update all documentation and functions to reflect name change

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2024
-COPYRIGHT HOLDER: satf authors
+COPYRIGHT HOLDER: stockplotr authors

NAMESPACE

@@ -11,6 +11,7 @@ export(plot_recruitment)
 export(plot_recruitment_deviations)
 export(plot_spawn_recruitment)
 export(plot_spawning_biomass)
+export(risk_table)
 export(table_bnc)
 export(table_indices)
 export(write_captions)

R/exp_all_figs_tables.R

@@ -95,7 +95,7 @@ exp_all_figs_tables <- function(
   # figures
 
   tryCatch({
-    satf::plot_recruitment(
+    stockplotr::plot_recruitment(
       dat,
       unit_label = recruitment_unit_label,
       scale_amount = recruitment_scale_amount,
@@ -115,7 +115,7 @@ exp_all_figs_tables <- function(
 
 
   tryCatch({
-    satf::plot_biomass(
+    stockplotr::plot_biomass(
       dat,
       unit_label = biomass_unit_label,
       scale_amount = biomass_scale_amount,
@@ -136,7 +136,7 @@ exp_all_figs_tables <- function(
 
 
   tryCatch({
-    satf::plot_landings(dat, unit_label = landings_unit_label, make_rda, rda_dir) |> suppressWarnings() |> invisible()
+    stockplotr::plot_landings(dat, unit_label = landings_unit_label, make_rda, rda_dir) |> suppressWarnings() |> invisible()
 
     message("Exported plot_landings")
 
@@ -146,7 +146,7 @@ exp_all_figs_tables <- function(
   })
 
   tryCatch({
-    satf::plot_recruitment_deviations(dat, end_year, n_projected_years, make_rda, rda_dir) |> suppressWarnings() |> invisible()
+    stockplotr::plot_recruitment_deviations(dat, end_year, n_projected_years, make_rda, rda_dir) |> suppressWarnings() |> invisible()
 
     message("Exported plot_recruitment_deviations")
 
@@ -157,7 +157,7 @@ exp_all_figs_tables <- function(
     print(e)
   })
 
-  # satf::plot_spawn_recruitment(dat,
+  # stockplotr::plot_spawn_recruitment(dat,
   #                        spawning_biomass_label,
   #                        recruitment_label = recruitment_unit_label,
   #                        end_year,
@@ -167,7 +167,7 @@ exp_all_figs_tables <- function(
   # message("Exported plot_spawn_recruitment")
 
   tryCatch({
-    satf::plot_spawning_biomass(
+    stockplotr::plot_spawning_biomass(
       dat,
       unit_label = spawning_biomass_label,
       scale_amount = spawning_biomass_scale_amount,
@@ -190,7 +190,7 @@ exp_all_figs_tables <- function(
   })
 
   # uncomment when this is working properly
-  # satf::plot_indices(dat,
+  # stockplotr::plot_indices(dat,
   #                    unit_label = indices_unit_label,
   #                    make_rda,
   #                    rda_dir) |> suppressWarnings() |> invisible()
@@ -199,7 +199,7 @@ exp_all_figs_tables <- function(
 
   # tables
   tryCatch({
-    satf::table_bnc(dat,
+    stockplotr::table_bnc(dat,
                     end_year,
                     biomass_unit_label,
                     catch_unit_label,
@@ -214,7 +214,7 @@ exp_all_figs_tables <- function(
   })
 
   tryCatch({
-    satf::table_indices(dat, make_rda, rda_dir) |> suppressWarnings() |> invisible()
+    stockplotr::table_indices(dat, make_rda, rda_dir) |> suppressWarnings() |> invisible()
 
     message("Exported table_indices")
 
@@ -224,7 +224,7 @@ exp_all_figs_tables <- function(
   })
 
   # uncomment when finished
-  # satf::table_landings(dat) |> suppressWarnings() |> invisible()
+  # stockplotr::table_landings(dat) |> suppressWarnings() |> invisible()
   #
   # message("Exported table_landings")
   #

R/export_rda.R

@@ -1,12 +1,12 @@
 #' Export a figure or table to rda
 #'
 #' Export a figure/table, and its caption and alternative text, to an rda object.
-#' Typically used after satf::extract_caps_alttext().
+#' Typically used after stockplotr::extract_caps_alttext().
 #'
 #' @param final The final figure (ggplot) or table (flextable) object.
 #' @param caps_alttext The object containing a figure's caption and alternative
 #' text, in a list, or a table's caption, likely generated with
-#' satf::extract_caps_alttext().
+#' stockplotr::extract_caps_alttext().
 #' @param rda_dir If the user has already created a folder containing .rda
 #' files with figures, tables, alt text, and captions, rda_dir represents
 #' the location of the folder containing these .rda files ("rda_files").

R/extract_caps_alttext.R

@@ -1,7 +1,7 @@
 #' Extract captions and alternative texts
 #'
 #' Extract a figure or table's caption and alternative text for usage when
-#' generating a figure or table. Typically used before satf::export_rda().
+#' generating a figure or table. Typically used before stockplotr::export_rda().
 #'
 #' @param topic_label A string that describes a figure or table's label. These
 #' labels are found in the "label" column of the "captions_alt_text.csv" file

R/plot_biomass.R

@@ -174,7 +174,7 @@ plot_biomass <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/plot_indices.R

@@ -138,7 +138,7 @@ plot_indices <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/plot_landings.R

@@ -79,7 +79,7 @@ plot_landings <- function(dat,
   if (!file.exists(
     fs::path(getwd(), "captions_alt_text.csv"))
   ) {
-    satf::write_captions(dat = dat,
+    stockplotr::write_captions(dat = dat,
                          dir = rda_dir,
                          year = NULL)
   }

R/plot_recruitment.R

@@ -122,7 +122,7 @@ plot_recruitment <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/plot_recruitment_deviations.R

@@ -97,7 +97,7 @@ plot_recruitment_deviations <- function (
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/plot_spawn_recruitment.R

@@ -78,7 +78,7 @@ plot_spawn_recruitment <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/plot_spawning_biomass.R

@@ -181,7 +181,7 @@ plot_spawning_biomass <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = end_year)
     }

R/table_afsc_tier.R

@@ -15,7 +15,7 @@ table_afsc_tier <- function() {
   if (!file.exists(
     fs::path(getwd(), "captions_alt_text.csv"))
   ) {
-    satf::write_captions(dat = dat,
+    stockplotr::write_captions(dat = dat,
                          dir = rda_dir,
                          year = NULL)
   }

R/table_bnc.R

@@ -132,7 +132,7 @@ table_bnc <- function(
   if (!file.exists(
     fs::path(getwd(), "captions_alt_text.csv"))
   ) {
-    satf::write_captions(dat = dat,
+    stockplotr::write_captions(dat = dat,
                          dir = rda_dir,
                          year = NULL)
   }

R/table_indices.R

@@ -112,7 +112,7 @@ table_indices <- function(
     if (!file.exists(
       fs::path(getwd(), "captions_alt_text.csv"))
     ) {
-      satf::write_captions(dat = dat,
+      stockplotr::write_captions(dat = dat,
                            dir = rda_dir,
                            year = NULL)
     }

R/write_captions.R

@@ -27,7 +27,7 @@ write_captions <- function(dat, # converted model output object
     # for key quantities (e.g., 'start_year' is the placeholder for the
     # assessment's start year)
     caps_alttext <- utils::read.csv(
-      system.file("resources", "captions_alt_text_template.csv", package = "satf")
+      system.file("resources", "captions_alt_text_template.csv", package = "stockplotr")
     )
 
     dat <- dat |>

R/zzz.R

@@ -1,8 +1,8 @@
-### Start up messages and actions to run for use of satf
+### Start up messages and actions to run for use of stockplotr
 # Start up message
 
 .onAttach <- function(libname, pkgname){
-  packageStartupMessage("Thanks for using satf! Please visit the GitHub pages for more information on this package as well as latest developments. If you have any issues or inquires, please use the Issues page on GitHub (https://github.com/nmfs-ost/satf/issues)")
+  packageStartupMessage("Thanks for using stockplotr! Please visit the GitHub pages for more information on this package as well as latest developments. If you have any issues or inquires, please use the Issues page on GitHub (https://github.com/nmfs-ost/satf/issues)")
 }
 
 # Things to load on start up

inst/WORDLIST

@@ -16,4 +16,3 @@ kable
 kableExtra
 rda
 rda's
-satf

pkgdown/_pkgdown.yml

@@ -1,4 +1,4 @@
-url: nmfs-ost.github.io/satf/
+url: nmfs-ost.github.io/stockplotr/
 
 navbar:
 
@@ -15,7 +15,7 @@ navbar:
     issue:
       text: Issues
       icon: fas fa-question-circle fa-lg
-      href: https://github.com/nmfs-ost/satf/issues
+      href: https://github.com/nmfs-ost/stockplotr/issues
 
     articles:
       text: Articles

tests/testthat.R

@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
-library(satf)
+library(stockplotr)
 
-test_check("satf")
+test_check("stockplotr")

vignettes/manual.Rmd

@@ -22,15 +22,15 @@ This manual is a work in progress. In the meantime, please read the function doc
 
 ## Updating alternative text and captions
 
-When a plotting function (e.g., `plot_biomass()`, `table_indices()`, `exp_all_figs_tables()`) is run, placeholders within the plot's associated alternative text and captions are replaced with key quantities (see the [`asar` package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and/or the [`satf::write_captions()` function](https://github.com/nmfs-ost/satf/blob/master/R/write_captions.R) for more details).
+When a plotting function (e.g., `plot_biomass()`, `table_indices()`, `exp_all_figs_tables()`) is run, placeholders within the plot's associated alternative text and captions are replaced with key quantities (see the [`asar` package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and/or the [`stockplotr::write_captions()` function](https://github.com/nmfs-ost/stockplotr/blob/master/R/write_captions.R) for more details).
 
 As stated in the [Accessibility vignette's "Your to-do list" section](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#your-to-do-list), **you should always:**
 
 **1. Check that these alternative texts and captions have been assembled correctly.**
 
 **2. Write the final component of each figure’s alt text.**
 
-Here's how to alter the alternative text and/or captions in `satf`, depending on what you wish to change:
+Here's how to alter the alternative text and/or captions in `stockplotr`, depending on what you wish to change:
 
 ### Add or Remove Text