Extracting more key quantities

.gitignore

@@ -7,3 +7,4 @@ captions_alt_text.csv
 converted_file_1126.csv
 rda_files
 petrale_sole_std_output.csv
+inst/doc

DESCRIPTION

@@ -41,7 +41,9 @@ Imports:
 Depends: 
     R (>= 2.10)
 Suggests: 
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Language: en-US
+VignetteBuilder: knitr

R/plot_biomass.R

@@ -179,6 +179,16 @@ plot_biomass <- function(
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      end_year = end_year,
+      units = unit_label,
+      ref_pt = ref_point
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,
@@ -189,6 +199,7 @@ plot_biomass <- function(
                rda_dir = rda_dir,
                topic_label = topic_label,
                fig_or_table = fig_or_table)
-  }
+
+    }
   return(final)
 }

R/plot_indices.R

@@ -143,6 +143,14 @@ plot_indices <- function(
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      units = unit_label
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,

R/plot_landings.R

@@ -84,6 +84,14 @@ plot_landings <- function(dat,
                          year = NULL)
   }
 
+  # add more key quantities included as arguments in this fxn
+  add_more_key_quants(
+    topic = topic_label,
+    fig_or_table = fig_or_table,
+    dir = rda_dir,
+    units = unit_label
+  )
+
   # extract this plot's caption and alt text
   caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                        fig_or_table = fig_or_table,

R/plot_recruitment.R

@@ -125,6 +125,15 @@ plot_recruitment <- function(
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      end_year = end_year,
+      units = unit_label
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,

R/plot_recruitment_deviations.R

@@ -102,6 +102,14 @@ plot_recruitment_deviations <- function (
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      end_year = end_year
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,

R/plot_spawn_recruitment.R

@@ -83,6 +83,17 @@ plot_spawn_recruitment <- function(
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      end_year = end_year,
+      sr_ssb_units = spawning_biomass_label,
+      sr_recruitment_units = recruitment_label,
+      units = NULL
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,

R/plot_spawning_biomass.R

@@ -186,6 +186,16 @@ plot_spawning_biomass <- function(
                            year = end_year)
     }
 
+    # add more key quantities included as arguments in this fxn
+    add_more_key_quants(
+      topic = topic_label,
+      fig_or_table = fig_or_table,
+      dir = rda_dir,
+      end_year = end_year,
+      units = unit_label,
+      ref_pt = ref_point
+    )
+
     # extract this plot's caption and alt text
     caps_alttext <- extract_caps_alttext(topic_label = topic_label,
                                          fig_or_table = fig_or_table,

R/utils.R

@@ -65,3 +65,124 @@ export_rda <- function(final = final,
                         "rda_files",
                         paste0(topic_label, "_", fig_or_table, ".rda")))
 }
+
+# substitute in more key quantities (units, end_years, reference points) to captions/alt text
+add_more_key_quants <- function(
+    topic = topic_label,
+    fig_or_table = fig_or_table,
+    dir = NULL,
+    end_year = NULL,
+    units = NULL,
+    sr_ssb_units = NULL,
+    sr_recruitment_units = NULL,
+    ref_pt = NULL){
+
+  # import csv
+  caps_alt_df <- read.csv(fs::path(getwd(), "captions_alt_text.csv"))
+
+  # make year character if not null
+  if (!is.null(end_year)){
+    end_year <- as.character(end_year)
+  }
+
+  # select specific fig/table's caption/alt text
+  topic_cap_alt <- caps_alt_df |>
+    dplyr::filter(label == topic,
+                  type == fig_or_table)
+
+  # replace placeholders (e.g., if "end.year" is found in topic_alt, replace it with end_year)
+  ## end_year-----
+  if(!is.null(end_year)){
+  ### alt text
+  ### this regex preserves the comma after the end year
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                      stringr::regex("(\\S*end\\.year\\S*)(?=\\s?,)"),
+                                                      end_year))
+
+  ### this regex removes a potential trailing space after the end year
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                      stringr::regex("\\S*end\\.year\\S*\\s*"),
+                                                      end_year))
+  }
+  ## units-----
+  if(!is.null(units)){
+  ### caption
+  ### this regex preserves the closing ) after the units
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(caption = stringr::str_replace_all(caption,
+                                                      stringr::regex("(\\S*units\\S*)(?=\\s?\\))"),
+                                                      as.character(units)))
+
+  ### this regex preserves the period after the units
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(caption = stringr::str_replace_all(caption,
+                                                     stringr::regex("(\\S*units\\S*)(?=\\s?.)"),
+                                                     as.character(units)))
+
+  ### this regex replaces the units if it's not found with the previous two commands
+  ### (i.e., there's no parenthesis or period adjacent to the units variable)
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(caption = stringr::str_replace_all(caption,
+                                                     stringr::regex("\\S*units\\S*"),
+                                                     as.character(units)))
+  }
+
+  if(!is.null(sr_ssb_units)){
+  ### this is for plot_spawn_recruitment, since there are two units
+  #### replace sr.ssb.units with sr_ssb_units
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                      "sr.ssb.units",
+                                                      as.character(sr_ssb_units)))
+  }
+
+  if(!is.null(sr_recruitment_units)){
+  ### this is for plot_spawn_recruitment, since there are two units
+  #### replace sr.units with sr_recruitment_units
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                      "sr.units",
+                                                      as.character(sr_recruitment_units)))
+  }
+
+  if(!is.null(units)){
+  ### alt text
+  ### this regex preserves the comma after the units
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                      stringr::regex("(\\S*units\\S*)(?=\\s?,)"),
+                                                      as.character(units)))
+
+  ### this regex replaces the units if it's not found with the previous command
+  ### (i.e., there's no comma adjacent to the units variable)
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(alt_text = stringr::str_replace_all(alt_text,
+                                                     stringr::regex("\\S*units\\S*"),
+                                                     as.character(units)))
+
+  }
+  ## reference points-----
+  if(!is.null(ref_pt)){
+  ### caption
+  ### this regex preserves the opening ( before the ref pt
+  topic_cap_alt <- topic_cap_alt |>
+    dplyr::mutate(caption = stringr::str_replace_all(caption,
+                                                     stringr::regex("\\(\\S*ref\\.pt*\\S*"),
+                                                     paste0("(", as.character(ref_pt))))
+  }
+
+  # remove row with old caption/alt text, then add new row
+  replaced_df <- dplyr::anti_join(caps_alt_df,
+                                  topic_cap_alt,
+                                  by = c("label", "type")) |>
+    dplyr::full_join(topic_cap_alt)
+
+  # export df with updated captions and alt text to csv
+  utils::write.csv(x = replaced_df,
+                   file = fs::path(dir,
+                                   "captions_alt_text.csv"),
+                   row.names=FALSE)
+
+  }