website update

martin3141 · Nov 27, 2023 · 26009d5 · 26009d5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spant
 Type: Package
 Title: MR Spectroscopy Analysis Tools
-Version: 2.17.9000
-Date: 2023-10-23
+Version: 2.17.0
+Date: 2023-11-27
 Authors@R: c(
     person("Martin", "Wilson", email = "martin@pipegrep.co.uk",
            role = c("cre", "aut"), comment = c(ORCID = "0000-0002-2089-3956")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 # spant 2.17.0
 * Simulation duration output is now rounded to 2dp.
 * sim_basis now accepts a character vector of molecular names.
+* Added get_1h_brain_basis_names function.
 
 # spant 2.16.0
 * Added subset option to mean_dyns function.

diff --git a/R/qm_simulation.R b/R/qm_simulation.R
@@ -506,20 +506,20 @@ get_1h_braino_basis_names <- function() {
 #' Note, this is a basic set and it may be appropriate to also include Asc, 
 #' Gly and PEth for high quality MRS data.
 #' 
-#' @param extra optional character vector of additional molecular names. Eg
+#' @param add optional character vector of additional molecular names. Eg
 #' c("asc", "gly", "peth").
 #' @param remove optional character vector of molecular names to remove from the
 #' set. Eg c("m_cr_ch2").
 #' @param inc_lip_mm include Lipid and MM basis signals.
 #' @return a character vector of molecule names.
 #' @export
-get_1h_brain_basis_names <- function(extra = NULL, remove = NULL,
+get_1h_brain_basis_names <- function(add = NULL, remove = NULL,
                                      inc_lip_mm = TRUE) {
 
   names <- c("m_cr_ch2", "ala", "asp", "cr", "gaba", "glc", "gln", "gsh", "glu",
              "gpc", "ins", "lac", "naa", "naag", "pch", "pcr", "sins", "tau")
 
-  if (!is.null(extra)) names <- sort(c(names, extra))
+  if (!is.null(add)) names <- sort(c(names, add))
 
   if (inc_lip_mm) {
     names <- c(names, "lip09", "lip13a", "lip13b", "lip20", "mm09", "mm12",

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/abfit-baseline-opts.html b/docs/articles/abfit-baseline-opts.html
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
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
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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
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
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
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html
diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html
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
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
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
diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html
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
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
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   spant-intro: spant-intro.html
   spant-metabolite-simulation: spant-metabolite-simulation.html
   spant-preprocessing: spant-preprocessing.html
-last_built: 2023-10-23T14:18Z
+last_built: 2023-11-27T10:00Z
 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
diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html
diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html
diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html
diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html
diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html
diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html
diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html
diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html
diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html
diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html
diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html
diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html
diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html
diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html
diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html
diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html
diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html
diff --git a/docs/reference/align.html b/docs/reference/align.html
diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html
diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html