rerun after sean and em merges and fixes to pkgdown page yml

afsc-gap-products · Apr 4, 2024 · c99f9d5 · c99f9d5
1 parent c9b4c58
commit c99f9d5
Show file tree

Hide file tree

Showing 11 changed files with 37 additions and 97 deletions.
diff --git a/README.md b/README.md
@@ -79,14 +79,14 @@ This package was last produced using:
     #> [19] ggplot2_3.5.0   tidyr_1.3.1     dplyr_1.1.4     plyr_1.8.9      RODBC_1.3-23    roxygen2_7.3.1  devtools_2.4.5  usethis_2.2.3   here_1.0.1     
     #> 
     #> loaded via a namespace (and not attached):
-    #>   [1] RColorBrewer_1.1-3  sys_3.4.2           rstudioapi_0.16.0   dlstats_0.1.7       jsonlite_1.8.8      rmarkdown_2.26      fs_1.6.3            vctrs_0.6.5         memoise_2.0.1       askpass_1.2.0       gh_1.4.1            htmltools_0.5.8     curl_5.2.1          KernSmooth_2.23-22 
-    #>  [15] htmlwidgets_1.6.4   desc_1.4.3          httr2_1.0.1         zoo_1.8-12          cachem_1.0.8        mime_0.12           lifecycle_1.0.4     pkgconfig_2.0.3     Matrix_1.6-5        R6_2.5.1            fastmap_1.1.1       shiny_1.8.1.1       digest_0.6.35       numDeriv_2016.8-1.1
-    #>  [29] colorspace_2.1-0    rprojroot_2.0.4     pkgload_1.3.4       fansi_1.0.6         timechange_0.3.0    httr_1.4.7          compiler_4.3.1      proxy_0.4-27        intervals_0.15.4    remotes_2.5.0       withr_3.0.0         DBI_1.2.2           pkgbuild_1.4.4      MASS_7.3-60.0.1    
-    #>  [43] openssl_2.1.1       rappdirs_0.3.3      sessioninfo_1.2.2   tools_4.3.1         units_0.8-5         httpuv_1.6.15       glue_1.7.0          promises_1.2.1      grid_4.3.1          generics_0.1.3      gtable_0.3.4        tzdb_0.4.0          class_7.3-22        data.table_1.15.4  
-    #>  [57] hms_1.1.3           sp_2.1-3            xml2_1.3.6          utf8_1.2.4          pillar_1.9.0        stringr_1.5.1       yulab.utils_0.1.4   later_1.3.2         lattice_0.22-6      FNN_1.1.4           deldir_2.0-4        tidyselect_1.2.1    rvcheck_0.2.1       miniUI_0.1.1.1     
-    #>  [71] knitr_1.45          gitcreds_0.1.2      xfun_0.43           credentials_2.0.1   stringi_1.8.3       lazyeval_0.2.2      yaml_2.3.8          evaluate_0.23       codetools_0.2-19    tibble_3.2.1        BiocManager_1.30.22 cli_3.6.2           xtable_1.8-4        munsell_0.5.1      
-    #>  [85] spacetime_1.3-1     Rcpp_1.0.12         gert_2.0.1          bdsmatrix_1.3-7     parallel_4.3.1      ellipsis_0.3.2      profvis_0.3.8       urlchecker_1.0.1    viridisLite_0.4.2   mvtnorm_1.2-4       scales_1.3.0        xts_0.13.2          e1071_1.7-14        purrr_1.0.2        
-    #>  [99] crayon_1.5.2        rlang_1.1.3
+    #>   [1] RColorBrewer_1.1-3  sys_3.4.2           rstudioapi_0.16.0   dlstats_0.1.7       jsonlite_1.8.8      rmarkdown_2.26      fs_1.6.3            vctrs_0.6.5         memoise_2.0.1       askpass_1.2.0       gh_1.4.1            janitor_2.2.0       htmltools_0.5.8     curl_5.2.1         
+    #>  [15] KernSmooth_2.23-22  htmlwidgets_1.6.4   desc_1.4.3          httr2_1.0.1         zoo_1.8-12          cachem_1.0.8        mime_0.12           lifecycle_1.0.4     pkgconfig_2.0.3     Matrix_1.6-5        R6_2.5.1            fastmap_1.1.1       shiny_1.8.1.1       snakecase_0.11.1   
+    #>  [29] digest_0.6.35       numDeriv_2016.8-1.1 colorspace_2.1-0    rprojroot_2.0.4     pkgload_1.3.4       fansi_1.0.6         timechange_0.3.0    httr_1.4.7          compiler_4.3.1      proxy_0.4-27        intervals_0.15.4    remotes_2.5.0       withr_3.0.0         DBI_1.2.2          
+    #>  [43] pkgbuild_1.4.4      MASS_7.3-60.0.1     openssl_2.1.1       rappdirs_0.3.3      sessioninfo_1.2.2   tools_4.3.1         units_0.8-5         httpuv_1.6.15       glue_1.7.0          promises_1.2.1      grid_4.3.1          generics_0.1.3      gtable_0.3.4        tzdb_0.4.0         
+    #>  [57] class_7.3-22        data.table_1.15.4   hms_1.1.3           sp_2.1-3            xml2_1.3.6          utf8_1.2.4          pillar_1.9.0        stringr_1.5.1       yulab.utils_0.1.4   later_1.3.2         lattice_0.22-6      FNN_1.1.4           deldir_2.0-4        tidyselect_1.2.1   
+    #>  [71] rvcheck_0.2.1       miniUI_0.1.1.1      knitr_1.45          gitcreds_0.1.2      xfun_0.43           credentials_2.0.1   stringi_1.8.3       lazyeval_0.2.2      yaml_2.3.8          evaluate_0.23       codetools_0.2-19    tibble_3.2.1        BiocManager_1.30.22 cli_3.6.2          
+    #>  [85] xtable_1.8-4        munsell_0.5.1       spacetime_1.3-1     Rcpp_1.0.12         gert_2.0.1          bdsmatrix_1.3-7     parallel_4.3.1      ellipsis_0.3.2      profvis_0.3.8       urlchecker_1.0.1    viridisLite_0.4.2   mvtnorm_1.2-4       scales_1.3.0        xts_0.13.2         
+    #>  [99] e1071_1.7-14        purrr_1.0.2         crayon_1.5.2        rlang_1.1.3
 
 ## NOAA README
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -65,14 +65,6 @@ reference:
       # - starts_with("get_")
       - '`convert_ted_btd`'
       - '`convert_ctd_btd`'
-      - '`convert_do_to_o2sat`'
-      - '`extract_calibration_xmlcon`'
-      - '`get_calibration_parameter`'
-      - '`integer_to_conductivity`'
-      - '`integer_to_ph`'
-      - '`integer_to_pressure`'
-      - '`integer_to_temperature`'
-      - '`oxygen_saturation`'
   - title: Estimate Net Spread
     contents:
       - '`calc_net_spread`'
@@ -83,14 +75,12 @@ reference:
   - title: Datasets
     contents:
       - '`public_data`'
+      - '`station_coords`'
       - '`species_data`'
       - '`PolySpecies`'
-      - '`station_coords`'
   - title: Helper Functions
     contents:
       - '`numbers0`'
       - '`fix_path`'
       - '`text_list`'
-      - '`hex_to_cnv`'
-      - '`tau_par`'
 
diff --git a/docs/articles/example-script.html b/docs/articles/example-script.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   example-script: example-script.html
-last_built: 2024-04-03T21:29Z
+last_built: 2024-04-04T08:37Z
 urls:
   reference: https://afsc-gap-products.github.io/GAPsurvey/reference
   article: https://afsc-gap-products.github.io/GAPsurvey/articles

diff --git a/docs/reference/2021_06_13_0003.cnv b/docs/reference/2021_06_13_0003.cnv
@@ -455,8 +455,8 @@
 # interval = seconds: 0.25
 # start_time = Jun 13 2021 12:13:29 [Instrument's time stamp, header]
 # bad_flag = -9.990e-29
-# gapctd_date = Apr 03 2024 14:30:06, gapctd 2.1.2
-# gapctd_in = C:/Users/emily.markowitz/AppData/Local/R/win-library/4.3/GAPsurvey/exdata/convert_ctd_btd/2021_06_13_0003.hex
+# gapctd_date = Apr 04 2024 01:37:49, GAPSurvey 2024.4.1
+# gapctd_in = C:/Users/emily.markowitz/AppData/Local/Temp/2/RtmpkvTLrr/temp_libpath111c4bce9c1/GAPsurvey/exdata/convert_ctd_btd/2021_06_13_0003.hex
 # file_type = ascii
 *END*
       0.000     5.5861     -0.251   0.000139        0.0

diff --git a/docs/reference/SBE19plus_01908106_2023_06_18_0001.cnv b/docs/reference/SBE19plus_01908106_2023_06_18_0001.cnv
@@ -501,8 +501,8 @@
 # interval = seconds: 0.25
 # start_time = Jun 18 2023 07:13:35 [Instrument's time stamp, header]
 # bad_flag = -9.990e-29
-# gapctd_date = Apr 03 2024 14:30:12, gapctd 2.1.2
-# gapctd_in = C:/Users/emily.markowitz/AppData/Local/R/win-library/4.3/GAPsurvey/exdata/convert_ctd_btd/SBE19plus_01908106_2023_06_18_0001.hex
+# gapctd_date = Apr 04 2024 01:37:56, GAPSurvey 2024.4.1
+# gapctd_in = C:/Users/emily.markowitz/AppData/Local/Temp/2/RtmpkvTLrr/temp_libpath111c4bce9c1/GAPsurvey/exdata/convert_ctd_btd/SBE19plus_01908106_2023_06_18_0001.hex
 # file_type = ascii
 *END*
       0.000     3.1821     -0.051   0.000776   3.349355      6.875        0.0

diff --git a/docs/reference/get_sunrise_sunset.html b/docs/reference/get_sunrise_sunset.html