[feat] Update indices table

.Rbuildignore

@@ -6,3 +6,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.positai$
+^\.claude$

.gitignore

@@ -13,3 +13,4 @@ docs
 stockplotr.Rproj
 *.Rproj
 !vignettes/figures/
+.positai

NAMESPACE

@@ -14,7 +14,7 @@ export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
 export(plot_fishing_mortality)
-export(plot_indices)
+export(plot_index)
 export(plot_landings)
 export(plot_natural_mortality)
 export(plot_obsvpred)
@@ -27,5 +27,6 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
+export(table_index)
 export(table_landings)
 export(theme_noaa)

R/convert_output.R

@@ -1933,7 +1933,7 @@ convert_output <- function(
             uncertainty = log_sd
           ) |>
           dplyr::mutate(
-            # label = "indices_observed",
+            # label = "index_observed",
             uncertainty_label = "log_sd",
             indices_predicted = dat$quantities$index_hat
           ) |>
@@ -1956,12 +1956,13 @@ convert_output <- function(
             values_to = "estimate"
           ) |>
           dplyr::mutate(
-            module_name = names(extract) # ,
+            module_name = names(extract),
             # era = dplyr::if_else(
             #   year > dat$data_list$endyr,
             #   "fore",
             #   NA_character_
             # )
+            label = stringr::str_replace_all(label, "indices", "index")
           )
 
         df_index_long[setdiff(tolower(names(out_new)), tolower(names(df_index_long)))] <- NA
@@ -2013,7 +2014,7 @@ convert_output <- function(
         df_comp_obs <- dat$data_list$comp_data |>
           dplyr::rename_with(tolower) |>
           dplyr::mutate(
-            label = "indices_observed"
+            label = "index_observed"
           )
 
         indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
@@ -2185,10 +2186,15 @@ convert_output <- function(
   # }
 
   # edit: here is a different way of loading in the csv sheets
-  con_file <- system.file("resources", glue::glue("{model}_var_names.csv"), package = "stockplotr", mustWork = TRUE)
+  con_file <- system.file("resources", glue::glue("{tolower(model)}_var_names.csv"), package = "stockplotr", mustWork = TRUE)
   # temporarily add call to local csv so I can test
   # con_file <- glue::glue("~/GitHub/stockplotr/inst/resources/{model}_var_names.csv")
   var_names_sheet <- utils::read.csv(con_file, na.strings = "")
+
+  if (tolower(model) == "bam") {
+    var_names_sheet <- var_names_sheet |> 
+      dplyr::mutate(label = tolower(label))
+  }
 
   if (file.exists(con_file)) {
     # Remove 'X' column if it exists

R/plot_indices.R → R/plot_index.R

@@ -13,7 +13,7 @@
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
 #' Default: NULL
-#' @returns A plot showing the expected and predicted indices.
+#' @returns A plot showing the expected and predicted index.
 #'
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -25,13 +25,13 @@
 #' @export
 #'
 #' @examples
-#' plot_indices(
+#' plot_index(
 #'   dat = stockplotr:::example_data,
 #'   unit_label = "fish/hr",
 #'   interactive = FALSE
 #' )
 #'
-plot_indices <- function(
+plot_index <- function(
   dat,
   unit_label = "",
   group = NULL,
@@ -57,7 +57,7 @@ plot_indices <- function(
   # Filter data
   prepared_data <- filter_data(
     dat,
-    label_name = "indices",
+    label_name = "index",
     era = NULL,
     geom = "line",
     # ifelse guarantees the code doesn't miss grouping when label has > 1 value
@@ -98,8 +98,8 @@ plot_indices <- function(
     dat = prepared_data,
     x = "year",
     y = "estimate",
-    observed_label = "indices_observed",
-    predicted_label = "indices_predicted",
+    observed_label = "index_observed",
+    predicted_label = "index_predicted",
     geom = "line",
     xlab = "Year",
     ylab = "Estimated Index",

R/process_data.R

@@ -532,8 +532,8 @@ process_table <- function(
       dplyr::rename(
         !!mod_uncert_lab := uncertainty
       ) |>
-      # set values to strings to include training zeros from rounding
-      dplyr::mutate(estimate = sprintf(glue::glue("%.{digits}f"), estimate)) |>
+    # set values to strings to include trailing zeros from rounding and     # format large estimate values with commas
+      dplyr::mutate(estimate = formatC(estimate, format = "f", digits = digits, big.mark = ",")) |>
       tidyr::pivot_wider(
         id_cols = dplyr::all_of(c(stringr::str_to_title(mod_cols))),
         values_from = dplyr::all_of(c("estimate", mod_uncert_lab)),

R/save_all_plots.R

@@ -80,7 +80,7 @@
 #'
 #' Default: "mt"
 #'
-#' @param indices_unit_label Units for index of abundance/CPUE
+#' @param index_unit_label Units for index of abundance/CPUE
 #'
 #' Default: ""
 #'
@@ -119,7 +119,7 @@
 #' save_all_plots(dat,
 #'   ref_line = "unfished",
 #'   ref_line_sb = "target",
-#'   indices_unit_label = "CPUE",
+#'   index_unit_label = "CPUE",
 #'   biomass_at_age_scale_amount = 1,
 #'   biomass_at_age_unit_label = "metric tons"
 #' )
@@ -150,15 +150,15 @@ save_all_plots <- function(
   # imported from plot_biomass_at_age
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  # imported from plot_indices
-  indices_unit_label = "",
+  # imported from plot_index
+  index_unit_label = "",
   # imported from table_afsc_tier- add potential unique arguments after dev
   # imported from table_bnc
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
   # imported from table_harvest_projection- add potential unique arguments after dev
-  # imported from table_indices- zero unique arguments
+  # imported from table_index- zero unique arguments
   # imported from table_landings- zero unique arguments
 ) {
   make_rda <- TRUE
@@ -419,18 +419,18 @@ save_all_plots <- function(
 
   tryCatch(
     {
-      cli::cli_h2("plot_indices")
-      plot_indices(dat,
-        unit_label = indices_unit_label,
+      cli::cli_h2("plot_index")
+      plot_index(dat,
+        unit_label = index_unit_label,
         make_rda = TRUE,
         interactive = FALSE,
         figures_dir = figures_tables_dir
       ) # |> suppressWarnings() |> invisible()
     },
     error = function(e) {
-      cli::cli_alert_danger("plot_indices failed to run.")
+      cli::cli_alert_danger("plot_index failed to run.")
       cli::cli_alert("Tip: check that your arguments are correct.")
-      cli::cli_li("indices_unit_label = {indices_unit_label}")
+      cli::cli_li("index_unit_label = {index_unit_label}")
       print(e)
     }
   )
@@ -460,23 +460,24 @@ save_all_plots <- function(
   #   }
   # )
 
-  # tryCatch(
-  #   {
-  #     cli::cli_h2("table_indices")
-  #     table_indices(
-  #       dat,
-  #       make_rda = TRUE,
-  #       tables_dir = figures_tables_dir
-  #     ) # |>
-  #     # suppressWarnings() |>
-  #     # invisible()
-  #   },
-  #   error = function(e) {
-  #     cli::cli_alert_danger("table_indices failed to run.")
-  #     cli::cli_alert("Tip: check that your arguments are correct.")
-  #     print(e)
-  #   }
-  # )
+  tryCatch(
+    {
+      cli::cli_h2("table_index")
+      table_index(
+        dat,
+        interactive = FALSE,
+        make_rda = TRUE,
+        tables_dir = figures_tables_dir
+      ) # |>
+      # suppressWarnings() |>
+      # invisible()
+    },
+    error = function(e) {
+      cli::cli_alert_danger("table_index failed to run.")
+      cli::cli_alert("Tip: check that your arguments are correct.")
+      print(e)
+    }
+  )
 
   tryCatch(
     {

R/table_afsc_tier.R

@@ -4,7 +4,7 @@ table_afsc_tier <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   # identify output

R/table_harvest_projection.R

@@ -4,7 +4,7 @@ table_harvest_projection <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   level <- c(