From 279abf0ab184f3558623b812fbf973fe67dfa608 Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Tue, 20 Oct 2026 20:55:54 +0000
Subject: [PATCH] style and docs: run devtools::document() and style with
 styler or air

---
 NAMESPACE                                     |   1 +
 R/convert_output.R                            |   7 +-
 R/extract_sis_data.R                          | 350 +++++++++---------
 R/plot_spr.R                                  |  33 +-
 R/plot_stock_recruitment.R                    |   2 +-
 R/table_total_catch.R                         |   8 +-
 R/utils_plot.R                                |  47 ++-
 man/calculate_reference_point.Rd              |   2 +-
 man/plot_spawning_potential_ratio.Rd          | 128 +++++++
 tests/testthat/helper-test_functions.R        |  42 ++-
 tests/testthat/test-convert_output.R          |   2 +-
 tests/testthat/test-extract_sis_data.R        |  20 +-
 tests/testthat/test-plot_natural_mortality.R  |   2 +-
 .../test-plot_spawning_potential_ratio.R      |   8 +-
 vignettes/extract-sis-data.Rmd                |   2 +-
 15 files changed, 403 insertions(+), 251 deletions(-)
 create mode 100644 man/plot_spawning_potential_ratio.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 0de5d9df..ab256ecd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,6 +23,7 @@ export(plot_recruitment)
 export(plot_recruitment_deviations)
 export(plot_selectivity)
 export(plot_spawning_biomass)
+export(plot_spawning_potential_ratio)
 export(plot_stock_recruitment)
 export(plot_timeseries)
 export(process_data)
diff --git a/R/convert_output.R b/R/convert_output.R
index b0b8b1f1..863a24de 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -48,18 +48,17 @@ convert_output <- function(
   fleet_names = NULL,
   save_dir = NULL
 ) {
-  
   if (is.character(file) && grepl("Report.sso", file)) {
     lifecycle::deprecate_warn(
-      when = "2.8.0", 
-      what = I("convert_output(file = 'Report.sso')"), 
+      when = "2.8.0",
+      what = I("convert_output(file = 'Report.sso')"),
       details = c(
         i = "Please use the returned object from `r4ss::ss_output()`",
         i = "File will be compatible until Oct. 1, 2027"
       )
     )
   }
-  
+
   # check if entered save_dir exists so doesn't waste user time finding this out at the end
   if (!is.null(save_dir)) {
     if (!grepl(".rda", save_dir)) {
diff --git a/R/extract_sis_data.R b/R/extract_sis_data.R
index 9176af07..e5f062a2 100644
--- a/R/extract_sis_data.R
+++ b/R/extract_sis_data.R
@@ -3,26 +3,26 @@
 #' Semi-automate the extraction of key quantities from model results and time
 #' series data from exported figure/table `.rda` files for eventual transmittance
 #' to SIS via `asar::export_to_sis()`.
-#' 
+#'
 #' @param sis_data_dir Path. Location to save the sis_assmt_template.csv and
 #' sis_ts_template.csv files or, if present, the location of the
 #' existing sis_assmt_template.csv file.
-#' 
+#'
 #' Default: The working directory.
-#' 
-#' @param key_quantities_dir Path. Location of the existing key_quantities.csv 
+#'
+#' @param key_quantities_dir Path. Location of the existing key_quantities.csv
 #' file.
-#' 
+#'
 #' Default: The working directory.
-#' 
-#' @param figures_tables_dir Path. Location of the existing 'figures' and 
+#'
+#' @param figures_tables_dir Path. Location of the existing 'figures' and
 #' 'tables' directories.
-#' 
+#'
 #' Default: The working directory.
-#' 
+#'
 #' @details See the "Automating data extraction for SIS" vignette for a
 #' detailed overview of the workflow and requirements for this function.
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -36,30 +36,33 @@
 #'
 extract_sis_data <- function(sis_data_dir = getwd(),
                              key_quantities_dir = getwd(),
-                             figures_tables_dir = getwd()
-                             ) {
+                             figures_tables_dir = getwd()) {
   # check if existing figures and tables folders exist; if both absent, throw an error
   if (!dir.exists(fs::path(figures_tables_dir, "figures")) & !dir.exists(fs::path(figures_tables_dir, "tables"))) {
     cli::cli_abort("Neither 'figures' nor 'tables' folders were found in {figures_tables_dir}. Please check the `figures_tables_dir` path, or export figures and tables, and then try again.")
-    }
-  
+  }
+
   # Check if existing data files exist; if not, start from blank templates
   if (!file.exists(fs::path(sis_data_dir, "sis_assmt_template.csv"))) {
     assmt_dat <- utils::read.csv(system.file("resources", "sis_assmt_template.csv", package = "stockplotr"))
     cli::cli_alert_info("No existing sis_assmt_template.csv found in {sis_data_dir}. Using blank template.")
   } else {
     assmt_dat <- read.csv(fs::path(sis_data_dir, "sis_assmt_template.csv"), stringsAsFactors = FALSE)
-        cli::cli_alert_success("Found existing sis_assmt_template.csv in {sis_data_dir}.")
+    cli::cli_alert_success("Found existing sis_assmt_template.csv in {sis_data_dir}.")
   }
-  
+
   ts_dat <- utils::read.csv(system.file("resources", "sis_ts_template.csv", package = "stockplotr"))
-  
+
   # extract key quantities from csv and assign to variables
   kqs_path <- fs::path(key_quantities_dir, "key_quantities.csv")
-  if (file.exists(kqs_path)){
-    kqs <- read.csv(fs::path(key_quantities_dir,
-                           "key_quantities.csv"), 
-                  stringsAsFactors = FALSE)
+  if (file.exists(kqs_path)) {
+    kqs <- read.csv(
+      fs::path(
+        key_quantities_dir,
+        "key_quantities.csv"
+      ),
+      stringsAsFactors = FALSE
+    )
     cli::cli_alert_success("Found existing key_quantities.csv in {key_quantities_dir}.")
   } else {
     cli::cli_alert_warning("No existing key_quantities.csv found in {key_quantities_dir}.")
@@ -69,8 +72,8 @@ extract_sis_data <- function(sis_data_dir = getwd(),
       "*" = "plot_biomass()"
     ))
   }
-  
-  if (file.exists(kqs_path)){
+
+  if (file.exists(kqs_path)) {
     # insert values into the sis_assmt_template.csv file
     mapping <- tibble::tribble(
       ~key_quantity,          ~Variable,
@@ -92,20 +95,20 @@ extract_sis_data <- function(sis_data_dir = getwd(),
       "F.MSY.terminal.max",   "AS_FMSY_MAX",
       "F.MSY.terminal.min",   "AS_FMSY_MIN"
     )
-    
+
     # Extract values and format into a key-value matching table
-    new_vals <- kqs |> 
-      dplyr::inner_join(mapping, by = "key_quantity") |> 
-      dplyr::mutate(value = as.numeric(value)) |> 
+    new_vals <- kqs |>
+      dplyr::inner_join(mapping, by = "key_quantity") |>
+      dplyr::mutate(value = as.numeric(value)) |>
       dplyr::select(Variable, new_value = value)
-    
+
     # Update assmt_dat
-    assmt_dat <- assmt_dat |> 
-      dplyr::left_join(new_vals, by = "Variable") |> 
-      dplyr::mutate(Value = ifelse(!is.na(new_value), new_value, Value)) |> 
+    assmt_dat <- assmt_dat |>
+      dplyr::left_join(new_vals, by = "Variable") |>
+      dplyr::mutate(Value = ifelse(!is.na(new_value), new_value, Value)) |>
       dplyr::select(-new_value)
   }
-  
+
   # obtain time series data
   if (!dir.exists(fs::path(figures_tables_dir, "figures"))) {
     cli::cli_alert_info("'figures' folder not found in {sis_data_dir}.")
@@ -127,76 +130,83 @@ extract_sis_data <- function(sis_data_dir = getwd(),
         biomass <<- NULL
       }
     )
-    
+
     # SPAWNERS (fits under "abundance" category)
-    tryCatch({
-      load(fs::path(figures_tables_dir, "figures", "spawning_biomass_figure.rda")) |> suppressWarnings()
-      sb <- rda[["figure"]][["layers"]][["geom_line"]]$data
-      spawning_biomass <- sb |>
-        dplyr::group_by(year) |>
-        dplyr::summarise(sum = sum(estimate)) |>
-        dplyr::rename(Spawners = sum)
-    },
-    error = function(e) {
-      cli::cli_alert_warning("Spawning biomass data was not extracted from the 'spawning_biomass_figure.rda' file.")
-      spawning_biomass <<- NULL
-    }
+    tryCatch(
+      {
+        load(fs::path(figures_tables_dir, "figures", "spawning_biomass_figure.rda")) |> suppressWarnings()
+        sb <- rda[["figure"]][["layers"]][["geom_line"]]$data
+        spawning_biomass <- sb |>
+          dplyr::group_by(year) |>
+          dplyr::summarise(sum = sum(estimate)) |>
+          dplyr::rename(Spawners = sum)
+      },
+      error = function(e) {
+        cli::cli_alert_warning("Spawning biomass data was not extracted from the 'spawning_biomass_figure.rda' file.")
+        spawning_biomass <<- NULL
+      }
     )
-    
+
     # RECRUITMENT
-    tryCatch({
-      load(fs::path(figures_tables_dir, "figures", "abundance_at_age_figure.rda")) |> suppressWarnings()
-      rec <- rda[["figure"]][["layers"]][["geom_point"]][["data"]]
-      recruitment <- rec |>
-        dplyr::filter(age == 1) |>
-        dplyr::group_by(year) |>
-        dplyr::summarise(sum = sum(estimate)) |>
-        dplyr::rename(Recruitment = sum)
-    },
-    error = function(e) {
-      cli::cli_alert_warning("Recruitment (age 1) data was not extracted from the 'abundance_at_age_figure.rda' file.")
-      recruitment <<- NULL
-      
-      # this is for recruitment in mt- not age-1, which is what SIS expects
-    #   load(fs::path(figures_tables_dir, "figures", "recruitment_figure.rda")) |> suppressWarnings()
-    #   rec <- rda[["figure"]][["layers"]][["geom_line"]]$data
-    #   recruitment <- rec |>
-    #     dplyr::group_by(year) |>
-    #     dplyr::summarise(sum = sum(predicted_recruitment)) |>
-    #     dplyr::rename(Recruitment = sum)
-    # },
-    # error = function(e) {
-    #   cli::cli_alert_warning("Recruitment data was not extracted from the 'recruitment_figure.rda' file.")
-    #   recruitment <<- NULL
-    })
-    
+    tryCatch(
+      {
+        load(fs::path(figures_tables_dir, "figures", "abundance_at_age_figure.rda")) |> suppressWarnings()
+        rec <- rda[["figure"]][["layers"]][["geom_point"]][["data"]]
+        recruitment <- rec |>
+          dplyr::filter(age == 1) |>
+          dplyr::group_by(year) |>
+          dplyr::summarise(sum = sum(estimate)) |>
+          dplyr::rename(Recruitment = sum)
+      },
+      error = function(e) {
+        cli::cli_alert_warning("Recruitment (age 1) data was not extracted from the 'abundance_at_age_figure.rda' file.")
+        recruitment <<- NULL
+
+        # this is for recruitment in mt- not age-1, which is what SIS expects
+        #   load(fs::path(figures_tables_dir, "figures", "recruitment_figure.rda")) |> suppressWarnings()
+        #   rec <- rda[["figure"]][["layers"]][["geom_line"]]$data
+        #   recruitment <- rec |>
+        #     dplyr::group_by(year) |>
+        #     dplyr::summarise(sum = sum(predicted_recruitment)) |>
+        #     dplyr::rename(Recruitment = sum)
+        # },
+        # error = function(e) {
+        #   cli::cli_alert_warning("Recruitment data was not extracted from the 'recruitment_figure.rda' file.")
+        #   recruitment <<- NULL
+      }
+    )
+
     # FISHING MORTALITY
-    tryCatch({
-      load(fs::path(figures_tables_dir, "figures", "fishing_mortality_figure.rda")) |> suppressWarnings()
-      fm <- rda[["figure"]][["layers"]][["geom_line"]]$data
-      fishing_mortality <- fm |>
-        dplyr::group_by(year) |>
-        dplyr::summarise(mean = mean(estimate)) |>
-        dplyr::rename(Fmort = mean)
-    },
-    error = function(e) {
-      cli::cli_alert_warning("Fishing mortality data was not extracted from the 'fishing_mortality_figure.rda' file.")
-      fishing_mortality <<- NULL
-    })
-    
+    tryCatch(
+      {
+        load(fs::path(figures_tables_dir, "figures", "fishing_mortality_figure.rda")) |> suppressWarnings()
+        fm <- rda[["figure"]][["layers"]][["geom_line"]]$data
+        fishing_mortality <- fm |>
+          dplyr::group_by(year) |>
+          dplyr::summarise(mean = mean(estimate)) |>
+          dplyr::rename(Fmort = mean)
+      },
+      error = function(e) {
+        cli::cli_alert_warning("Fishing mortality data was not extracted from the 'fishing_mortality_figure.rda' file.")
+        fishing_mortality <<- NULL
+      }
+    )
+
     # INDEX
-    tryCatch({
-      load(fs::path(figures_tables_dir, "figures", "index_figure.rda")) |> suppressWarnings()
-      index <- rda[["figure"]][["layers"]][["geom_line"]]$data
-      index <- index |>
-        dplyr::group_by(year) |>
-        dplyr::summarise(mean = mean(estimate)) |>
-        dplyr::rename(Index = mean)
-    },
-    error = function(e) {
-      cli::cli_alert_warning("Index data was not extracted from the 'index_figure.rda' file.")
-      index <<- NULL
-    })
+    tryCatch(
+      {
+        load(fs::path(figures_tables_dir, "figures", "index_figure.rda")) |> suppressWarnings()
+        index <- rda[["figure"]][["layers"]][["geom_line"]]$data
+        index <- index |>
+          dplyr::group_by(year) |>
+          dplyr::summarise(mean = mean(estimate)) |>
+          dplyr::rename(Index = mean)
+      },
+      error = function(e) {
+        cli::cli_alert_warning("Index data was not extracted from the 'index_figure.rda' file.")
+        index <<- NULL
+      }
+    )
   }
   if (!dir.exists(fs::path(figures_tables_dir, "tables"))) {
     cli::cli_alert_info("'tables' folder not found in {sis_data_dir}.")
@@ -205,38 +215,38 @@ extract_sis_data <- function(sis_data_dir = getwd(),
   } else {
     table_ts <- TRUE
     tryCatch(
-    {
-      load(fs::path(figures_tables_dir, "tables", "total_catch_table.rda")) |> suppressWarnings()
-      catch <- rda[["table"]][["_data"]]
-      catch_cols <- colnames(catch)
-      cols_without_catch <- c("Sex", "Area", "Season", "Type")
-      if (any(cols_without_catch %in% catch_cols)) {
+      {
+        load(fs::path(figures_tables_dir, "tables", "total_catch_table.rda")) |> suppressWarnings()
+        catch <- rda[["table"]][["_data"]]
+        catch_cols <- colnames(catch)
+        cols_without_catch <- c("Sex", "Area", "Season", "Type")
+        if (any(cols_without_catch %in% catch_cols)) {
+          catch <- catch |>
+            dplyr::select(-dplyr::any_of(cols_without_catch))
+        }
         catch <- catch |>
-          dplyr::select(-dplyr::any_of(cols_without_catch))
+          # remove values in parentheses, if present
+          dplyr::mutate(dplyr::across(!Year, ~ stringr::str_remove_all(.x, "\\s*\\(.*?\\)"))) |>
+          dplyr::mutate(dplyr::across(!Year, ~ stringr::str_remove_all(.x, ","))) |>
+          dplyr::mutate(dplyr::across(!Year, ~ as.numeric(.x))) |>
+          # summarize non-Year rows
+          dplyr::rowwise() |>
+          dplyr::mutate(Catch = sum(dplyr::c_across(!Year), na.rm = TRUE)) |>
+          dplyr::ungroup() |>
+          dplyr::select(Year, Catch)
+      },
+      error = function(e) {
+        cli::cli_alert_warning("Catch data will not be extracted from the 'total_catch_table.rda' file.")
+        catch <<- NULL
       }
-      catch <- catch |>
-        # remove values in parentheses, if present
-        dplyr::mutate(dplyr::across(!Year, ~ stringr::str_remove_all(.x, "\\s*\\(.*?\\)"))) |>
-        dplyr::mutate(dplyr::across(!Year, ~ stringr::str_remove_all(.x, ","))) |>
-        dplyr::mutate(dplyr::across(!Year, ~ as.numeric(.x))) |>
-        # summarize non-Year rows
-        dplyr::rowwise() |>
-        dplyr::mutate(Catch = sum(dplyr::c_across(!Year), na.rm = TRUE)) |>
-        dplyr::ungroup() |>
-        dplyr::select(Year, Catch)
-    },
-    error = function(e) {
-      cli::cli_alert_warning("Catch data will not be extracted from the 'total_catch_table.rda' file.")
-      catch <<- NULL
-    }
     )
   }
-  
-  if(exists("fig_ts")){
+
+  if (exists("fig_ts")) {
     summaries <- c("biomass", "spawning_biomass", "recruitment", "fishing_mortality", "index")
-    
-    summaries <- summaries[sapply(summaries, function(x) !is.null(get(x)))] 
-    
+
+    summaries <- summaries[sapply(summaries, function(x) !is.null(get(x)))]
+
     # join all summaries by year
     all_summaries <- c()
     for (i in seq_along(summaries)) {
@@ -244,25 +254,27 @@ extract_sis_data <- function(sis_data_dir = getwd(),
         all_summaries <- get(summaries[i])
       } else {
         all_summaries <- dplyr::full_join(all_summaries,
-                                          get(summaries[i]),
-                                          by = "year")
+          get(summaries[i]),
+          by = "year"
+        )
       }
     }
   }
-  if (exists("table_ts") & !is.null(catch)){
-    if (!is.null(all_summaries) & exists("fig_ts")){
+  if (exists("table_ts") & !is.null(catch)) {
+    if (!is.null(all_summaries) & exists("fig_ts")) {
       catch <- catch |>
         dplyr::rename(year = Year)
       all_summaries <- dplyr::full_join(all_summaries,
-                                      catch,
-                                      by = "year")
+        catch,
+        by = "year"
+      )
       summaries <- c(summaries, "catch")
     } else {
       all_summaries <- get("catch")
       summaries <- "catch"
     }
   }
-  
+
   ts_options <- summaries[!is.na(summaries)]
   cli::cli_alert_info("The following time series summaries were extracted:")
   cli::cli_ul(ts_options)
@@ -281,23 +293,25 @@ extract_sis_data <- function(sis_data_dir = getwd(),
   if (all(primary_options2 %in% ts_options)) {
     cli::cli_alert_info("One of the following categories can be a Primary time series:")
     cli::cli_ul(primary_options2)
-      if (interactive()) {
+    if (interactive()) {
       primary1 <- readline("Which category should be chosen? ")
-        if (primary1 %notin% primary_options2) {
-          cli::cli_abort("Invalid Primary category specified. Please choose from: {primary_options2}.")
-        } else {
-          primary <- c(primary, primary1)
-        }
+      if (primary1 %notin% primary_options2) {
+        cli::cli_abort("Invalid Primary category specified. Please choose from: {primary_options2}.")
       } else {
-        primary <- c(primary, primary_options2[1])
-        cli::cli_alert_info("Primary categor{?y/ies} set to {primary} by default in non-interactive mode.")
+        primary <- c(primary, primary1)
       }
+    } else {
+      primary <- c(primary, primary_options2[1])
+      cli::cli_alert_info("Primary categor{?y/ies} set to {primary} by default in non-interactive mode.")
+    }
   } else if (any(primary_options2 %in% ts_options)) {
     primary <- c(primary, ts_options[ts_options %in% primary_options2])
   }
-  
-  if (length(primary) == 0) {primary <- NA} 
-  
+
+  if (length(primary) == 0) {
+    primary <- NA
+  }
+
   category_pairs <- list(
     "fishing_mortality" = "Fmort",
     "recruitment" = "Recruitment",
@@ -306,41 +320,41 @@ extract_sis_data <- function(sis_data_dir = getwd(),
     "biomass" = "Biomass",
     "index" = "Index"
   )
-  
+
   primary <- unlist(lapply(primary, function(x) category_pairs[[x]]))
-  
+
   # identify sis_assmt_template AS_B_UNIT values if coded
   b_unit <- assmt_dat$Value[assmt_dat$Variable == "AS_B_UNIT"]
   if (as.numeric(b_unit) %in% 1:8) {
     b_unit <- switch(b_unit,
-                     "1" = "Metric Tons",
-                     "2" = "Thousand Metric Tons",
-                     "3" = "Adult spawners - Natural & Hatchery - Escapement",
-                     "4" = "Adult spawners - Hatchery - Escapement",
-                     "5" = "Adult spawners - Natural - Escapement",
-                     "6" = "Number of Eggs",
-                     "7" = "kg / tow",
-                     "8" = "Number of Fish"
+      "1" = "Metric Tons",
+      "2" = "Thousand Metric Tons",
+      "3" = "Adult spawners - Natural & Hatchery - Escapement",
+      "4" = "Adult spawners - Hatchery - Escapement",
+      "5" = "Adult spawners - Natural - Escapement",
+      "6" = "Number of Eggs",
+      "7" = "kg / tow",
+      "8" = "Number of Fish"
     )
   }
-  
+
   # identify sis_assmt_template AS_F_UNIT values if coded
   f_unit <- assmt_dat$Value[assmt_dat$Variable == "AS_F_UNIT"]
   if (as.numeric(f_unit) %in% 1:7) {
     f_unit <- switch(f_unit,
-                     "1" = "Apical F",
-                     "2" = "Fully-selected F",
-                     "3" = "Exploitation Rate",
-                     "4" = "Relative F",
-                     "5" = "Metric Tons",
-                     "6" = "1 - SPR",
-                     "7" = "Z - M"
+      "1" = "Apical F",
+      "2" = "Fully-selected F",
+      "3" = "Exploitation Rate",
+      "4" = "Relative F",
+      "5" = "Metric Tons",
+      "6" = "1 - SPR",
+      "7" = "Z - M"
     )
   }
-  
-  
+
+
   ts_dat_filled <- all_summaries |>
-    dplyr::rename_with(~ "Year", .cols = matches("^year$")) |>
+    dplyr::rename_with(~"Year", .cols = matches("^year$")) |>
     tidyr::pivot_longer(cols = -Year, names_to = "Category", values_to = "Value") |>
     dplyr::mutate(Primary = ifelse(tolower(Category) %in% tolower(primary), "Y", "")) |>
     dplyr::mutate(Description = dplyr::case_when(
@@ -356,16 +370,16 @@ extract_sis_data <- function(sis_data_dir = getwd(),
       Category == "Biomass" ~ as.character(b_unit),
       Category == "Spawners" ~ as.character(b_unit),
       Category == "Fmort" ~ as.character(f_unit),
-      Category == "Index" ~ "", 
+      Category == "Index" ~ "",
       Category == "Catch" ~ ifelse(kqs$value[kqs$key_quantity == "tot.catch.units"] == " (mt)", "Metric Tons", kqs$value[kqs$key_quantity == "tot.catch.units"]),
       Category == "Recruitment" ~ "Number of Fish",
       TRUE ~ NA
     )) |>
     dplyr::relocate(Value, .after = Unit)
-  
+
   # Ensure ts_dat_filled has same cols as ts_dat
   if (isFALSE(any(colnames(ts_dat_filled) == colnames(ts_dat)))) {
-      cli::cli_abort("Time series data does not match template structure.")
+    cli::cli_abort("Time series data does not match template structure.")
   }
 
   # if assmt_dat$Value is NA and Default is 95, change it to Default
@@ -374,11 +388,11 @@ extract_sis_data <- function(sis_data_dir = getwd(),
       assmt_dat$Value[i] <- assmt_dat$Default[i]
     }
   }
-  
+
   # export files
   assmt_dat_path <- fs::path(sis_data_dir, "sis_assmt_template.csv")
   ts_dat_path <- fs::path(sis_data_dir, "sis_ts_template.csv")
-  
+
   if (file.exists(assmt_dat_path) | file.exists(ts_dat_path)) {
     cli::cli_alert_info("Existing sis_assmt_template.csv or sis_ts_template.csv found in {sis_data_dir}.")
     overwrite <- readline("Do you want to overwrite the existing files? (y/n): ")
diff --git a/R/plot_spr.R b/R/plot_spr.R
index 7b6e00b8..a818c1e2 100644
--- a/R/plot_spr.R
+++ b/R/plot_spr.R
@@ -1,7 +1,7 @@
 #' Plot spawning potential ratio (SPR)
 #'
 #' @inheritParams plot_spawning_biomass
-#' 
+#'
 #' @param ylab String. Y-axis label to show.
 #'
 #' @returns A plot showing spawning potential ratio (SPR).
@@ -47,13 +47,12 @@ plot_spawning_potential_ratio <- function(
   ylab = NULL,
   ...
 ) {
-  
   # Filter data for spr
   prepared_data <- filter_data(
     dat = dat,
     label_name = "spr",
     geom = geom,
-    #TODO: change this to era once stockplotr::example_data updated
+    # TODO: change this to era once stockplotr::example_data updated
     era = NULL,
     group = group,
     facet = facet,
@@ -63,19 +62,19 @@ plot_spawning_potential_ratio <- function(
   ) |>
     # filter NA from year
     dplyr::filter(!is.na(year))
-  
-  if(nrow(prepared_data)==0){
+
+  if (nrow(prepared_data) == 0) {
     # We could potentially make this more informative if we know the model type
     # by reporting the common MODULE used by other packages (e.g., DERIVED_QUANTITIES
     # for SS3 models, or t.series for BAM models).
     cli::cli_alert(glue::glue("There is no data available to be plotted. Try selecting a different module."))
   }
-  
+
   # Process data
   processed_data <- process_data(
     dat = prepared_data,
     group = group,
-    facet = facet#
+    facet = facet #
     # method = "sum"
   )
   prepared_data <- processed_data[[1]]
@@ -93,7 +92,7 @@ plot_spawning_potential_ratio <- function(
   if (!is.null(group)) {
     if (group %notin% colnames(prepared_data)) group <- NULL
   }
-  
+
   # inital base plot
   plt <- plot_timeseries(
     dat = prepared_data,
@@ -104,10 +103,14 @@ plot_spawning_potential_ratio <- function(
     facet = facet,
     ...
   ) +
-    ggplot2::geom_hline(yintercept = 1,
-                        color = "grey") +
-    ggplot2::geom_hline(yintercept = 0,
-                        color = "grey") +
+    ggplot2::geom_hline(
+      yintercept = 1,
+      color = "grey"
+    ) +
+    ggplot2::geom_hline(
+      yintercept = 0,
+      color = "grey"
+    ) +
     add_reference_line(
       dat = dat,
       ref_line = ref_line,
@@ -115,7 +118,7 @@ plot_spawning_potential_ratio <- function(
       scale_amount = 1
     ) +
     theme_noaa()
-  
+
 
   if (length(unique(prepared_data$group_var)) == 1) {
     plt <- plt + ggplot2::theme(legend.position = "none")
@@ -125,13 +128,13 @@ plot_spawning_potential_ratio <- function(
   if (make_rda) {
     # TODO: Update caption, alt text, and quantities once plot is finalized
     # Obtain relevant key quantities for captions/alt text
-    
+
     spr.start.year <- min(prepared_data$year)
     spr.end.year <- max(prepared_data$year)
     spr.min <- min(prepared_data$estimate) |> round(digits = 3)
     spr.max <- max(prepared_data$estimate) |> round(digits = 3)
     spr.ref.pt <- as.character(ref_line)
-    
+
     # calculate & export key quantities
     export_kqs(
       spr.start.year,
diff --git a/R/plot_stock_recruitment.R b/R/plot_stock_recruitment.R
index a7dbe279..aa0f60f6 100644
--- a/R/plot_stock_recruitment.R
+++ b/R/plot_stock_recruitment.R
@@ -100,7 +100,7 @@ plot_stock_recruitment <- function(
   # Extract spawning biomass
   sb <- filter_data(
     dat = dat |>
-    dplyr::filter(!is.na(year)),
+      dplyr::filter(!is.na(year)),
     label_name = "spawning biomass",
     geom = "point",
     era = era,
diff --git a/R/table_total_catch.R b/R/table_total_catch.R
index bb1f3529..e2d3ca60 100644
--- a/R/table_total_catch.R
+++ b/R/table_total_catch.R
@@ -58,9 +58,11 @@ table_total_catch <- function(
   # Filter data for catch
   prepared_data <- filter_data(
     dat = dat |>
-      dplyr::filter(!is.na(year),
-                    !is.na(estimate),
-                    label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")),
+      dplyr::filter(
+        !is.na(year),
+        !is.na(estimate),
+        label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")
+      ),
     label_name = "^catch",
     geom = "line",
     era = era,
diff --git a/R/utils_plot.R b/R/utils_plot.R
index 691b52fd..086eb490 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -568,32 +568,32 @@ reference_line <- function(
   ref_line_val <- ref_line[[1]]
   reference <- names(ref_line)
 
-  switch(direction, 
+  switch(direction,
     "h" = {
-        list(
-          # Add geom for ref line
-          ggplot2::geom_hline(
-            data = data.frame(yintercept = ref_line_val, model = model_name, group_var = "1"),
-            ggplot2::aes(
-              yintercept = ref_line_val / scale_amount,
-              color = interaction(model, group_var) # model
-            ),
-            linetype = "dashed",
-            show.legend = FALSE
+      list(
+        # Add geom for ref line
+        ggplot2::geom_hline(
+          data = data.frame(yintercept = ref_line_val, model = model_name, group_var = "1"),
+          ggplot2::aes(
+            yintercept = ref_line_val / scale_amount,
+            color = interaction(model, group_var) # model
           ),
-          # add line annotation
-          ggplot2::annotate(
-            geom = "text",
-            # TODO: need to change this for general process
-            x = -Inf,
-            y = ref_line_val / scale_amount,
-            label = glue::glue("{reference}"), # glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
-            parse = TRUE,
-            hjust = -0.05, # slight offset so text doesn't hit border
-            vjust = -0.5 # , #slightly above line
-            # size = 5 # this is not foolproof
-          )
+          linetype = "dashed",
+          show.legend = FALSE
+        ),
+        # add line annotation
+        ggplot2::annotate(
+          geom = "text",
+          # TODO: need to change this for general process
+          x = -Inf,
+          y = ref_line_val / scale_amount,
+          label = glue::glue("{reference}"), # glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
+          parse = TRUE,
+          hjust = -0.05, # slight offset so text doesn't hit border
+          vjust = -0.5 # , #slightly above line
+          # size = 5 # this is not foolproof
         )
+      )
     },
     "v" = {
       list(
@@ -622,7 +622,6 @@ reference_line <- function(
       )
     }
   )
-  
 }
 
 #------------------------------------------------------------------------------
diff --git a/man/calculate_reference_point.Rd b/man/calculate_reference_point.Rd
index 86e38307..e7f50726 100644
--- a/man/calculate_reference_point.Rd
+++ b/man/calculate_reference_point.Rd
@@ -13,7 +13,7 @@ returned from \link[stockplotr]{convert_output}.
 If inputting a list of tibbles, the first tibble's reference point defined
 in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.}
 
-\item{reference_name}{a string of the name of the reference point (e.g. "spawning biomass msy")}
+\item{reference_name}{String. Name of the reference point (e.g. "spawning biomass msy")}
 
 \item{lbs}{Logical. TRUE/FALSE; indicate whether to convert the y-axis values from
 kilograms to pounds. The default units match the default in the
diff --git a/man/plot_spawning_potential_ratio.Rd b/man/plot_spawning_potential_ratio.Rd
new file mode 100644
index 00000000..a424822d
--- /dev/null
+++ b/man/plot_spawning_potential_ratio.Rd
@@ -0,0 +1,128 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_spr.R
+\name{plot_spawning_potential_ratio}
+\alias{plot_spawning_potential_ratio}
+\title{Plot spawning potential ratio (SPR)}
+\usage{
+plot_spawning_potential_ratio(
+  dat,
+  geom = "line",
+  group = NULL,
+  facet = NULL,
+  ref_line = "target",
+  era = "time",
+  module = NULL,
+  interactive = TRUE,
+  make_rda = FALSE,
+  figures_dir = getwd(),
+  ylab = NULL,
+  ...
+)
+}
+\arguments{
+\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()})
+returned from \link[stockplotr]{convert_output}.
+
+If inputting a list of tibbles, the first tibble's reference point defined
+in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.}
+
+\item{geom}{String. Geom used for the plot.
+
+Default: "line".
+
+Options: "line", "point", or "area"}
+
+\item{group}{String. Single column that groups the data.
+
+Set group = "none" to summarize data over all indexing values.
+
+Default: NULL
+Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL}
+
+\item{facet}{Character vector. Column name or names used for faceting.
+
+Default: NULL}
+
+\item{ref_line}{String or named vector. Reference point name (and value if
+custom). When multiple models are being compared, a reference line for each
+model will appear, if desired. The following options can be used to customize
+the reference line:
+\enumerate{
+\item all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc
+\item custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+\item input vector of labels - ref_line = c("msy", "target")
+}
+
+Default: "msy"
+
+Options: (including, but not limited to) "target", "msy", and "unfished"
+If the reference point is not found in the data, set ref_line = c("name" = value).}
+
+\item{era}{String. Era of data.
+
+Default: "time"
+
+Options: "early", "time", "fore" (forecast), or NULL (all data)}
+
+\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}.
+If selecting >1 module, place them in a vector like c("module1", "module2").
+
+Default: NULL
+
+If the interactive and >1 module_name is found, user will select the
+module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}}
+
+\item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive.
+
+Default: \code{FALSE}}
+
+\item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and
+make an automated caption and alternative text in the form of an \code{rda} object. If TRUE,
+the rda will be exported to the folder indicated in the argument "figures_dir".
+
+Default: \code{FALSE}.}
+
+\item{figures_dir}{Path. Path to the "figures" folder.
+
+Default: \code{getwd()}
+
+The folder is created within the path if it does not exist.}
+
+\item{ylab}{String. Y-axis label to show.}
+
+\item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}}
+}
+\value{
+A plot showing spawning potential ratio (SPR).
+}
+\description{
+Plot spawning potential ratio (SPR)
+}
+\details{
+The input is from an assessment model output file
+translated to a standardized output (\link[stockplotr]{convert_output}).
+There are options to return a \code{ggplot2} object or export an .rda object
+containing associated caption and alternative text for the figure.
+}
+\examples{
+plot_spawning_potential_ratio(
+  dat = stockplotr:::example_data,
+  unit_label = "metric tons",
+  group = "fleet",
+  interactive = FALSE,
+  make_rda = FALSE,
+  ylab = "SPR"
+)
+plot_spawning_potential_ratio(
+  dat = stockplotr:::example_data,
+  unit_label = "metric tons",
+  facet = "fleet",
+  module = "DERIVED_QUANTITIES",
+  interactive = FALSE,
+  make_rda = FALSE,
+  ylab = "(1-SPR)/(1-SPR_ref)"
+)
+}
+\seealso{
+\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}}
+}
diff --git a/tests/testthat/helper-test_functions.R b/tests/testthat/helper-test_functions.R
index 78688e07..7b35a04e 100644
--- a/tests/testthat/helper-test_functions.R
+++ b/tests/testthat/helper-test_functions.R
@@ -1,32 +1,34 @@
 #' Check for the existence and remove .rda files from test environment
-#' 
+#'
 #' Checks for the existence of `dir` and `filename` as well as the
-#' existence of "captions_alt_text.csv" and "key_quantities.csv". 
-#' Files are removed upon completion of checks. 
-#' 
+#' existence of "captions_alt_text.csv" and "key_quantities.csv".
+#' Files are removed upon completion of checks.
+#'
 #' For testing only.
-#' 
+#'
 #' @param filename String. filename of figure/table .rda file
 #' @param dir String. directory where filename exists
 #' @param figs_or_tables String. whether check for a "figures" or "tables" internal directory
-#' 
+#'
 #' DEFAULT: "figures"
-#' 
-check_and_remove_tmp_files <- function(filename, dir=fs::path(getwd()), figs_or_tables="figures"){
-    # expect that both figures dir and the abundance_at_age_figure.rda file exist
-    expect_true(dir.exists(dir)) # this check needs to exist in case save dir isnt getwd()
-    expect_true(dir.exists(fs::path(dir, figs_or_tables)))
-    expect_true(file.exists(fs::path(dir, figs_or_tables, filename)))
+#'
+check_and_remove_tmp_files <- function(filename, dir = fs::path(getwd()), figs_or_tables = "figures") {
+  # expect that both figures dir and the abundance_at_age_figure.rda file exist
+  expect_true(dir.exists(dir)) # this check needs to exist in case save dir isnt getwd()
+  expect_true(dir.exists(fs::path(dir, figs_or_tables)))
+  expect_true(file.exists(fs::path(dir, figs_or_tables, filename)))
 
-    # erase temporary testing files
-    captions_file <- fs::path(dir, "captions_alt_text.csv")
-    keyquant_file <- fs::path(dir, "key_quantities.csv")
+  # erase temporary testing files
+  captions_file <- fs::path(dir, "captions_alt_text.csv")
+  keyquant_file <- fs::path(dir, "key_quantities.csv")
 
-    if(fs::file_exists(captions_file))
-        fs::file_delete(captions_file)
+  if (fs::file_exists(captions_file)) {
+    fs::file_delete(captions_file)
+  }
 
-    if(fs::file_exists(keyquant_file))
-        fs::file_delete(keyquant_file)
+  if (fs::file_exists(keyquant_file)) {
+    fs::file_delete(keyquant_file)
+  }
 
-    unlink(fs::path(dir, figs_or_tables), recursive = T)
+  unlink(fs::path(dir, figs_or_tables), recursive = T)
 }
diff --git a/tests/testthat/test-convert_output.R b/tests/testthat/test-convert_output.R
index 12b477a8..fc495216 100644
--- a/tests/testthat/test-convert_output.R
+++ b/tests/testthat/test-convert_output.R
@@ -14,7 +14,7 @@ test_that("convert_output works for SS3", {
     "BigSkate_2019"
   )
 
-  models_to_test <- all_models[grepl(paste0(model_names, collapse="|"), all_models)]
+  models_to_test <- all_models[grepl(paste0(model_names, collapse = "|"), all_models)]
 
   # Loop through each model directory and check convert_output function
   for (i in seq_along(models_to_test)) {
diff --git a/tests/testthat/test-extract_sis_data.R b/tests/testthat/test-extract_sis_data.R
index 60a09c1f..0d2eb31c 100644
--- a/tests/testthat/test-extract_sis_data.R
+++ b/tests/testthat/test-extract_sis_data.R
@@ -1,16 +1,20 @@
 test_that("extract_sis_data() runs with all possible rdas present", {
   save_all_plots(stockplotr::example_data)
   table_total_catch(stockplotr::example_data,
-                    module = "TIME_SERIES",
-                    interactive = FALSE,
-                    make_rda = TRUE)
+    module = "TIME_SERIES",
+    interactive = FALSE,
+    make_rda = TRUE
+  )
 
   files <- c(
-    fs::path("figures",
-             c("biomass_figure.rda", "spawning_biomass_figure.rda", "abundance_at_age_figure.rda", "fishing_mortality_figure.rda",  "index_figure.rda")
-             ),
-    fs::path("tables",
-             "total_catch_table.rda")
+    fs::path(
+      "figures",
+      c("biomass_figure.rda", "spawning_biomass_figure.rda", "abundance_at_age_figure.rda", "fishing_mortality_figure.rda", "index_figure.rda")
+    ),
+    fs::path(
+      "tables",
+      "total_catch_table.rda"
+    )
   )
 
   expect_true(all(file.exists(files)))
diff --git a/tests/testthat/test-plot_natural_mortality.R b/tests/testthat/test-plot_natural_mortality.R
index fb241f72..59cd88a7 100644
--- a/tests/testthat/test-plot_natural_mortality.R
+++ b/tests/testthat/test-plot_natural_mortality.R
@@ -2,7 +2,7 @@ test_that("plot_natural_mortality generate without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
     plot_natural_mortality(
-      stockplotr::example_data, 
+      stockplotr::example_data,
       module = "Natural_Mortality",
       interactive = FALSE
     )
diff --git a/tests/testthat/test-plot_spawning_potential_ratio.R b/tests/testthat/test-plot_spawning_potential_ratio.R
index 75b19161..aec6d6d9 100644
--- a/tests/testthat/test-plot_spawning_potential_ratio.R
+++ b/tests/testthat/test-plot_spawning_potential_ratio.R
@@ -3,7 +3,7 @@ test_that("plot_spawning_potential_ratio generates plots without errors", {
   expect_no_error(
     plot_spawning_potential_ratio(stockplotr::example_data, interactive = FALSE)
   )
-  
+
   # expect error-free plot with many arguments
   expect_no_error(
     plot_spawning_potential_ratio(
@@ -14,7 +14,7 @@ test_that("plot_spawning_potential_ratio generates plots without errors", {
     )
   )
 
-  
+
   # expect ggplot object is returned
   expect_s3_class(
     plot_spawning_potential_ratio(
@@ -35,11 +35,11 @@ test_that("rda file made when indicated", {
     make_rda = TRUE,
     figures_dir = getwd()
   )
-  
+
   # expect that both figures dir and the spawning_biomass_figure.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "figures")))
   expect_true(file.exists(fs::path(getwd(), "figures", "spawning_potential_ratio_figure.rda")))
-  
+
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
   file.remove(fs::path(getwd(), "key_quantities.csv"))
diff --git a/vignettes/extract-sis-data.Rmd b/vignettes/extract-sis-data.Rmd
index 2c52b7e0..cfe7f33c 100644
--- a/vignettes/extract-sis-data.Rmd
+++ b/vignettes/extract-sis-data.Rmd
@@ -134,4 +134,4 @@ The `extract_sis_data()` workflow extracts at most one time series for each cate
 
 * **Fmort, Recruitment, & Catch**: Multiple time series allowed per category, but exactly one must be marked Primary = Y per category.
 * **Spawners & Biomass**: Multiple time series allowed across both categories, but only one time series combined across both Spawners and Biomass can be marked Primary = Y.
-* **Index**: Multiple time series allowed, but none can be marked Primary = Y (always N).
\ No newline at end of file
+* **Index**: Multiple time series allowed, but none can be marked Primary = Y (always N).