

    Plot a 2D slice from an MRSI fit result object.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    map
    +
    map

    fit result values to display as a colour map. Can be specified as a character string or array of numeric values. Defaults to "tNAA".

    -
    map_denom
    +
    map_denom

    fit result values to divide the map argument by. Can be specified as a character string (eg "tCr") or array of numeric values.

    -
    slice
    +
    slice

    slice to plot in the z direction.

    -
    zlim
    +
    zlim

    range of values to plot.

    -
    interp
    +
    interp

    interpolation factor.

    @@ -129,15 +131,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html index 4eed104a..e06ec73d 100644 --- a/docs/reference/plot_slice_fit_inter.html +++ b/docs/reference/plot_slice_fit_inter.html @@ -1,9 +1,9 @@ -Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant)Plot a 2D slice from an MRSI fit result object. — plot_slice_fit_inter • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,33 +91,35 @@

    Plot a 2D slice from an MRSI fit result object.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    map
    +
    map

    fit result values to display as a colour map. Can be specified as a character string or array of numeric values. Defaults to "tNAA".

    -
    map_denom
    +
    map_denom

    fit result values to divide the map argument by. Can be specified as a character string (eg "tCr") or array of numeric values.

    -
    slice
    +
    slice

    slice to plot in the z direction.

    -
    zlim
    +
    zlim

    range of values to plot.

    -
    interp
    +
    interp

    interpolation factor.

    -
    xlim
    +
    xlim

    spectral plot limits for the x axis.

    @@ -134,15 +136,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html index 553e9ac8..f3074a86 100644 --- a/docs/reference/plot_slice_map.html +++ b/docs/reference/plot_slice_map.html @@ -1,9 +1,9 @@ -Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant)Plot a slice from a 7 dimensional array. — plot_slice_map • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -95,48 +95,50 @@

    Plot a slice from a 7 dimensional array.

    Arguments

    -
    data
    + + +
    data

    7d array of values to be plotted.

    -
    zlim
    +
    zlim

    smallest and largest values to be plotted.

    -
    mask_map
    +
    mask_map

    matching map with logical values to indicate if the corresponding values should be plotted.

    -
    mask_cutoff
    +
    mask_cutoff

    minimum values to plot (as a percentage of the maximum).

    -
    interp
    +
    interp

    map interpolation factor.

    -
    slice
    +
    slice

    the slice index to plot.

    -
    dyn
    +
    dyn

    the dynamic index to plot.

    -
    coil
    +
    coil

    the coil element number to plot.

    -
    ref
    +
    ref

    reference index to plot.

    -
    denom
    +
    denom

    map to use as a denominator.

    -
    horizontal
    +
    horizontal

    display the colourbar horizontally (logical).

    @@ -153,15 +155,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html index 40d33b42..a75caff8 100644 --- a/docs/reference/plot_slice_map_inter.html +++ b/docs/reference/plot_slice_map_inter.html @@ -1,12 +1,10 @@ -Plot an interactive slice map from a data array where voxels can be selected -to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant)Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum. — plot_slice_map_inter • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Plot an interactive slice map from a data array where voxels can be selected -to display a corresponding spectrum.

    +

    Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.

    Source: R/interactive_plotting.R
    @@ -103,62 +100,64 @@

    Plot an interactive slice map from a data array where voxels can be selected

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    spectral data.

    -
    map
    +
    map

    array of values to be plotted, defaults to the integration of the modulus of the full spectral width.

    -
    xlim
    +
    xlim

    spectral region to plot.

    -
    slice
    +
    slice

    the slice index to plot.

    -
    zlim
    +
    zlim

    smallest and largest values to be plotted.

    -
    mask_map
    +
    mask_map

    matching map with logical values to indicate if the corresponding values should be plotted.

    -
    denom
    +
    denom

    map to use as a denominator.

    -
    mask_cutoff
    +
    mask_cutoff

    minimum values to plot (as a percentage of the maximum).

    -
    interp
    +
    interp

    map interpolation factor.

    -
    mode
    +
    mode

    representation of the complex spectrum to be plotted, can be one of: "re", "im", "mod" or "arg".

    -
    y_scale
    +
    y_scale

    option to display the y-axis values (logical).

    -
    ylim
    +
    ylim

    intensity range to plot.

    -
    coil
    +
    coil

    coil element to plot.

    -
    fd
    +
    fd

    display data in the frequency-domain (default), or time-domain (logical).

    @@ -176,15 +175,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_spec_sd.html b/docs/reference/plot_spec_sd.html index 14667514..c4a430b3 100644 --- a/docs/reference/plot_spec_sd.html +++ b/docs/reference/plot_spec_sd.html @@ -1,9 +1,9 @@ -Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant)Plot the spectral standard deviation. — plot_spec_sd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,21 @@

    Plot the spectral standard deviation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be plotted.

    -
    xlim
    +
    xlim

    plotting limits in ppm.

    -
    scale_sd
    +
    scale_sd

    scaling factor for the standard deviation trace.

    -
    ...
    +
    ...

    other arguments passed to the stackplot function.

    @@ -112,15 +114,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html index 9a782e88..26e30b26 100644 --- a/docs/reference/plot_voi_overlay.html +++ b/docs/reference/plot_voi_overlay.html @@ -1,9 +1,9 @@ -Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant)Plot a volume as an image overlay. — plot_voi_overlay • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,25 @@

    Plot a volume as an image overlay.

    Arguments

    -
    mri
    + + +
    mri

    image data as a nifti object or path to data file.

    -
    voi
    +
    voi

    volume data as a nifti object or path to data file.

    -
    export_path
    +
    export_path

    optional path to save the image in png format.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    ...
    +
    ...

    additional arguments to the ortho3 function.

    @@ -116,15 +118,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html index 3d4e74ff..2aac9b38 100644 --- a/docs/reference/plot_voi_overlay_seg.html +++ b/docs/reference/plot_voi_overlay_seg.html @@ -1,9 +1,9 @@ -Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant)Plot a volume as an overlay on a segmented brain volume. — plot_voi_overlay_seg • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,21 @@

    Plot a volume as an overlay on a segmented brain volume.

    Arguments

    -
    mri_seg
    + + +
    mri_seg

    segmented brain volume as a nifti object.

    -
    voi
    +
    voi

    volume data as a nifti object.

    -
    export_path
    +
    export_path

    optional path to save the image in png format.

    -
    ...
    +
    ...

    additional arguments to the ortho3 function.

    @@ -112,15 +114,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ppm.fit_result.html b/docs/reference/ppm.fit_result.html new file mode 100644 index 00000000..9251b9b6 --- /dev/null +++ b/docs/reference/ppm.fit_result.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html index c352327a..9198a903 100644 --- a/docs/reference/ppm.html +++ b/docs/reference/ppm.html @@ -1,9 +1,9 @@ -Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant)Return the ppm scale of an MRS dataset or fit result. — ppm • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -80,44 +80,44 @@

    Return the ppm scale of an MRS dataset or fit result.

    ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)
 
-# S3 method for fit_result
+# S3 method for class 'fit_result'
 ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)

    Arguments

    -
    x
    + + +
    x

    MRS dataset of fit result.

    -
    ft
    +
    ft

    transmitter frequency in Hz, does not apply when the object is a fit result.

    -
    ref
    +
    ref

    reference value for ppm scale, does not apply when the object is a fit result.

    -
    fs
    +
    fs

    sampling frequency in Hz, does not apply when the object is a fit result.

    -
    N
    +
    N

    number of data points in the spectral dimension, does not apply when the object is a fit result.

    Value

    - - -

    ppm scale.

    +

    ppm scale.

    @@ -132,15 +132,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ppm.mrs_data.html b/docs/reference/ppm.mrs_data.html new file mode 100644 index 00000000..9251b9b6 --- /dev/null +++ b/docs/reference/ppm.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html index 822d7336..63154148 100644 --- a/docs/reference/precomp.html +++ b/docs/reference/precomp.html @@ -1,12 +1,10 @@ -Save function results to file and load on subsequent calls to avoid repeat -computation. — precomp • Spectroscopy Analysis Tools (spant)Save function results to file and load on subsequent calls to avoid repeat computation. — precomp • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Save function results to file and load on subsequent calls to avoid repeat -computation.

    +

    Save function results to file and load on subsequent calls to avoid repeat computation.

    Source: R/precomp.R
    @@ -88,15 +85,17 @@

    Save function results to file and load on subsequent calls to avoid repeat

    Arguments

    -
    file
    + + +
    file

    file name to write the results.

    -
    fun
    +
    fun

    function to run.

    -
    ...
    +
    ...

    arguments to be passed to fun.

    @@ -113,15 +112,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/preproc_svs.html b/docs/reference/preproc_svs.html new file mode 100644 index 00000000..db5ef900 --- /dev/null +++ b/docs/reference/preproc_svs.html @@ -0,0 +1,129 @@ + +Preprocess and perform quality assessment of a single SVS data set. — preproc_svs • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Preprocess and perform quality assessment of a single SVS data set.

    + Source: R/fmrs.R + +
    + +
    +

    Preprocess and perform quality assessment of a single SVS data set.

    +
    + +
    + 
    preproc_svs(path, label = NULL, output_dir = NULL, ref_inds = NULL)
    +
    + +
    +

    Arguments

    + + +
    path
    +

    path to the fMRS data file or IMA directory.

    + + +
    label
    +

    a label to describe the data set.

    + + +
    output_dir
    +

    output directory.

    + + +
    ref_inds
    +

    a vector of 1-based indices for any water reference dynamic +scans.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html new file mode 100644 index 00000000..6746af9c --- /dev/null +++ b/docs/reference/preproc_svs_dataset.html @@ -0,0 +1,150 @@ + +Preprocess and perform quality assessment of one or more SVS data sets. — preproc_svs_dataset • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Preprocess and perform quality assessment of one or more SVS data sets.

    + Source: R/fmrs.R + +
    + +
    +

    Preprocess and perform quality assessment of one or more SVS data sets.

    +
    + +
    + 
    preproc_svs_dataset(
+  paths,
+  labels = NULL,
+  output_dir = "spant_analysis",
+  exclude_labels = NULL,
+  overwrite = FALSE,
+  ref_inds = NULL,
+  return_results = FALSE
+)
    +
    + +
    +

    Arguments

    + + +
    paths
    +

    paths to the fMRS data file or IMA directory.

    + + +
    labels
    +

    labels to describe each data set.

    + + +
    output_dir
    +

    output directory.

    + + +
    exclude_labels
    +

    vector of labels of scans to exclude, eg poor quality +data.

    + + +
    overwrite
    +

    overwrite saved results, defaults to FALSE.

    + + +
    ref_inds
    +

    a vector of 1-based indices for any water reference dynamic +scans.

    + + +
    return_results
    +

    function will return key outputs, defaults to FALSE.

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html index 297f28dc..9f28ea0b 100644 --- a/docs/reference/print.fit_result.html +++ b/docs/reference/print.fit_result.html @@ -1,9 +1,9 @@ -Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant)Print a summary of an object of class fit_result. — print.fit_result • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,17 +78,19 @@

    Print a summary of an object of class fit_result.

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 print(x, ...)

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    ...
    +
    ...

    further arguments.

    @@ -105,15 +107,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html index 51199017..9d7645f3 100644 --- a/docs/reference/print.mrs_data.html +++ b/docs/reference/print.mrs_data.html @@ -1,9 +1,9 @@ -Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant)Print a summary of mrs_data parameters. — print.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,21 +78,23 @@

    Print a summary of mrs_data parameters.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 print(x, full = FALSE, ...)

    Arguments

    -
    x
    + + +
    x

    mrs_data object.

    -
    full
    +
    full

    print all parameters (default FALSE).

    -
    ...
    +
    ...

    further arguments.

    @@ -109,15 +111,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html index 0f42f2f9..a779afa7 100644 --- a/docs/reference/qn_states.html +++ b/docs/reference/qn_states.html @@ -1,9 +1,9 @@ -Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant)Get the quantum coherence matrix for a spin system. — qn_states • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Get the quantum coherence matrix for a spin system.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    Value

    - - -

    quantum coherence number matrix.

    +

    quantum coherence number matrix.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rats.html b/docs/reference/rats.html index 5a39a396..ee7897ea 100644 --- a/docs/reference/rats.html +++ b/docs/reference/rats.html @@ -1,9 +1,9 @@ -Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant)Robust Alignment to a Target Spectrum (RATS). — rats • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -103,95 +103,95 @@

    Robust Alignment to a Target Spectrum (RATS).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ref
    +
    ref

    optional MRS data to use as a reference, the mean of all dynamics is used if this argument is not supplied.

    -
    xlim
    +
    xlim

    optional frequency range to perform optimisation, set to NULL to use the full range.

    -
    max_shift
    +
    max_shift

    maximum allowable frequency shift in Hz.

    -
    p_deg
    +
    p_deg

    polynomial degree used for baseline modelling. Negative values disable baseline modelling.

    -
    sp_N
    +
    sp_N

    number of spline functions, note the true number will be sp_N + sp_deg.

    -
    sp_deg
    +
    sp_deg

    degree of spline functions.

    -
    max_t
    +
    max_t

    truncate the FID when longer than max_t to reduce time taken, set to NULL to use the entire FID.

    -
    basis_type
    +
    basis_type

    may be one of "poly" or "spline".

    -
    rescale_output
    +
    rescale_output

    rescale the bl_matched_spec and bl output to improve consistency between dynamic scans.

    -
    phase_corr
    +
    phase_corr

    apply phase correction (in addition to frequency). TRUE by default.

    -
    ret_corr_only
    +
    ret_corr_only

    return the corrected mrs_data object only.

    -
    zero_freq_shift_t0
    +
    zero_freq_shift_t0

    perform a linear fit to the frequency shifts and set the (linearly modeled) shift to be 0 Hz for the first dynamic scan.

    -
    remove_freq_outliers
    +
    remove_freq_outliers

    remove dynamics based on their frequency shift.

    -
    freq_outlier_thresh
    +
    freq_outlier_thresh

    threshold to remove frequency outliers.

    -
    remove_phase_outliers
    +
    remove_phase_outliers

    remove dynamics based on their phase shift.

    -
    phase_outlier_thresh
    +
    phase_outlier_thresh

    threshold to remove phase outliers.

    -
    remove_amp_outliers
    +
    remove_amp_outliers

    remove dynamics based on their amplitude change.

    -
    amp_outlier_thresh
    +
    amp_outlier_thresh

    threshold to remove amplitude outliers.

    Value

    - - -

    a list containing the corrected data; phase and shift values in units +

    a list containing the corrected data; phase and shift values in units of degrees and Hz respectively.

    @@ -207,15 +207,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html index d21caf21..a285a35f 100644 --- a/docs/reference/re_weighting.html +++ b/docs/reference/re_weighting.html @@ -1,9 +1,9 @@ -Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant)Apply a weighting to the FID to enhance spectral resolution. — re_weighting • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Apply a weighting to the FID to enhance spectral resolution.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be enhanced.

    -
    re
    +
    re

    resolution enhancement factor (rising exponential factor).

    -
    alpha
    +
    alpha

    alpha factor (Gaussian decay)

    Value

    - - -

    resolution enhanced mrs_data.

    +

    resolution enhanced mrs_data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/readNifti.html b/docs/reference/readNifti.html new file mode 100644 index 00000000..3d3d7357 --- /dev/null +++ b/docs/reference/readNifti.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html index da9b94af..0f8aa9a7 100644 --- a/docs/reference/read_basis.html +++ b/docs/reference/read_basis.html @@ -1,9 +1,9 @@ -Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant)Read a basis file in LCModel .basis format. — read_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Read a basis file in LCModel .basis format.

    Arguments

    -
    basis_file
    + + +
    basis_file

    path to basis file.

    -
    ref
    +
    ref

    assumed ppm reference value.

    -
    sort_basis
    +
    sort_basis

    sort the basis set based on signal names.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html index 28c02de0..8cd6cd03 100644 --- a/docs/reference/read_ima_coil_dir.html +++ b/docs/reference/read_ima_coil_dir.html @@ -1,15 +1,11 @@ -Read a directory containing Siemens MRS IMA files and combine along the coil -dimension. Note that the coil ID is inferred from the sorted file name and -should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant)Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories. — read_ima_coil_dir • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Read a directory containing Siemens MRS IMA files and combine along the coil -dimension. Note that the coil ID is inferred from the sorted file name and -should be checked when consistency is required between two directories.

    +

    Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.

    Source: R/mrs_read_ima.R
    @@ -93,24 +87,24 @@

    Read a directory containing Siemens MRS IMA files and combine along the coil

    Arguments

    -
    dir
    + + +
    dir

    data directory path.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    -
    verbose
    +
    verbose

    output extra information to the console.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -125,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_ima_dyn_dir.html b/docs/reference/read_ima_dyn_dir.html index afd997e7..1a995eea 100644 --- a/docs/reference/read_ima_dyn_dir.html +++ b/docs/reference/read_ima_dyn_dir.html @@ -1,15 +1,11 @@ -Read a directory containing Siemens MRS IMA files and combine along the -dynamic dimension. Note that the coil ID is inferred from the sorted file -name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant)Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required. — read_ima_dyn_dir • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +30,7 @@
    • - +
    -

    Read a directory containing Siemens MRS IMA files and combine along the -dynamic dimension. Note that the coil ID is inferred from the sorted file -name and should be checked when consistency is required.

    +

    Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.

    Source: R/mrs_read_ima.R
    @@ -93,24 +87,24 @@

    Read a directory containing Siemens MRS IMA files and combine along the

    Arguments

    -
    dir
    + + +
    dir

    data directory path.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    -
    verbose
    +
    verbose

    output extra information to the console.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -125,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_lcm_coord.html b/docs/reference/read_lcm_coord.html index 47c6b99f..3fff4be1 100644 --- a/docs/reference/read_lcm_coord.html +++ b/docs/reference/read_lcm_coord.html @@ -1,9 +1,9 @@ -Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant)Read an LCModel formatted coord file containing fit information. — read_lcm_coord • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Read an LCModel formatted coord file containing fit information.

    Arguments

    -
    coord_f
    + + +
    coord_f

    path to the coord file.

    Value

    - - -

    list containing a table of fit point and results structure containing +

    list containing a table of fit point and results structure containing signal amplitudes, errors and fitting diagnostics.

    @@ -107,15 +107,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html index 3ac2a36b..a9dd7053 100644 --- a/docs/reference/read_mrs.html +++ b/docs/reference/read_mrs.html @@ -1,9 +1,9 @@ -Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant)Read MRS data from a file. — read_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -88,64 +88,72 @@

    Read MRS data from a file.

    full_fid = FALSE, omit_svs_ref_scans = TRUE, verbose = FALSE, - extra = NULL + extra = NULL, + fid_filt_dist = NULL )

    Arguments

    -
    fname
    + + +
    fname

    filename of the dpt format MRS data.

    -
    format
    +
    format

    string describing the data format. Must be one of the following : "spar_sdat", "rda", "dicom", "twix", "pfile", "list_data", "paravis", "dpt", "lcm_raw", "rds", "nifti", "varian", "jmrui_txt". If not specified, the format will be guessed from the filename extension.

    -
    ft
    +
    ft

    transmitter frequency in Hz (required for list_data format).

    -
    fs
    +
    fs

    sampling frequency in Hz (required for list_data format).

    -
    ref
    +
    ref

    reference value for ppm scale (required for list_data format).

    -
    n_ref_scans
    +
    n_ref_scans

    override the number of water reference scans detected in the file header (GE p-file only).

    -
    full_fid
    +
    full_fid

    export all data points, including those before the start of the FID (default = FALSE), TWIX format only.

    -
    omit_svs_ref_scans
    +
    omit_svs_ref_scans

    remove any reference scans sometimes saved in SVS twix data (default = TRUE).

    -
    verbose
    +
    verbose

    print data file information (default = FALSE).

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    + +
    fid_filt_dist
    +

    indicate if the data has a distorted FID due to a +brick-wall filter being used to downsample the data. Default is to auto +detect this from the data, but TRUE or FALSE options can be given to override +detection.

    +

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    @@ -183,15 +191,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html index 5766362f..0715cefa 100644 --- a/docs/reference/read_mrs_tqn.html +++ b/docs/reference/read_mrs_tqn.html @@ -1,9 +1,9 @@ -Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant)Read MRS data using the TARQUIN software package. — read_mrs_tqn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,40 +83,40 @@

    Read MRS data using the TARQUIN software package.

    Arguments

    -
    fname
    + + +
    fname

    the filename containing the MRS data.

    -
    fname_ref
    +
    fname_ref

    a second filename containing reference MRS data.

    -
    format
    +
    format

    format of the MRS data. Can be one of the following: siemens, philips, ge, dcm, dpt, rda, lcm, varian, bruker, jmrui_txt.

    -
    id
    +
    id

    optional ID string.

    -
    group
    +
    group

    optional group string.

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    Examples

    fname <- system.file("extdata","philips_spar_sdat_WS.SDAT",package="spant")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 mrs_data <- read_mrs_tqn(fname, format="philips")
-}
+} # }
    @@ -131,15 +131,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html index c9e0d43c..de0e661b 100644 --- a/docs/reference/read_pulse_ascii.html +++ b/docs/reference/read_pulse_ascii.html @@ -1,9 +1,9 @@ -Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant)Read an ASCII formatted pulse file. — read_pulse_ascii • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Read an ASCII formatted pulse file.

    Arguments

    -
    fname
    + + +
    fname

    ASCII formatted pulse file path.

    -
    deg2rad
    +
    deg2rad

    convert phase values stored in degrees to radians.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html index c92bf76a..1728446e 100644 --- a/docs/reference/read_pulse_bruker.html +++ b/docs/reference/read_pulse_bruker.html @@ -1,9 +1,9 @@ -Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant)Read a Bruker formatted pulse file — read_pulse_bruker • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Read a Bruker formatted pulse file

    Arguments

    -
    fname
    + + +
    fname

    Bruker formatted pulse file path.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html index 72e1b6d4..7cb51f4c 100644 --- a/docs/reference/read_pulse_pta.html +++ b/docs/reference/read_pulse_pta.html @@ -1,9 +1,9 @@ -Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant)Read a .pta formatted pulse file compatible with Siemens PulseTool. — read_pulse_pta • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Read a .pta formatted pulse file compatible with Siemens PulseTool.

    Arguments

    -
    fname
    + + +
    fname

    pta formatted pulse file path.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html index 23fb8c70..0565e854 100644 --- a/docs/reference/read_siemens_txt_hdr.html +++ b/docs/reference/read_siemens_txt_hdr.html @@ -1,9 +1,9 @@ -Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant)Read the text format header found in Siemens IMA and TWIX data files. — read_siemens_txt_hdr • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,32 +78,32 @@

    Read the text format header found in Siemens IMA and TWIX data files.

    - 
    read_siemens_txt_hdr(input, version = "vd", verbose, offset = 0)
    + 
    read_siemens_txt_hdr(input, version = "vd", verbose = FALSE, offset = 0)

    Arguments

    -
    input
    + + +
    input

    file name to read or raw data.

    -
    version
    +
    version

    software version, can be "vb" or "vd".

    -
    verbose
    +
    verbose

    print information to the console.

    -
    offset
    +
    offset

    offset to begin searching for the text header.

    Value

    - - -

    a list of parameter values

    +

    a list of parameter values

    @@ -118,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html index 4da6c25e..3c80aa9f 100644 --- a/docs/reference/read_tqn_fit.html +++ b/docs/reference/read_tqn_fit.html @@ -1,9 +1,9 @@ -Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant)Reader for csv fit results generated by TARQUIN. — read_tqn_fit • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,22 +83,22 @@

    Reader for csv fit results generated by TARQUIN.

    Arguments

    -
    fit_f
    + + +
    fit_f

    TARQUIN fit file.

    Value

    - - -

    A data frame of the fit data points.

    +

    A data frame of the fit data points.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 fit <- read_tqn_fit(system.file("extdata","fit.csv",package="spant"))
-}
+} # }
    @@ -113,15 +113,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html index 36659714..50899561 100644 --- a/docs/reference/read_tqn_result.html +++ b/docs/reference/read_tqn_result.html @@ -1,9 +1,9 @@ -Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant)Reader for csv results generated by TARQUIN. — read_tqn_result • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,26 +83,26 @@

    Reader for csv results generated by TARQUIN.

    Arguments

    -
    result_f
    + + +
    result_f

    TARQUIN result file.

    -
    remove_rcs
    +
    remove_rcs

    omit row, column and slice ids from output.

    Value

    - - -

    list of amplitudes, crlbs and diagnostics.

    +

    list of amplitudes, crlbs and diagnostics.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 result <- read_tqn_result(system.file("extdata","result.csv",package="spant"))
-}
+} # }
    @@ -117,15 +117,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html index d2a72225..1866e759 100644 --- a/docs/reference/recon_imag.html +++ b/docs/reference/recon_imag.html @@ -1,12 +1,10 @@ -Reconstruct complex time-domain data from the real part of frequency-domain -data. — recon_imag • Spectroscopy Analysis Tools (spant)Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Reconstruct complex time-domain data from the real part of frequency-domain -data.

    +

    Reconstruct complex time-domain data from the real part of frequency-domain data.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Reconstruct complex time-domain data from the real part of frequency-domain

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    reconstructed MRS data.

    +

    reconstructed MRS data.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/recon_imag_vec.html b/docs/reference/recon_imag_vec.html index f72c0998..b9e053a6 100644 --- a/docs/reference/recon_imag_vec.html +++ b/docs/reference/recon_imag_vec.html @@ -1,12 +1,10 @@ -Reconstruct complex time-domain data from the real part of frequency-domain -data. — recon_imag_vec • Spectroscopy Analysis Tools (spant)Reconstruct complex time-domain data from the real part of frequency-domain data. — recon_imag_vec • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Reconstruct complex time-domain data from the real part of frequency-domain -data.

    +

    Reconstruct complex time-domain data from the real part of frequency-domain data.

    Source: R/mrs_data_proc.R
    @@ -88,15 +85,15 @@

    Reconstruct complex time-domain data from the real part of frequency-domain

    Arguments

    -
    data
    + + +
    data

    data points in the frequency domain.

    Value

    - - -

    reconstructed signal.

    +

    reconstructed signal.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/recon_twix_2d_mrsi.html b/docs/reference/recon_twix_2d_mrsi.html index 22ed7907..0fd8cd40 100644 --- a/docs/reference/recon_twix_2d_mrsi.html +++ b/docs/reference/recon_twix_2d_mrsi.html @@ -1,9 +1,9 @@ -Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant)Reconstruct 2D MRSI data from a twix file loaded with read_mrs. — recon_twix_2d_mrsi • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Reconstruct 2D MRSI data from a twix file loaded with read_mrs.

    Arguments

    -
    twix_mrs
    + + +
    twix_mrs

    raw dynamic data.

    Value

    - - -

    reconstructed data.

    +

    reconstructed data.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html index a2117283..7f38b601 100644 --- a/docs/reference/rectangular_mask.html +++ b/docs/reference/rectangular_mask.html @@ -1,9 +1,9 @@ -Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant)Create a rectangular mask stored as a matrix of logical values. — rectangular_mask • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,39 +83,39 @@

    Create a rectangular mask stored as a matrix of logical values.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of rectangle in the x direction in units of pixels.

    -
    y0
    +
    y0

    centre of rectangle in the y direction in units of pixels.

    -
    xw
    +
    xw

    width in the x direction in units of pixels.

    -
    yw
    +
    yw

    width in the y direction in units of pixels.

    -
    angle
    +
    angle

    angle of rotation in degrees.

    Value

    - - -

    logical mask matrix with dimensions fov_yN x fov_xN.

    +

    logical mask matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +130,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 694a75d1..a06a4a92 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,5 +1,5 @@ -Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant)Objects exported from other packages — reexports • Spectroscopy Analysis Tools (spant) - +
    @@ -35,7 +35,7 @@
    • - +
    @@ -103,15 +103,15 @@

    Objects exported from other packages

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html index b9c49b4a..cc0327aa 100644 --- a/docs/reference/rep_array_dim.html +++ b/docs/reference/rep_array_dim.html @@ -1,9 +1,9 @@ -Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant)Repeat an array over a given dimension. — rep_array_dim • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Repeat an array over a given dimension.

    Arguments

    -
    x
    + + +
    x

    array.

    -
    rep_dim
    +
    rep_dim

    dimension to extend.

    -
    n
    +
    n

    number of times to repeat.

    Value

    - - -

    extended array.

    +

    extended array.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html index 6bbfb0ef..8a33d1ef 100644 --- a/docs/reference/rep_dyn.html +++ b/docs/reference/rep_dyn.html @@ -1,9 +1,9 @@ -Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant)Replicate a scan in the dynamic dimension. — rep_dyn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Replicate a scan in the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be replicated.

    -
    times
    +
    times

    number of times to replicate.

    Value

    - - -

    replicated data object.

    +

    replicated data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html index 67730b5c..57b5fe03 100644 --- a/docs/reference/rep_mrs.html +++ b/docs/reference/rep_mrs.html @@ -1,9 +1,9 @@ -Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant)Replicate a scan over a given dimension. — rep_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,39 +91,39 @@

    Replicate a scan over a given dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be replicated.

    -
    x_rep
    +
    x_rep

    number of x replications.

    -
    y_rep
    +
    y_rep

    number of y replications.

    -
    z_rep
    +
    z_rep

    number of z replications.

    -
    dyn_rep
    +
    dyn_rep

    number of dynamic replications.

    -
    coil_rep
    +
    coil_rep

    number of coil replications.

    -
    warn
    +
    warn

    print a warning when the data dimensions do not change.

    Value

    - - -

    replicated data object.

    +

    replicated data object.

    @@ -138,15 +138,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html index b0f2ab17..e26a44e8 100644 --- a/docs/reference/resample_basis.html +++ b/docs/reference/resample_basis.html @@ -1,9 +1,9 @@ -Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant)Resample a basis-set to match a mrs_data acquisition. — resample_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Resample a basis-set to match a mrs_data acquisition.

    Arguments

    -
    basis
    + + +
    basis

    the basis to be resampled.

    -
    mrs_data
    +
    mrs_data

    the mrs_data to match the number of data points and sampling frequency.

    -
    ref_freq_match
    +
    ref_freq_match

    apply a frequency shift to the basis to match the reference frequency (usually 4.65 or 4.68) of the mrs_data.

    Value

    - - -

    resampled basis set object.

    +

    resampled basis set object.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html index f1e7beaf..88d1de35 100644 --- a/docs/reference/resample_img.html +++ b/docs/reference/resample_img.html @@ -1,9 +1,9 @@ -Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant)Resample an image to match a target image space. — resample_img • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Resample an image to match a target image space.

    Arguments

    -
    source
    + + +
    source

    image data as a nifti object.

    -
    target
    +
    target

    image data as a nifti object.

    -
    interp
    +
    interp

    interpolation parameter, see nifyreg.linear definition.

    Value

    - - -

    resampled image data as a nifti object.

    +

    resampled image data as a nifti object.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html index 8fbfa836..524cb29c 100644 --- a/docs/reference/resample_voi.html +++ b/docs/reference/resample_voi.html @@ -1,12 +1,10 @@ -Resample a VOI to match a target image space using nearest-neighbour -interpolation. — resample_voi • Spectroscopy Analysis Tools (spant)Resample a VOI to match a target image space using nearest-neighbour interpolation. — resample_voi • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Resample a VOI to match a target image space using nearest-neighbour -interpolation.

    +

    Resample a VOI to match a target image space using nearest-neighbour interpolation.

    Source: R/image_reg.R
    @@ -88,19 +85,19 @@

    Resample a VOI to match a target image space using nearest-neighbour

    Arguments

    -
    voi
    + + +
    voi

    volume data as a nifti object.

    -
    mri
    +
    mri

    image data as a nifti object.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -115,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reslice_to_mrs.html b/docs/reference/reslice_to_mrs.html index 2da67870..2f4f33b3 100644 --- a/docs/reference/reslice_to_mrs.html +++ b/docs/reference/reslice_to_mrs.html @@ -1,9 +1,9 @@ -Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant)Reslice a nifti object to match the orientation of mrs data. — reslice_to_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Reslice a nifti object to match the orientation of mrs data.

    Arguments

    -
    mri
    + + +
    mri

    nifti object to be resliced.

    -
    mrs
    +
    mrs

    mrs_data object for the target orientation.

    -
    interp
    +
    interp

    interpolation parameter, see nifyreg.linear definition.

    Value

    - - -

    resliced imaging data.

    +

    resliced imaging data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html index d75579ee..333bb54e 100644 --- a/docs/reference/reson_table2mrs_data.html +++ b/docs/reference/reson_table2mrs_data.html @@ -1,9 +1,9 @@ -Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant)Generate mrs_data from a table of single Lorentzian resonances. — reson_table2mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -87,24 +87,24 @@

    Generate mrs_data from a table of single Lorentzian resonances.

    Arguments

    -
    reson_table
    + + +
    reson_table

    as produced by the hsvd function.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters. See

    -
    back_extrap_pts
    +
    back_extrap_pts

    number of data points to back extrapolate def_acq_paras

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -119,15 +119,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html index 5d5ef692..a146fb4f 100644 --- a/docs/reference/rm_dyns.html +++ b/docs/reference/rm_dyns.html @@ -1,9 +1,9 @@ -Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant)Remove a subset of dynamic scans. — rm_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Remove a subset of dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be removed.

    Value

    - - -

    MRS data without the specified dynamic scans.

    +

    MRS data without the specified dynamic scans.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html index aaeee1f2..044d28db 100644 --- a/docs/reference/scale_amp_molal.html +++ b/docs/reference/scale_amp_molal.html @@ -1,7 +1,5 @@ -Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant)Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal • Spectroscopy Analysis Tools (spant) - +
    @@ -36,7 +34,7 @@
    • - +
    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

    Source: R/amp_scaling.R
    @@ -108,47 +105,47 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    te
    +
    te

    the MRS TE in seconds.

    -
    tr
    +
    tr

    the MRS TR in seconds.

    -
    water_t1
    +
    water_t1

    assumed water T1 value.

    -
    water_t2
    +
    water_t2

    assumed water T2 value.

    -
    metab_t1
    +
    metab_t1

    assumed metabolite T1 value.

    -
    metab_t2
    +
    metab_t2

    assumed metabolite T2 value.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    A fit_result object with a rescaled results table.

    +

    A fit_result object with a rescaled results table.

    @@ -163,15 +160,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html index 962d6afc..d001ad9e 100644 --- a/docs/reference/scale_amp_molal_pvc.html +++ b/docs/reference/scale_amp_molal_pvc.html @@ -1,7 +1,5 @@ -Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water). — scale_amp_molal_pvc • Spectroscopy Analysis Tools (spant) - +
    @@ -35,7 +33,7 @@
    • - +
    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / kg of tissue water).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

    Source: R/amp_scaling.R
    @@ -96,37 +93,37 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. For example, a voxel containing 100% white matter tissue would use : p_vols = c(WM = 100, GM = 0, CSF = 0).

    -
    te
    +
    te

    the MRS TE in seconds.

    -
    tr
    +
    tr

    the MRS TR in seconds.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    A fit_result object with a rescaled results table.

    +

    A fit_result object with a rescaled results table.

    @@ -141,15 +138,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html index 02358d91..c24e1831 100644 --- a/docs/reference/scale_amp_molar.html +++ b/docs/reference/scale_amp_molar.html @@ -1,14 +1,12 @@ -Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant)Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). — scale_amp_molar • Spectroscopy Analysis Tools (spant) - +
    @@ -33,7 +31,7 @@
    • - +
    -

    Apply water reference scaling to a fitting results object to yield metabolite -quantities in millimolar (mM) units (mol / Litre of tissue).

    +

    Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).

    Source: R/amp_scaling.R
    @@ -92,34 +89,34 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    w_att
    +
    w_att

    water attenuation factor (default = 0.7). Assumes water T2 of 80ms and a TE = 30 ms. exp(-30ms / 80ms) ~ 0.7.

    -
    w_conc
    +
    w_conc

    assumed water concentration (default = 35880). Default value corresponds to typical white matter. Set to 43300 for gray matter, and 55556 for phantom measurements.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -134,15 +131,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_molar2molal_pvc.html b/docs/reference/scale_amp_molar2molal_pvc.html index c1cab0b7..4bdb2cfa 100644 --- a/docs/reference/scale_amp_molar2molal_pvc.html +++ b/docs/reference/scale_amp_molar2molal_pvc.html @@ -1,12 +1,10 @@ -Convert default LCM/TARQUIN concentration scaling to molal units with partial -volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant)Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction. — scale_amp_molar2molal_pvc • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert default LCM/TARQUIN concentration scaling to molal units with partial -volume correction.

    +

    Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.

    Source: R/amp_scaling.R
    @@ -88,30 +85,30 @@

    Convert default LCM/TARQUIN concentration scaling to molal units with partia

    Arguments

    -
    fit_result
    + + +
    fit_result

    a fit_result object to apply partial volume correction.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. For example, a voxel containing 100% white matter tissue would use : p_vols = c(WM = 100, GM = 0, CSF = 0).

    -
    te
    +
    te

    the MRS TE.

    -
    tr
    +
    tr

    the MRS TR.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -126,15 +123,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_ratio.html b/docs/reference/scale_amp_ratio.html index 756eb144..46c57eb6 100644 --- a/docs/reference/scale_amp_ratio.html +++ b/docs/reference/scale_amp_ratio.html @@ -1,9 +1,9 @@ -Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant)Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,25 +83,25 @@

    Scale fitted amplitudes to a ratio of signal amplitude.

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    name
    +
    name

    the signal name to use as a denominator (usually, "tCr" or "tNAA").

    -
    use_mean_value
    +
    use_mean_value

    scales the result by the mean of the signal when set to TRUE.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -116,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html index 2036837a..07cc5d26 100644 --- a/docs/reference/scale_amp_ratio_value.html +++ b/docs/reference/scale_amp_ratio_value.html @@ -1,9 +1,9 @@ -Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant)Scale fitted amplitudes to a ratio of signal amplitude. — scale_amp_ratio_value • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Scale fitted amplitudes to a ratio of signal amplitude.

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    value
    +
    value

    the number use as a denominator.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html index 5b25e884..22888e7a 100644 --- a/docs/reference/scale_amp_water_ratio.html +++ b/docs/reference/scale_amp_water_ratio.html @@ -1,9 +1,9 @@ -Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant)Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude. — scale_amp_water_ratio • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude.<

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    ref_data
    +
    ref_data

    a water reference MRS data object.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html index 9401c3f1..d6bd1b47 100644 --- a/docs/reference/scale_basis_amp.html +++ b/docs/reference/scale_basis_amp.html @@ -1,9 +1,9 @@ -Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant)Scale a basis object by a scalar. — scale_basis_amp • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Scale a basis object by a scalar.

    Arguments

    -
    basis
    + + +
    basis

    basis_set object to be scaled.

    -
    amp
    +
    amp

    multiplicative factor with length 1.

    Value

    - - -

    basis_set object multiplied by the amplitude scale factor.

    +

    basis_set object multiplied by the amplitude scale factor.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html index 0d542bc8..c2f5145a 100644 --- a/docs/reference/scale_basis_from_singlet.html +++ b/docs/reference/scale_basis_from_singlet.html @@ -1,5 +1,5 @@ -Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant)Scale a basis-set to be consistent with spant assumptions for water scaling. — scale_basis_from_singlet • Spectroscopy Analysis Tools (spant) - +
    @@ -34,7 +34,7 @@
    • - +
    @@ -95,24 +95,24 @@

    Scale a basis-set to be consistent with spant assumptions for water scaling.

    Arguments

    -
    basis
    + + +
    basis

    basis set to be scaled.

    -
    name
    +
    name

    the name of the singlet to be used as a scaling reference.

    -
    protons
    +
    protons

    the number of MRS visible protons contributing to the singlet resonance.

    Value

    - - -

    a scaled basis.

    +

    a scaled basis.

    @@ -127,15 +127,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html index b5501a0d..dc6991df 100644 --- a/docs/reference/scale_mrs_amp.html +++ b/docs/reference/scale_mrs_amp.html @@ -1,9 +1,9 @@ -Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant)Scale an mrs_data object by a scalar or vector or amplitudes. — scale_mrs_amp • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,20 +83,20 @@

    Scale an mrs_data object by a scalar or vector or amplitudes.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be scaled.

    -
    amp
    +
    amp

    multiplicative factor, must have length equal to 1 or Nspec(mrs_data).

    Value

    - - -

    mrs_data object multiplied by the amplitude scale factor.

    +

    mrs_data object multiplied by the amplitude scale factor.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html index 4f6ea835..826c17a9 100644 --- a/docs/reference/scale_spec.html +++ b/docs/reference/scale_spec.html @@ -1,9 +1,9 @@ -Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant)Scale mrs_data to a spectral region. — scale_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,42 +91,42 @@

    Scale mrs_data to a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    -
    operator
    +
    operator

    can be "sum" (default), "mean", "l2", "max", "min" or "max-min".

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "Hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    -
    mean_dyns
    +
    mean_dyns

    mean the dynamic scans before applying the operator. The same scaling value will be applied to each individual dynamic.

    -
    ret_scale_factor
    +
    ret_scale_factor

    option to return the scaling factor in addition to the scaled data.

    Value

    - - -

    normalised data.

    +

    normalised data.

    @@ -141,15 +141,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sd.html b/docs/reference/sd.html index ea1eec9f..7a533d35 100644 --- a/docs/reference/sd.html +++ b/docs/reference/sd.html @@ -1,9 +1,9 @@ -Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant)Calculate the standard deviation spectrum from an mrs_data object. — sd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Calculate the standard deviation spectrum from an mrs_data object.

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    na.rm
    +
    na.rm

    remove NA values.

    Value

    - - -

    sd mrs_data object.

    +

    sd mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html index 3f92a49f..4bfecd0f 100644 --- a/docs/reference/sd.mrs_data.html +++ b/docs/reference/sd.mrs_data.html @@ -1,9 +1,9 @@ -Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant)Calculate the standard deviation spectrum from an mrs_data object. — sd.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,25 +78,25 @@

    Calculate the standard deviation spectrum from an mrs_data object.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 sd(x, na.rm = FALSE)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    na.rm
    +
    na.rm

    remove NA values.

    Value

    - - -

    sd mrs_data object.

    +

    sd mrs_data object.

    @@ -111,15 +111,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html index b34d6627..fee752f4 100644 --- a/docs/reference/seconds.html +++ b/docs/reference/seconds.html @@ -1,9 +1,9 @@ -Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant)Return a time scale vector to match the FID of an MRS data object. — seconds • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return a time scale vector to match the FID of an MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    time scale vector in units of seconds.

    +

    time scale vector in units of seconds.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html index 547e96ab..01f17fde 100644 --- a/docs/reference/seq_cpmg_ideal.html +++ b/docs/reference/seq_cpmg_ideal.html @@ -1,9 +1,9 @@ -CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant)CPMG style sequence with ideal pulses. — seq_cpmg_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    CPMG style sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    echo time in seconds.

    -
    echoes
    +
    echoes

    number of echoes.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html index 0769b8b4..3f264b3c 100644 --- a/docs/reference/seq_mega_press_ideal.html +++ b/docs/reference/seq_mega_press_ideal.html @@ -1,12 +1,10 @@ -MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped -editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant)MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse. — seq_mega_press_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped -editing pulse.

    +

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.

    Source: R/pulse_sequences.R
    @@ -97,43 +94,43 @@

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    ed_freq
    +
    ed_freq

    editing pulse frequency in ppm.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    -
    BW
    +
    BW

    editing pulse bandwidth in Hz.

    -
    steps
    +
    steps

    number of hard pulses used to approximate the editing pulse.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -148,15 +145,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_press_2d_shaped.html b/docs/reference/seq_press_2d_shaped.html index 258f5c38..a9a112c8 100644 --- a/docs/reference/seq_press_2d_shaped.html +++ b/docs/reference/seq_press_2d_shaped.html @@ -1,9 +1,9 @@ -PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant)PRESS sequence with shaped refocusing pulses. — seq_press_2d_shaped • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -96,61 +96,61 @@

    PRESS sequence with shaped refocusing pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    -
    pulse_file
    +
    pulse_file

    path to refocusing pulse file.

    -
    pulse_dur
    +
    pulse_dur

    refocusing pulse duration.

    -
    pulse_file_format
    +
    pulse_file_format

    file format for the refocusing pulse.

    -
    refoc_flip_angle
    +
    refoc_flip_angle

    refocusing pulse flip angle in degrees (defaults to 180).

    -
    xy_pulse_ppm
    +
    xy_pulse_ppm

    a vector of ppm values for the offset of each sub-simulation.

    -
    resamp
    +
    resamp

    option to resample the pulse shape.

    -
    fs_resamp
    +
    fs_resamp

    sampling frequency (Hz) to resample.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -165,15 +165,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html index 8c976856..9b86db44 100644 --- a/docs/reference/seq_press_ideal.html +++ b/docs/reference/seq_press_ideal.html @@ -1,9 +1,9 @@ -PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant)PRESS sequence with ideal pulses. — seq_press_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    PRESS sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html index 4a88fc64..4dc30c94 100644 --- a/docs/reference/seq_pulse_acquire.html +++ b/docs/reference/seq_pulse_acquire.html @@ -1,9 +1,9 @@ -Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant)Simple pulse and acquire sequence with ideal pulses. — seq_pulse_acquire • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Simple pulse and acquire sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    acquisition nucleus.

    -
    acq_delay
    +
    acq_delay

    delay between excitation and acquisition.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html index 74688f4d..d1a6e261 100644 --- a/docs/reference/seq_slaser_ideal.html +++ b/docs/reference/seq_slaser_ideal.html @@ -1,9 +1,9 @@ -sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant)sLASER sequence with ideal pulses. — seq_slaser_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,35 +83,35 @@

    sLASER sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    first echo time (between exc. and 1st echo) in seconds.

    -
    TE2
    +
    TE2

    second echo time (between 2nd echo and 4th echo) in seconds.

    -
    TE3
    +
    TE3

    third echo time (between 4th echo and 5th echo) in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -126,15 +126,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html index e23271de..05f365bc 100644 --- a/docs/reference/seq_spin_echo_ideal.html +++ b/docs/reference/seq_spin_echo_ideal.html @@ -1,9 +1,9 @@ -Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant)Spin echo sequence with ideal pulses. — seq_spin_echo_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Spin echo sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    acquisition nucleus.

    -
    TE
    +
    TE

    echo time in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html index a60685a8..a2f8b97b 100644 --- a/docs/reference/seq_steam_ideal.html +++ b/docs/reference/seq_steam_ideal.html @@ -1,9 +1,9 @@ -STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant)STEAM sequence with ideal pulses. — seq_steam_ideal • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,29 @@

    STEAM sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -111,9 +113,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -128,15 +128,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html index 8f225740..0d0ea60e 100644 --- a/docs/reference/seq_steam_ideal_cof.html +++ b/docs/reference/seq_steam_ideal_cof.html @@ -1,12 +1,10 @@ -STEAM sequence with ideal pulses and coherence order filtering to simulate -gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant)STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers. — seq_steam_ideal_cof • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    STEAM sequence with ideal pulses and coherence order filtering to simulate -gradient crushers.

    +

    STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.

    Source: R/pulse_sequences.R
    @@ -88,27 +85,29 @@

    STEAM sequence with ideal pulses and coherence order filtering to simulate

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -116,9 +115,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -133,15 +130,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/seq_steam_ideal_young.html b/docs/reference/seq_steam_ideal_young.html index 994f41b9..9bead9f7 100644 --- a/docs/reference/seq_steam_ideal_young.html +++ b/docs/reference/seq_steam_ideal_young.html @@ -1,12 +1,10 @@ -STEAM sequence with ideal pulses using the z-rotation gradient simulation -method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant)STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999). — seq_steam_ideal_young • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    STEAM sequence with ideal pulses using the z-rotation gradient simulation -method described by Young et al JMR 140, 146-152 (1999).

    +

    STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).

    Source: R/pulse_sequences.R
    @@ -95,27 +92,29 @@

    STEAM sequence with ideal pulses using the z-rotation gradient simulation

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -123,9 +122,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -140,15 +137,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_Ntrans.html b/docs/reference/set_Ntrans.html index f306da68..11fbfecd 100644 --- a/docs/reference/set_Ntrans.html +++ b/docs/reference/set_Ntrans.html @@ -1,9 +1,9 @@ -Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant)Set the number of transients for an mrs_data object. — set_Ntrans • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Set the number of transients for an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    n_trans
    +
    n_trans

    number of acquired transients.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html index 3e1b4004..b52ecf94 100644 --- a/docs/reference/set_def_acq_paras.html +++ b/docs/reference/set_def_acq_paras.html @@ -1,9 +1,9 @@ -Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant)Set the default acquisition parameters. — set_def_acq_paras • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -89,23 +89,25 @@

    Set the default acquisition parameters.

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    @@ -122,15 +124,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html index 2056ed01..c7929d87 100644 --- a/docs/reference/set_lcm_cmd.html +++ b/docs/reference/set_lcm_cmd.html @@ -1,9 +1,9 @@ -Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant)Set the command to run the LCModel command-line program. — set_lcm_cmd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Set the command to run the LCModel command-line program.

    Arguments

    -
    cmd
    + + +
    cmd

    path to binary.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html index b64ec851..c4b57b38 100644 --- a/docs/reference/set_lw.html +++ b/docs/reference/set_lw.html @@ -1,9 +1,9 @@ -Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant)Apply line-broadening to an mrs_data object to achieve a specified linewidth. — set_lw • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,32 +83,32 @@

    Apply line-broadening to an mrs_data object to achieve a specified linewidth

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data in.

    -
    lw
    +
    lw

    target linewidth in units of ppm.

    -
    xlim
    +
    xlim

    region to search for peaks to obtain a linewidth estimate.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter.

    -
    mask_narrow
    +
    mask_narrow

    masks spectra where the requested linewidth is too narrow, if set FALSE the spectra are not changed.

    Value

    - - -

    line-broadened data.

    +

    line-broadened data.

    @@ -123,15 +123,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html index 49dc5d4e..6c1c931c 100644 --- a/docs/reference/set_mask_xy_mat.html +++ b/docs/reference/set_mask_xy_mat.html @@ -1,9 +1,9 @@ -Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant)Set the masked voxels in a 2D MRSI dataset to given spectrum. — set_mask_xy_mat • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Set the masked voxels in a 2D MRSI dataset to given spectrum.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data object.

    -
    mask
    +
    mask

    matrix of boolean values specifying the voxels to set, where a value of TRUE indicates the voxel should be set to mask_mrs_data.

    -
    mask_mrs_data
    +
    mask_mrs_data

    the spectral data to be assigned to the masked voxels.

    Value

    - - -

    updated dataset.

    +

    updated dataset.

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html index f44bd5d3..0feb353d 100644 --- a/docs/reference/set_precomp_mode.html +++ b/docs/reference/set_precomp_mode.html @@ -1,9 +1,9 @@ -Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant)Set the precompute mode. — set_precomp_mode • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Set the precompute mode.

    Arguments

    -
    mode
    + + +
    mode

    can be one of: "default", "overwrite", "clean" or "disabled".

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html index 1453a231..9dadc897 100644 --- a/docs/reference/set_precomp_verbose.html +++ b/docs/reference/set_precomp_verbose.html @@ -1,9 +1,9 @@ -Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant)Set the verbosity of the precompute function. — set_precomp_verbose • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Set the verbosity of the precompute function.

    Arguments

    -
    verbose
    + + +
    verbose

    can be TRUE or FALSE.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html index 8953fa50..c63c49fb 100644 --- a/docs/reference/set_ref.html +++ b/docs/reference/set_ref.html @@ -1,9 +1,9 @@ -Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant)Set the ppm reference value (eg ppm value at 0Hz). — set_ref • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Set the ppm reference value (eg ppm value at 0Hz).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    ref
    +
    ref

    reference value for ppm scale.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html index 8a80d42a..056199b3 100644 --- a/docs/reference/set_td_pts.html +++ b/docs/reference/set_td_pts.html @@ -1,12 +1,10 @@ -Set the number of time-domain data points, truncating or zero-filling as -appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant)Set the number of time-domain data points, truncating or zero-filling as appropriate. — set_td_pts • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Set the number of time-domain data points, truncating or zero-filling as -appropriate.

    +

    Set the number of time-domain data points, truncating or zero-filling as appropriate.

    Source: R/mrs_data_proc.R
    @@ -88,19 +85,19 @@

    Set the number of time-domain data points, truncating or zero-filling as

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of data points.

    Value

    - - -

    MRS data with pts data points.

    +

    MRS data with pts data points.

    @@ -115,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_tqn_cmd.html b/docs/reference/set_tqn_cmd.html index 7083886d..55b9a7f4 100644 --- a/docs/reference/set_tqn_cmd.html +++ b/docs/reference/set_tqn_cmd.html @@ -1,9 +1,9 @@ -Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant)Set the command to run the TARQUIN command-line program. — set_tqn_cmd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,9 @@

    Set the command to run the TARQUIN command-line program.

    Arguments

    -
    cmd
    + + +
    cmd

    path to binary.

    @@ -100,15 +102,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html index b2109ab0..d2f085a0 100644 --- a/docs/reference/set_tr.html +++ b/docs/reference/set_tr.html @@ -1,9 +1,9 @@ -Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant)Set the repetition time of an MRS dataset. — set_tr • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Set the repetition time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    tr
    +
    tr

    repetition time in seconds.

    Value

    - - -

    updated mrs_data set.

    +

    updated mrs_data set.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/shift.html b/docs/reference/shift.html index ab0fe724..87b9ec01 100644 --- a/docs/reference/shift.html +++ b/docs/reference/shift.html @@ -1,9 +1,9 @@ -Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant)Apply a frequency shift to MRS data. — shift • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,23 +83,23 @@

    Apply a frequency shift to MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    shift
    +
    shift

    frequency shift (in ppm by default).

    -
    units
    +
    units

    of the shift ("ppm" or "hz").

    Value

    - - -

    frequency shifted MRS data.

    +

    frequency shifted MRS data.

    @@ -114,15 +114,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html index 2884be19..51fbea77 100644 --- a/docs/reference/shift_basis.html +++ b/docs/reference/shift_basis.html @@ -1,9 +1,9 @@ -Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant)Apply frequency shifts to basis set signals. — shift_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Apply frequency shifts to basis set signals.

    Arguments

    -
    basis
    + + +
    basis

    the basis to apply the shift to.

    -
    shifts
    +
    shifts

    a vector of frequency shifts to apply in ppm units. Must be the same length as there are basis elements, or one value to be applied to all elements.

    @@ -95,9 +97,7 @@

    Arguments

    Value

    - - -

    modified basis set object.

    +

    modified basis set object.

    @@ -112,15 +112,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html index c7838c46..22fb4597 100644 --- a/docs/reference/sim_basis.html +++ b/docs/reference/sim_basis.html @@ -1,9 +1,9 @@ -Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant)Simulate a basis set object. — sim_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -90,38 +90,38 @@

    Simulate a basis set object.

    Arguments

    -
    mol_list
    + + +
    mol_list

    list of mol_parameter objects. Alternatively, a character vector matching molecules may also be provided. Use the get_mol_names function for a full list of molecules.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    -
    xlim
    +
    xlim

    ppm range limiting signals to be simulated.

    -
    verbose
    +
    verbose

    output simulation progress and timings.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -136,15 +136,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html index 62ed7389..2ede607d 100644 --- a/docs/reference/sim_basis_1h_brain.html +++ b/docs/reference/sim_basis_1h_brain.html @@ -1,12 +1,10 @@ -Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant)Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.

    +

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

    Source: R/qm_simulation.R
    @@ -94,33 +91,33 @@

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRES

    Arguments

    -
    pul_seq
    + + +
    pul_seq

    pulse sequence function to use.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras.

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    lcm_compat
    +
    lcm_compat

    exclude lipid and MM signals for use with default LCModel options.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -135,15 +132,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_basis_1h_brain_press.html b/docs/reference/sim_basis_1h_brain_press.html index adc077c1..de660c8f 100644 --- a/docs/reference/sim_basis_1h_brain_press.html +++ b/docs/reference/sim_basis_1h_brain_press.html @@ -1,12 +1,10 @@ -Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant)Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed. — sim_basis_1h_brain_press • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS -sequence. Note, ideal pulses are assumed.

    +

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

    Source: R/qm_simulation.R
    @@ -94,33 +91,33 @@

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRES

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    lcm_compat
    +
    lcm_compat

    exclude lipid and MM signals for use with default LCModel options.

    -
    TE1
    +
    TE1

    TE1 of PRESS sequence (TE = TE1 + TE2).

    -
    TE2
    +
    TE2

    TE2 of PRESS sequence.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -135,15 +132,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_basis_mm_lip_lcm.html b/docs/reference/sim_basis_mm_lip_lcm.html index df2fd120..82343152 100644 --- a/docs/reference/sim_basis_mm_lip_lcm.html +++ b/docs/reference/sim_basis_mm_lip_lcm.html @@ -1,12 +1,10 @@ -Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS -analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant)Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis. — sim_basis_mm_lip_lcm • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS -analysis.

    +

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.

    Source: R/qm_simulation.R
    @@ -88,16 +85,16 @@

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -112,15 +109,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_basis_tqn.html b/docs/reference/sim_basis_tqn.html index cd16d362..cbc7f176 100644 --- a/docs/reference/sim_basis_tqn.html +++ b/docs/reference/sim_basis_tqn.html @@ -1,9 +1,9 @@ -Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant)Simulate a basis file using TARQUIN. — sim_basis_tqn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -89,32 +89,34 @@

    Simulate a basis file using TARQUIN.

    Arguments

    -
    fs
    + + +
    fs

    sampling frequency

    -
    ft
    +
    ft

    transmitter frequency

    -
    N
    +
    N

    number of data points

    -
    ref
    +
    ref

    chemical shift reference

    -
    opts
    +
    opts

    list of options to pass to TARQUIN.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 write_basis_tqn('test.basis',mrs_data,c("--echo","0.04"))
-}
+} # }
    @@ -129,15 +131,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html index 2044cf1a..3b76a138 100644 --- a/docs/reference/sim_brain_1h.html +++ b/docs/reference/sim_brain_1h.html @@ -1,9 +1,9 @@ -Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant)Simulate MRS data with a similar appearance to normal brain (by default). — sim_brain_1h • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,57 +94,57 @@

    Simulate MRS data with a similar appearance to normal brain (by default).

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras.

    -
    type
    +
    type

    type of spectrum, only "normal" is implemented currently.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    full_output
    +
    full_output

    when FALSE (default) only output the simulated MRS data. When TRUE output a list containing the MRS data, basis set object and corresponding amplitudes.

    -
    amps
    +
    amps

    a vector of basis amplitudes may be specified to modify the output spectrum.

    -
    basis_lb
    +
    basis_lb

    apply additional Gaussian line-broadening to the basis (Hz).

    -
    zero_lip_mm
    +
    zero_lip_mm

    zero the amplitudes of any lipid or macromolecular components based on their name starting with "MM" or "Lip".

    -
    remove_lip_mm
    +
    remove_lip_mm

    remove any lipid or macromolecular basis components based on their name starting with "MM" or "Lip".

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    see full_output option.

    +

    see full_output option.

    @@ -159,15 +159,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html index 23bcef50..0c4ca366 100644 --- a/docs/reference/sim_mol.html +++ b/docs/reference/sim_mol.html @@ -1,9 +1,9 @@ -Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant)Simulate a mol_parameter object. — sim_mol • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -92,43 +92,43 @@

    Simulate a mol_parameter object.

    Arguments

    -
    mol
    + + +
    mol

    mol_parameter object.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    xlim
    +
    xlim

    ppm range limiting signals to be simulated.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -143,15 +143,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html index 23875f79..16a35773 100644 --- a/docs/reference/sim_noise.html +++ b/docs/reference/sim_noise.html @@ -1,9 +1,9 @@ -Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant)Simulate an mrs_data object containing simulated Gaussian noise. — sim_noise • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,6 +84,7 @@

    Simulate an mrs_data object containing simulated Gaussian noise.

    ft = def_ft(), N = def_N(), ref = def_ref(), + nuc = def_nuc(), dyns = 1, fd = TRUE )
    @@ -91,39 +92,43 @@

    Simulate an mrs_data object containing simulated Gaussian noise.

    Arguments

    -
    sd
    + + +
    sd

    standard deviation of the noise.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    dyns
    +
    nuc
    +

    resonant nucleus.

    + + +
    dyns

    number of dynamic scans to generate.

    -
    fd
    +
    fd

    return data in the frequency-domain (TRUE) or time-domain (FALSE)

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -138,15 +143,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html index 19e9a8a4..a84f6321 100644 --- a/docs/reference/sim_resonances.html +++ b/docs/reference/sim_resonances.html @@ -1,9 +1,9 @@ -Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant)Simulate a MRS data object containing a set of simulated resonances. — sim_resonances • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -94,54 +94,54 @@

    Simulate a MRS data object containing a set of simulated resonances.

    Arguments

    -
    freq
    + + +
    freq

    resonance frequency.

    -
    amp
    +
    amp

    resonance amplitude.

    -
    lw
    +
    lw

    line width in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    -
    phase
    +
    phase

    phase in degrees.

    -
    freq_ppm
    +
    freq_ppm

    frequencies are given in ppm units if set to TRUE, otherwise Hz are assumed.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters. See def_acq_paras

    -
    fp_scale
    +
    fp_scale

    multiply the first data point by 0.5.

    -
    back_extrap_pts
    +
    back_extrap_pts

    number of data points to back extrapolate.

    -
    sum_resonances
    +
    sum_resonances

    sum all resonances (default is TRUE), otherwise return a dynamic mrs_data object.

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    @@ -161,15 +161,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html index 5535c5ef..91bd8b33 100644 --- a/docs/reference/sim_th_excit_profile.html +++ b/docs/reference/sim_th_excit_profile.html @@ -1,12 +1,10 @@ -Simulate an ideal pulse excitation profile by smoothing a top-hat function -with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant)Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian. — sim_th_excit_profile • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate an ideal pulse excitation profile by smoothing a top-hat function -with a Gaussian.

    +

    Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.

    Source: R/utils.R
    @@ -88,23 +85,23 @@

    Simulate an ideal pulse excitation profile by smoothing a top-hat function

    Arguments

    -
    bw
    + + +
    bw

    top-hat bandwidth (Hz).

    -
    sigma
    +
    sigma

    Gaussian width smoothing parameter (Hz).

    -
    fa
    +
    fa

    intended flip angle of the pulse.

    Value

    - - -

    data frame containing the frequency scale, excitation profile and +

    data frame containing the frequency scale, excitation profile and corresponding flip-angles.

    @@ -120,15 +117,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sim_zero.html b/docs/reference/sim_zero.html index ffb85e0f..46b650d0 100644 --- a/docs/reference/sim_zero.html +++ b/docs/reference/sim_zero.html @@ -1,9 +1,9 @@ -Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant)Simulate an mrs_data object containing complex zero valued samples. — sim_zero • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,36 +78,47 @@

    Simulate an mrs_data object containing complex zero valued samples.

    - 
    sim_zero(fs = def_fs(), ft = def_ft(), N = def_N(), ref = def_ref(), dyns = 1)
    + 
    sim_zero(
+  fs = def_fs(),
+  ft = def_ft(),
+  N = def_N(),
+  ref = def_ref(),
+  nuc = def_nuc(),
+  dyns = 1
+)

    Arguments

    -
    fs
    + + +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    dyns
    +
    nuc
    +

    resonant nucleus.

    + + +
    dyns

    number of dynamic scans to generate.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -122,15 +133,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html index 4cc8da50..0c9bb9f3 100644 --- a/docs/reference/smooth_dyns.html +++ b/docs/reference/smooth_dyns.html @@ -1,9 +1,9 @@ -Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant)Smooth data across the dynamic dimension with a Gaussian kernel. — smooth_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Smooth data across the dynamic dimension with a Gaussian kernel.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be smoothed.

    -
    sigma
    +
    sigma

    standard deviation of the underlying Gaussian kernel in seconds.

    Value

    - - -

    smoothed mrs_data object.

    +

    smoothed mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html index 6a676ea2..83349782 100644 --- a/docs/reference/sort_basis.html +++ b/docs/reference/sort_basis.html @@ -1,9 +1,9 @@ -Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant)Sort the basis-set elements alphabetically. — sort_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Sort the basis-set elements alphabetically.

    Arguments

    -
    basis
    + + +
    basis

    input basis.

    Value

    - - -

    sorted basis.

    +

    sorted basis.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html index b3dd8e21..2dce089b 100644 --- a/docs/reference/spant-package.html +++ b/docs/reference/spant-package.html @@ -1,10 +1,10 @@ -spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant)spant: spectroscopy analysis tools. — spant-package • Spectroscopy Analysis Tools (spant) - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -117,15 +117,15 @@

    Author

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spant.html b/docs/reference/spant.html new file mode 100644 index 00000000..8b056250 --- /dev/null +++ b/docs/reference/spant.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/spant_abfit_benchmark.html b/docs/reference/spant_abfit_benchmark.html index 4d54df4c..f37e8b64 100644 --- a/docs/reference/spant_abfit_benchmark.html +++ b/docs/reference/spant_abfit_benchmark.html @@ -1,12 +1,10 @@ -Simulate and fit some spectra with ABfit for benchmarking purposes. Basic -timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant)Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed. — spant_abfit_benchmark • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic -timing and performance metrics will be printed.

    +

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.

    Source: R/benchmark.R
    @@ -88,15 +85,17 @@

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic

    Arguments

    -
    noise_reps
    + + +
    noise_reps

    number of spectra to fit with differing noise samples.

    -
    return_res
    +
    return_res

    return a list of fit_result objects.

    -
    opts
    +
    opts

    ABfit options structure.

    @@ -113,15 +112,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spant_mpress_drift.html b/docs/reference/spant_mpress_drift.html index 0555ef15..11ba2b66 100644 --- a/docs/reference/spant_mpress_drift.html +++ b/docs/reference/spant_mpress_drift.html @@ -1,9 +1,9 @@ -Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant)Example MEGA-PRESS data with significant B0 drift. — spant_mpress_drift • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,7 +83,7 @@

    Example MEGA-PRESS data with significant B0 drift.

    Format

    -

    An object of class mrs_data of length 13.

    +

    An object of class mrs_data of dimension 1 x 1 x 1 x 1 x 40 x 1 x 1024.

    @@ -98,15 +98,15 @@

    Format

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html new file mode 100644 index 00000000..f11f93a2 --- /dev/null +++ b/docs/reference/spant_sim_fmrs_dataset.html @@ -0,0 +1,119 @@ + +Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure. — spant_sim_fmrs_dataset • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.

    + Source: R/fmrs.R + +
    + +
    +

    Simulate an example fMRS dataset for a block design fMRS experiment and +export a BIDS structure.

    +
    + +
    + 
    spant_sim_fmrs_dataset(output_dir = NULL)
    +
    + +
    +

    Arguments

    + + +
    output_dir
    +

    output directory for the BIDS data. Defaults to : +"HOME/sim_fmrs_dataset/data".

    + +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html index 32daa8bf..e4a21000 100644 --- a/docs/reference/spant_simulation_benchmark.html +++ b/docs/reference/spant_simulation_benchmark.html @@ -1,12 +1,10 @@ -Simulate a typical metabolite basis set for benchmarking. Timing metrics will -be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant)Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion. — spant_simulation_benchmark • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Simulate a typical metabolite basis set for benchmarking. Timing metrics will -be printed on completion.

    +

    Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.

    Source: R/benchmark.R
    @@ -88,11 +85,13 @@

    Simulate a typical metabolite basis set for benchmarking. Timing metrics wil

    Arguments

    -
    sim_reps
    + + +
    sim_reps

    number of times to simulate the basis set.

    -
    N
    +
    N

    number of FID data points to simulate.

    @@ -109,15 +108,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spec_decomp.html b/docs/reference/spec_decomp.html index ffe7b3e1..6aa0c52f 100644 --- a/docs/reference/spec_decomp.html +++ b/docs/reference/spec_decomp.html @@ -1,11 +1,11 @@ -Decompose an mrs_data object into white and gray matter spectra. — spec_decomp • Spectroscopy Analysis Tools (spant) - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -87,27 +87,27 @@

    Decompose an mrs_data object into white and gray matter spectra.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be decomposed into white and gray matter spectra.

    -
    wm
    +
    wm

    vector of white matter contributions to each voxel.

    -
    gm
    +
    gm

    vector of gray matter contributions to each voxel.

    -
    norm_fractions
    +
    norm_fractions

    option to normalise the wm, gm vectors for each voxel.

    Value

    - - -

    a list of two mrs_data objects corresponding to the two tissue types.

    +

    a list of two mrs_data objects corresponding to the two tissue types.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spec_op.html b/docs/reference/spec_op.html index d0f264ef..d633d488 100644 --- a/docs/reference/spec_op.html +++ b/docs/reference/spec_op.html @@ -1,9 +1,9 @@ -Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant)Perform a mathematical operation on a spectral region. — spec_op • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -89,32 +89,32 @@

    Perform a mathematical operation on a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    -
    operator
    -

    can be "sum" (default), "mean", "l2", "max", "min" or -"max-min".

    +
    operator
    +

    can be "sum" (default), "mean", "l2", "max", "max_cplx, +"min" or "max-min".

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    Value

    - - -

    an array of integral values.

    +

    an array of integral values.

    @@ -129,15 +129,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html index 853423a4..b1a0a203 100644 --- a/docs/reference/spin_sys.html +++ b/docs/reference/spin_sys.html @@ -1,9 +1,9 @@ -Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant)Create a spin system object for pulse sequence simulation. — spin_sys • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,31 +83,31 @@

    Create a spin system object for pulse sequence simulation.

    Arguments

    -
    spin_params
    + + +
    spin_params

    an object describing the spin system properties.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    precomp_jc_H
    +
    precomp_jc_H

    use a precomputed J-coupling H matrix to save time.

    -
    precomp_Iz
    +
    precomp_Iz

    use precomputed Iz matrices to save time.

    Value

    - - -

    spin system object.

    +

    spin system object.

    @@ -122,15 +122,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html index 23a1bad9..6f129eac 100644 --- a/docs/reference/spm_pve2categorical.html +++ b/docs/reference/spm_pve2categorical.html @@ -1,12 +1,10 @@ -Convert SPM style segmentation files to a single categorical image where -the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant)Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM. — spm_pve2categorical • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Convert SPM style segmentation files to a single categorical image where -the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.

    +

    Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.

    Source: R/image_reg.R
    @@ -88,15 +85,15 @@

    Convert SPM style segmentation files to a single categorical image where

    Arguments

    -
    fname
    + + +
    fname

    any of the segmentation files (eg c1_MY_T1.nii).

    Value

    - - -

    nifti object.

    +

    nifti object.

    @@ -111,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/ssp.html b/docs/reference/ssp.html index 6e7d3cd5..9b8eb04a 100644 --- a/docs/reference/ssp.html +++ b/docs/reference/ssp.html @@ -1,12 +1,12 @@ -Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant)Signal space projection method for lipid suppression. — ssp • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -89,23 +89,23 @@

    Signal space projection method for lipid suppression.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    comps
    +
    comps

    the number of spatial components to use.

    -
    xlim
    +
    xlim

    spectral range (in ppm) covering the lipid signals.

    Value

    - - -

    lipid suppressed mrs_data object.

    +

    lipid suppressed mrs_data object.

    @@ -120,15 +120,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/stackplot.fit_result.html b/docs/reference/stackplot.fit_result.html index 4112e3fd..cb13e97e 100644 --- a/docs/reference/stackplot.fit_result.html +++ b/docs/reference/stackplot.fit_result.html @@ -1,12 +1,10 @@ -Plot the fitting results of an object of class fit_result with -individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant)Plot the fitting results of an object of class fit_result with individual basis set components shown. — stackplot.fit_result • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Plot the fitting results of an object of class fit_result with -individual basis set components shown.

    +

    Plot the fitting results of an object of class fit_result with individual basis set components shown.

    Source: R/fit_display.R
    @@ -83,7 +80,7 @@

    Plot the fitting results of an object of class fit_result with

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 stackplot(
   x,
   xlim = NULL,
@@ -113,103 +110,105 @@ 
    Plot the fitting results of an object of class fit_result with
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    fit_result object.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    y_offset
    
+
    y_offset
    
 
    separate basis signals in the y-axis direction by this value.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    n
    
+
    n
    
 
    single index element to plot (overrides other indices when given).
    
 
 
-
    sub_bl
    
+
    sub_bl
    
 
    subtract the baseline from the data and fit (logical).
    
 
 
-
    labels
    
+
    labels
    
 
    print signal labels at the right side of the plot.
    
 
 
-
    label_names
    
+
    label_names
    
 
    provide a character vector of signal names to replace the
 defaults determined from the basis set.
    
 
 
-
    sig_col
    
+
    sig_col
    
 
    colour of individual signal components.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    omit_signals
    
+
    omit_signals
    
 
    a character vector of basis signal names to be removed
 from the plot.
    
 
 
-
    combine_lipmm
    
+
    combine_lipmm
    
 
    combine all basis signals with names starting with "Lip"
 or "MM".
    
 
 
-
    combine_metab
    
+
    combine_metab
    
 
    combine all basis signals with names not starting with
 "Lip" or "MM".
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    invert_fit
    
+
    invert_fit
    
 
    show the fit result "upside-down"/
    
 
 
-
    ...
    
+
    ...
    
 
    further arguments to plot method.
    
 
 
    
@@ -226,15 +225,15 @@ 
    Arguments
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/stackplot.html b/docs/reference/stackplot.html index be569e29..b62bdcf4 100644 --- a/docs/reference/stackplot.html +++ b/docs/reference/stackplot.html @@ -1,9 +1,9 @@ -Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant)Produce a plot with multiple traces. — stackplot • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Produce a plot with multiple traces.

    Arguments

    -
    x
    + + +
    x

    object for plotting.

    -
    ...
    +
    ...

    arguments to be passed to methods.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html index 17ff5648..014a429e 100644 --- a/docs/reference/stackplot.mrs_data.html +++ b/docs/reference/stackplot.mrs_data.html @@ -1,9 +1,9 @@ -Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant)Stackplot plotting method for objects of class mrs_data. — stackplot.mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -78,7 +78,7 @@

    Stackplot plotting method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 stackplot(
   x,
   xlim = NULL,
@@ -114,131 +114,133 @@ 
    Stackplot plotting method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    x_units
    
+
    x_units
    
 
    the units to use for the x-axis, can be one of: "ppm", "hz",
 "points" or "seconds".
    
 
 
-
    fd
    
+
    fd
    
 
    display data in the frequency-domain (default), or time-domain
 (logical).
    
 
 
-
    col
    
+
    col
    
 
    set the colour of the line, eg col = rgb(1, 0, 0, 0.5).
    
 
 
-
    alpha
    
+
    alpha
    
 
    set the line transparency, eg alpha = 0.5 is 50% transparency.
 Overrides any transparency levels set by col.
    
 
 
-
    x_offset
    
+
    x_offset
    
 
    separate plots in the x-axis direction by this value.
 Default value is 0.
    
 
 
-
    y_offset
    
+
    y_offset
    
 
    separate plots in the y-axis direction by this value.
    
 
 
-
    plot_dim
    
+
    plot_dim
    
 
    the dimension to display on the y-axis, can be one of: "dyn",
 "x", "y", "z", "coil" or NULL. If NULL (the default) all spectra will be
 collapsed into the dynamic dimension and displayed.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    labels
    
+
    labels
    
 
    add labels to each data item.
    
 
 
-
    lab_cex
    
+
    lab_cex
    
 
    label size.
    
 
 
-
    bl_lty
    
+
    bl_lty
    
 
    linetype for the y = 0 baseline trace. A default value NULL
 results in no baseline being plotted.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    lwd
    
+
    lwd
    
 
    plot linewidth.
    
 
 
-
    vline
    
+
    vline
    
 
    x-value to draw a vertical line.
    
 
 
-
    vline_lty
    
+
    vline_lty
    
 
    linetype for the vertical line.
    
 
 
-
    vline_col
    
+
    vline_col
    
 
    colour for the vertical line.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the matplot method.
    
 
 
    
@@ -255,15 +257,15 @@ 
    Arguments
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html index dbd7f831..b4408de6 100644 --- a/docs/reference/sub_first_dyn.html +++ b/docs/reference/sub_first_dyn.html @@ -1,9 +1,9 @@ -Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant)Subtract the first dynamic spectrum from a dynamic series. — sub_first_dyn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Subtract the first dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the first spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html index 6e3bb2df..0b686470 100644 --- a/docs/reference/sub_mean_dyns.html +++ b/docs/reference/sub_mean_dyns.html @@ -1,9 +1,9 @@ -Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant)Subtract the mean dynamic spectrum from a dynamic series. — sub_mean_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Subtract the mean dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the mean spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html index 134c495d..3205624a 100644 --- a/docs/reference/sub_median_dyns.html +++ b/docs/reference/sub_median_dyns.html @@ -1,9 +1,9 @@ -Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant)Subtract the median dynamic spectrum from a dynamic series. — sub_median_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Subtract the median dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the medium spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html index 7bf559f2..e25c34e8 100644 --- a/docs/reference/sum_coils.html +++ b/docs/reference/sum_coils.html @@ -1,9 +1,9 @@ -Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant)Calculate the sum across receiver coil elements. — sum_coils • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the sum across receiver coil elements.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data split across receiver coil elements.

    Value

    - - -

    sum across coil elements.

    +

    sum across coil elements.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html index a0be19d3..747eed2b 100644 --- a/docs/reference/sum_dyns.html +++ b/docs/reference/sum_dyns.html @@ -1,9 +1,9 @@ -Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant)Calculate the sum of data dynamics. — sum_dyns • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Calculate the sum of data dynamics.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    sum of data dynamics.

    +

    sum of data dynamics.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html index a22f215b..51d8493c 100644 --- a/docs/reference/sum_mrs.html +++ b/docs/reference/sum_mrs.html @@ -1,9 +1,9 @@ -Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant)Sum two mrs_data objects. — sum_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Sum two mrs_data objects.

    Arguments

    -
    a
    + + +
    a

    first mrs_data object to be summed.

    -
    b
    +
    b

    second mrs_data object to be summed.

    -
    force
    +
    force

    set to TRUE to force mrs_data objects to be summed, even if they are in different time/frequency domains.

    Value

    - - -

    a + b

    +

    a + b

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html index f4e09aea..17d5e17a 100644 --- a/docs/reference/sum_mrs_list.html +++ b/docs/reference/sum_mrs_list.html @@ -1,9 +1,9 @@ -Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant)Return the sum of a list of mrs_data objects. — sum_mrs_list • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the sum of a list of mrs_data objects.

    Arguments

    -
    mrs_list
    + + +
    mrs_list

    list of mrs_data objects.

    Value

    - - -

    sum mrs_data object.

    +

    sum mrs_data object.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html index 8ce514db..d6a57625 100644 --- a/docs/reference/svs_1h_brain_analysis.html +++ b/docs/reference/svs_1h_brain_analysis.html @@ -1,9 +1,9 @@ -Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -102,89 +102,89 @@

    Standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab
    + + +
    metab

    filepath or mrs_data object containing MRS metabolite data.

    -
    basis
    +
    basis

    basis set object to use for analysis.

    -
    w_ref
    +
    w_ref

    filepath or mrs_data object containing MRS water reference data.

    -
    mri_seg
    +
    mri_seg

    filepath or nifti object containing segmented MRI data.

    -
    mri
    +
    mri

    filepath or nifti object containing anatomical MRI data.

    -
    output_dir
    +
    output_dir

    directory path to output fitting results.

    -
    extra
    +
    extra

    data.frame with one row containing additional information to be attached to the fit results table.

    -
    decimate
    +
    decimate

    option to decimate the input data by a factor of two. The default value of NULL does not perform decimation unless the spectral width is greater than 20 PPM.

    -
    rats_corr
    +
    rats_corr

    option to perform rats correction, defaults to TRUE.

    -
    ecc
    +
    ecc

    option to perform water reference based eddy current correction, defaults to FALSE.

    -
    comb_dyns
    +
    comb_dyns

    option to combine dynamic scans, defaults to TRUE.

    -
    hsvd_filt
    +
    hsvd_filt

    option to apply hsvd water removal, defaults to FALSE.

    -
    scale_amps
    +
    scale_amps

    option to scale metabolite amplitude estimates, defaults to TRUE.

    -
    te
    +
    te

    metabolite mrs data echo time in seconds.

    -
    tr
    +
    tr

    metabolite mrs data repetition time in seconds.

    -
    preproc_only
    +
    preproc_only

    only perform the preprocessing steps and omit fitting. The preprocessed metabolite data will be returned in this case.

    -
    method
    +
    method

    analysis method to use, see fit_mrs help.

    -
    opts
    +
    opts

    options to pass to the analysis method.

    Value

    - - -

    a fit_result or mrs_data object depending on the preproc_only option.

    +

    a fit_result or mrs_data object depending on the preproc_only option.

    @@ -199,15 +199,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html index d70a14d3..b5540ca2 100644 --- a/docs/reference/svs_1h_brain_analysis_dev.html +++ b/docs/reference/svs_1h_brain_analysis_dev.html @@ -1,9 +1,9 @@ -Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant)Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis_dev • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -99,73 +99,75 @@

    Standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab
    + + +
    metab

    filepath or mrs_data object containing MRS metabolite data.

    -
    w_ref
    +
    w_ref

    filepath or mrs_data object containing MRS water reference data.

    -
    output_dir
    +
    output_dir

    directory path to output fitting results.

    -
    basis
    +
    basis

    precompiled basis set object to use for analysis.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. Defaults to 100% white matter. A voxel containing 100% gray matter tissue would use : p_vols = c(WM = 0, GM = 100, CSF = 0).

    -
    append_basis
    +
    append_basis

    names of extra signals to add to the default basis. Eg append_basis = c("peth", "cit"). Cannot be used with precompiled basis sets.

    -
    remove_basis
    +
    remove_basis

    names of signals to remove from the basis. Cannot be used with precompiled basis sets.

    -
    dfp_corr
    +
    dfp_corr

    perform dynamic frequency and phase correction using the RATS method.

    -
    omit_bad_dynamics
    +
    omit_bad_dynamics

    detect and remove bad dynamics.

    -
    te
    +
    te

    metabolite mrs data echo time in seconds. If not supplied this will be guessed from the metab data file.

    -
    tr
    +
    tr

    metabolite mrs data repetition time in seconds. If not supplied this will be guessed from the metab data file.

    -
    output_ratio
    +
    output_ratio

    optional string to specify a metabolite ratio to output. Defaults to "tCr" and multiple metabolites may be specified for multiple outputs. Set as NULL to omit.

    -
    ecc
    +
    ecc

    option to perform water reference based eddy current correction, defaults to FALSE.

    -
    abfit_opts
    +
    abfit_opts

    options to pass to ABfit.

    -
    verbose
    +
    verbose

    output potentially useful information.

    @@ -176,9 +178,9 @@

    Examples

    package = "spant") w_ref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant") -if (FALSE) { +if (FALSE) { # \dontrun{ fit_result <- svs_1h_brain_analysis(metab, w_ref, "fit_res_dir") -} +} # }
    @@ -193,15 +195,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html index 5631e8cc..7145c1e5 100644 --- a/docs/reference/svs_1h_brain_batch_analysis.html +++ b/docs/reference/svs_1h_brain_batch_analysis.html @@ -1,9 +1,9 @@ -Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant)Batch interface to the standard SVS 1H brain analysis pipeline. — svs_1h_brain_batch_analysis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,45 +91,45 @@

    Batch interface to the standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab_list
    + + +
    metab_list

    list of file paths or mrs_data objects containing MRS metabolite data.

    -
    w_ref_list
    +
    w_ref_list

    list of file paths or mrs_data objects containing MRS water reference data.

    -
    mri_seg_list
    +
    mri_seg_list

    list of file paths or nifti objects containing segmented MRI data.

    -
    mri_list
    +
    mri_list

    list of file paths or nifti objects containing anatomical MRI data.

    -
    output_dir_list
    +
    output_dir_list

    list of directory paths to output fitting results.

    -
    extra
    +
    extra

    a data frame with the same number of rows as metab_list, containing additional information to be attached to the fit results table.

    -
    ...
    +
    ...

    additional options to be passed to the svs_1h_brain_analysis function.

    Value

    - - -

    a list of fit_result objects.

    +

    a list of fit_result objects.

    @@ -144,15 +144,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html new file mode 100644 index 00000000..daa4cbac --- /dev/null +++ b/docs/reference/t_test_spec.html @@ -0,0 +1,124 @@ + +Perform a t-test on spectral data points. — t_test_spec • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Perform a t-test on spectral data points.

    + Source: R/fmrs.R + +
    + +
    +

    Perform a t-test on spectral data points.

    +
    + +
    + 
    t_test_spec(mrs_data, group)
    +
    + +
    +

    Arguments

    + + +
    mrs_data
    +

    an mrs_data object with spectra in the dynamic dimension.

    + + +
    group
    +

    vector describing the group membership of each dynamic spectrum.

    + +
    +
    +

    Value

    +

    a list of statistical results.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html index 6748a6a8..0cebf786 100644 --- a/docs/reference/td2fd.html +++ b/docs/reference/td2fd.html @@ -1,9 +1,9 @@ -Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant)Transform time-domain data to the frequency-domain. — td2fd • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Transform time-domain data to the frequency-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data in time-domain representation.

    Value

    - - -

    MRS data in frequency-domain representation.

    +

    MRS data in frequency-domain representation.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html index a9f340c3..dee2ff71 100644 --- a/docs/reference/td_conv_filt.html +++ b/docs/reference/td_conv_filt.html @@ -1,12 +1,12 @@ -Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant)Time-domain convolution based filter. — td_conv_filt • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -89,15 +89,17 @@

    Time-domain convolution based filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    K
    +
    K

    window width in data points.

    -
    ext
    +
    ext

    point separation for linear extrapolation.

    @@ -114,15 +116,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/tdsr.html b/docs/reference/tdsr.html index 25eebe37..71410e08 100644 --- a/docs/reference/tdsr.html +++ b/docs/reference/tdsr.html @@ -1,9 +1,9 @@ -Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant)Time-domain spectral registration. — tdsr • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,29 +83,29 @@

    Time-domain spectral registration.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ref
    +
    ref

    optional MRS data to use as a reference, the mean of all dynamics is used if this argument is not supplied.

    -
    xlim
    +
    xlim

    optional frequency range to perform optimisation, set to NULL to use the full range.

    -
    max_t
    +
    max_t

    truncate the FID when longer than max_t to reduce time taken.

    Value

    - - -

    a list containing the corrected data; phase and shift values in units +

    a list containing the corrected data; phase and shift values in units of degrees and Hz respectively.

    @@ -121,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/te.html b/docs/reference/te.html index 010361b1..2ed213a0 100644 --- a/docs/reference/te.html +++ b/docs/reference/te.html @@ -1,9 +1,9 @@ -Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant)Return the echo time of an MRS dataset. — te • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the echo time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    echo time in seconds.

    +

    echo time in seconds.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/tr.html b/docs/reference/tr.html index 0c0bd63b..77d4e175 100644 --- a/docs/reference/tr.html +++ b/docs/reference/tr.html @@ -1,9 +1,9 @@ -Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant)Return the repetition time of an MRS dataset. — tr • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,15 @@

    Return the repetition time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    repetition time in seconds.

    +

    repetition time in seconds.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html index c2270a16..720480ab 100644 --- a/docs/reference/varpro_3_para_opts.html +++ b/docs/reference/varpro_3_para_opts.html @@ -1,9 +1,9 @@ -Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant)Return a list of options for VARPRO based fitting with 3 free parameters. — varpro_3_para_opts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -91,42 +91,42 @@

    Return a list of options for VARPRO based fitting with 3 free parameters.

    Arguments

    -
    nstart
    + + +
    nstart

    position in the time-domain to start fitting, units of data points.

    -
    init_damping
    +
    init_damping

    starting value for the global Gaussian line-broadening term - measured in Hz.

    -
    maxiters
    +
    maxiters

    maximum number of levmar iterations to perform.

    -
    max_shift
    +
    max_shift

    maximum global shift allowed, measured in Hz.

    -
    max_damping
    +
    max_damping

    maximum damping allowed, FWHM measured in Hz.

    -
    anal_jac
    +
    anal_jac

    option to use the analytic or numerical Jacobian (logical).

    -
    bl_smth_pts
    +
    bl_smth_pts

    number of data points to use in the baseline smoothing calculation.

    Value

    - - -

    list of options.

    +

    list of options.

    @@ -141,15 +141,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html index 32c86d22..e048448a 100644 --- a/docs/reference/varpro_basic_opts.html +++ b/docs/reference/varpro_basic_opts.html @@ -1,9 +1,9 @@ -Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant)Return a list of options for a basic VARPRO analysis. — varpro_basic_opts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,27 +83,27 @@

    Return a list of options for a basic VARPRO analysis.

    Arguments

    -
    method
    + + +
    method

    one of "td", "fd", "fd_re".

    -
    nnls
    +
    nnls

    restrict basis amplitudes to non-negative values.

    -
    ppm_left
    +
    ppm_left

    downfield frequency limit for the fitting range (ppm).

    -
    ppm_right
    +
    ppm_right

    upfield frequency limit for the fitting range (ppm).

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -118,15 +118,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html index 2aabf11d..2778671a 100644 --- a/docs/reference/varpro_opts.html +++ b/docs/reference/varpro_opts.html @@ -1,9 +1,9 @@ -Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant)Return a list of options for VARPRO based fitting. — varpro_opts • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -92,48 +92,48 @@

    Return a list of options for VARPRO based fitting.

    Arguments

    -
    nstart
    + + +
    nstart

    position in the time-domain to start fitting, units of data points.

    -
    init_g_damping
    +
    init_g_damping

    starting value for the global Gaussian line-broadening term - measured in Hz.

    -
    maxiters
    +
    maxiters

    maximum number of levmar iterations to perform.

    -
    max_shift
    +
    max_shift

    maximum shift allowed to each element in the basis set, measured in Hz.

    -
    max_g_damping
    +
    max_g_damping

    maximum permitted global Gaussian line-broadening.

    -
    max_ind_damping
    +
    max_ind_damping

    maximum permitted Lorentzian line-broadening for each element in the basis set, measured in Hz.

    -
    anal_jac
    +
    anal_jac

    option to use the analytic or numerical Jacobian (logical).

    -
    bl_smth_pts
    +
    bl_smth_pts

    number of data points to use in the baseline smoothing calculation.

    Value

    - - -

    list of options.

    +

    list of options.

    @@ -177,15 +177,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html index 0cccd73b..01ce4670 100644 --- a/docs/reference/vec2mrs_data.html +++ b/docs/reference/vec2mrs_data.html @@ -1,9 +1,9 @@ -Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant)Convert a vector into a mrs_data object. — vec2mrs_data • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -80,10 +80,11 @@

    Convert a vector into a mrs_data object.

    vec2mrs_data(
   vec,
-  fs = def_fs(),
-  ft = def_ft(),
-  ref = def_ref(),
-  nuc = def_nuc(),
+  mrs_data = NULL,
+  fs = NULL,
+  ft = NULL,
+  ref = NULL,
+  nuc = NULL,
   dyns = 1,
   fd = FALSE
 )
    @@ -91,39 +92,43 @@

    Convert a vector into a mrs_data object.

    Arguments

    -
    vec
    + + +
    vec

    the data vector.

    -
    fs
    +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    -
    dyns
    +
    dyns

    replicate the data across the dynamic dimension.

    -
    fd
    -

    flag to indicate if the matrix is in the frequency domain (logical).

    +
    fd
    +

    flag to indicate if the vector is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -138,15 +143,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/writeNifti.html b/docs/reference/writeNifti.html new file mode 100644 index 00000000..3d3d7357 --- /dev/null +++ b/docs/reference/writeNifti.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html index b6e27cbd..b32b08b5 100644 --- a/docs/reference/write_basis.html +++ b/docs/reference/write_basis.html @@ -1,9 +1,9 @@ -Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant)Write a basis object to an LCModel .basis formatted file. — write_basis • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,15 +83,17 @@

    Write a basis object to an LCModel .basis formatted file.

    Arguments

    -
    basis
    + + +
    basis

    basis object to be exported.

    -
    basis_file
    +
    basis_file

    path to basis file to be generated.

    -
    fwhmba
    +
    fwhmba

    parameter used by LCModel.

    @@ -108,15 +110,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html index 6aa51c1d..7630b0ef 100644 --- a/docs/reference/write_basis_tqn.html +++ b/docs/reference/write_basis_tqn.html @@ -1,9 +1,9 @@ -Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant)Generate a basis file using TARQUIN. — write_basis_tqn • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,26 @@

    Generate a basis file using TARQUIN.

    Arguments

    -
    basis_file
    + + +
    basis_file

    filename of the basis file to be generated.

    -
    metab_data
    +
    metab_data

    MRS data object to match the generated basis parameters.

    -
    opts
    +
    opts

    list of options to pass to TARQUIN.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 write_basis_tqn('test.basis',mrs_data,c("--echo","0.04"))
-}
+} # }
    @@ -115,15 +117,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html index fff25f15..8f13fa08 100644 --- a/docs/reference/write_mrs.html +++ b/docs/reference/write_mrs.html @@ -1,9 +1,9 @@ -Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant)Write MRS data object to file. — write_mrs • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,21 +83,23 @@

    Write MRS data object to file.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    object to be written to file, or list of mrs_data objects.

    -
    fname
    +
    fname

    one or more filenames to output.

    -
    format
    +
    format

    string describing the data format. Must be one of the following : "nifti", "dpt", "lcm_raw", "rds". If not specified, the format will be guessed from the filename extension.

    -
    force
    +
    force

    set to TRUE to overwrite any existing files.

    @@ -114,15 +116,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html index f4bf1921..552bf0a8 100644 --- a/docs/reference/write_mrs_nifti.html +++ b/docs/reference/write_mrs_nifti.html @@ -1,9 +1,9 @@ -Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant)Write MRS data object to file in NIFTI format. — write_mrs_nifti • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Write MRS data object to file in NIFTI format.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    object to be written to file.

    -
    fname
    +
    fname

    the filename of the output NIFTI MRS data.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html index 067ae086..ab071455 100644 --- a/docs/reference/write_pulse_ascii.html +++ b/docs/reference/write_pulse_ascii.html @@ -1,9 +1,9 @@ -Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant)Write an ASCII formatted pulse file. — write_pulse_ascii • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Write an ASCII formatted pulse file.

    Arguments

    -
    pulse
    + + +
    pulse

    pulse data object.

    -
    path
    +
    path

    file path for export.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html index c703745c..1364a3c5 100644 --- a/docs/reference/zero_fade_spec.html +++ b/docs/reference/zero_fade_spec.html @@ -1,12 +1,10 @@ -Fade a spectrum to zero by frequency domain multiplication with a tanh -function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant)Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID. — zero_fade_spec • Spectroscopy Analysis Tools (spant) - +
    @@ -31,7 +29,7 @@
    • - +
    -

    Fade a spectrum to zero by frequency domain multiplication with a tanh -function. Note this operation distorts data points at the end of the FID.

    +

    Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.

    Source: R/mrs_data_proc.R
    @@ -88,23 +85,23 @@

    Fade a spectrum to zero by frequency domain multiplication with a tanh

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be faded.

    -
    start_ppm
    +
    start_ppm

    start point of the fade in ppm units.

    -
    end_ppm
    +
    end_ppm

    end point of the fade in ppm units.

    Value

    - - -

    modified mrs_data object.

    +

    modified mrs_data object.

    @@ -119,15 +116,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/zero_higher_orders.html b/docs/reference/zero_higher_orders.html index f703876d..a35d60c0 100644 --- a/docs/reference/zero_higher_orders.html +++ b/docs/reference/zero_higher_orders.html @@ -1,9 +1,9 @@ -Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant)Zero all coherences including and above a given order. — zero_higher_orders • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,24 @@

    Zero all coherences including and above a given order.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    order
    +
    order

    states higher than or equal to this argument will be set to zero.

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -115,15 +115,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html index 8c1123c8..3384f7da 100644 --- a/docs/reference/zero_td_pts_end.html +++ b/docs/reference/zero_td_pts_end.html @@ -1,9 +1,9 @@ -Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant)Set mrs_data object data points at the end of the FID to zero. — zero_td_pts_end • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,19 @@

    Set mrs_data object data points at the end of the FID to zero.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of end points to set to zero.

    Value

    - - -

    modified mrs_data object.

    +

    modified mrs_data object.

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/zf.basis_set.html b/docs/reference/zf.basis_set.html new file mode 100644 index 00000000..2da37483 --- /dev/null +++ b/docs/reference/zf.basis_set.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/zf.html b/docs/reference/zf.html index 85e2013c..5adcbf65 100644 --- a/docs/reference/zf.html +++ b/docs/reference/zf.html @@ -1,9 +1,9 @@ -Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant)Zero-fill MRS data in the time domain. — zf • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -80,37 +80,37 @@

    Zero-fill MRS data in the time domain.

    zf(x, factor = 2, offset = 0)
 
-# S3 method for list
+# S3 method for class 'list'
 zf(x, factor = 2, offset = 0)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 zf(x, factor = 2, offset = 0)
 
-# S3 method for basis_set
+# S3 method for class 'basis_set'
 zf(x, factor = 2, offset = 0)

    Arguments

    -
    x
    + + +
    x

    input mrs_data or basis_set object.

    -
    factor
    +
    factor

    zero-filling factor, factor of 2 returns a dataset with twice the original data points.

    -
    offset
    +
    offset

    number of points from the end of the FID to insert the zero values.

    Value

    - - -

    zero-filled data.

    +

    zero-filled data.

    @@ -125,15 +125,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/zf.list.html b/docs/reference/zf.list.html new file mode 100644 index 00000000..2da37483 --- /dev/null +++ b/docs/reference/zf.list.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/zf.mrs_data.html b/docs/reference/zf.mrs_data.html new file mode 100644 index 00000000..2da37483 --- /dev/null +++ b/docs/reference/zf.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html index ebca3999..b50bfd71 100644 --- a/docs/reference/zf_xy.html +++ b/docs/reference/zf_xy.html @@ -1,9 +1,9 @@ -Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant)Zero-fill MRSI data in the k-space x-y direction. — zf_xy • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,11 +83,13 @@

    Zero-fill MRSI data in the k-space x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    -
    factor
    +
    factor

    zero-filling factor, a factor of 2 returns a dataset with twice the original points in the x-y directions. Factors smaller than one are permitted, such that a factor of 0.5 returns half the k-space points in @@ -96,9 +98,7 @@

    Arguments

    Value

    - - -

    zero-filled data.

    +

    zero-filled data.

    @@ -113,15 +113,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index e2139f71..47d5c994 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,1182 +1,411 @@ - - - - https://martin3141.github.io/spant/404.html - - - https://martin3141.github.io/spant/CONTRIBUTING.html - - - https://martin3141.github.io/spant/LICENSE-text.html - - - https://martin3141.github.io/spant/articles/abfit-baseline-opts.html - - - https://martin3141.github.io/spant/articles/index.html - - - https://martin3141.github.io/spant/articles/spant-basis-simulation.html - - - https://martin3141.github.io/spant/articles/spant-intro.html - - - https://martin3141.github.io/spant/articles/spant-metabolite-simulation.html - - - https://martin3141.github.io/spant/articles/spant-preprocessing.html - - - https://martin3141.github.io/spant/authors.html - - - https://martin3141.github.io/spant/index.html - - - https://martin3141.github.io/spant/news/index.html - - - https://martin3141.github.io/spant/reference/Arg.mrs_data.html - - - https://martin3141.github.io/spant/reference/Conj.mrs_data.html - - - https://martin3141.github.io/spant/reference/Im.mrs_data.html - - - https://martin3141.github.io/spant/reference/Imzap.html - - - https://martin3141.github.io/spant/reference/Mod.mrs_data.html - - - https://martin3141.github.io/spant/reference/N.html - - - https://martin3141.github.io/spant/reference/Ncoils.html - - - https://martin3141.github.io/spant/reference/Ndyns.html - - - https://martin3141.github.io/spant/reference/Npts.html - - - https://martin3141.github.io/spant/reference/Nspec.html - - - https://martin3141.github.io/spant/reference/Ntrans.html - - - https://martin3141.github.io/spant/reference/Nx.html - - - https://martin3141.github.io/spant/reference/Ny.html - - - https://martin3141.github.io/spant/reference/Nz.html - - - https://martin3141.github.io/spant/reference/Re.mrs_data.html - - - https://martin3141.github.io/spant/reference/abfit_opts.html - - - https://martin3141.github.io/spant/reference/abfit_opts_v1_9_0.html - - - https://martin3141.github.io/spant/reference/acquire.html - - - https://martin3141.github.io/spant/reference/add_noise.html - - - https://martin3141.github.io/spant/reference/add_noise_spec_snr.html - - - https://martin3141.github.io/spant/reference/align.html - - - https://martin3141.github.io/spant/reference/apodise_xy.html - - - https://martin3141.github.io/spant/reference/append_basis.html - - - https://martin3141.github.io/spant/reference/append_coils.html - - - https://martin3141.github.io/spant/reference/append_dyns.html - - - https://martin3141.github.io/spant/reference/append_regs.html - - - https://martin3141.github.io/spant/reference/apply_axes.html - - - https://martin3141.github.io/spant/reference/apply_mrs.html - - - https://martin3141.github.io/spant/reference/apply_pulse.html - - - https://martin3141.github.io/spant/reference/apply_pvc.html - - - https://martin3141.github.io/spant/reference/array2mrs_data.html - - - https://martin3141.github.io/spant/reference/auto_phase.html - - - https://martin3141.github.io/spant/reference/back_extrap.html - - - https://martin3141.github.io/spant/reference/back_extrap_ar.html - - - https://martin3141.github.io/spant/reference/basis2dyn_mrs_data.html - - - https://martin3141.github.io/spant/reference/basis2mrs_data.html - - - https://martin3141.github.io/spant/reference/bbase.html - - - https://martin3141.github.io/spant/reference/bc_als.html - - - https://martin3141.github.io/spant/reference/bc_constant.html - - - https://martin3141.github.io/spant/reference/bc_gauss.html - - - https://martin3141.github.io/spant/reference/bc_poly.html - - - https://martin3141.github.io/spant/reference/bc_spline.html - - - https://martin3141.github.io/spant/reference/beta2lw.html - - - https://martin3141.github.io/spant/reference/bin_spec.html - - - 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