From 300efc8516291d47b2deade5de0ed679559222d2 Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Mon, 11 May 2026 19:39:17 +0000
Subject: [PATCH] style and docs: run devtools::document() and style with
 styler or air

---
 DESCRIPTION                                 |   2 +-
 R/convert_output.R                          | 165 ++++++++++----------
 R/data.R                                    |   6 +-
 R/html_all_figs_tables.R                    |   4 +-
 R/plot_abundance_at_age.R                   |   6 +-
 R/plot_biomass.R                            |  12 +-
 R/plot_biomass_at_age.R                     |   8 +-
 R/plot_catch_comp.R                         |   2 +-
 R/plot_fishing_mortality.R                  |  11 +-
 R/plot_indices.R                            |  10 +-
 R/plot_landings.R                           |   8 +-
 R/plot_natural_mortality.R                  |   6 +-
 R/plot_recruitment.R                        |   8 +-
 R/plot_spawning_biomass.R                   |  44 +++---
 R/plot_stock_recruitment.R                  |   8 +-
 R/process_data.R                            |  18 +--
 R/save_all_plots.R                          |   4 +-
 R/table_landings.R                          |   6 +-
 R/utils.R                                   |  27 ++--
 R/utils_plot.R                              |   3 +-
 R/utils_rda.R                               |   6 +-
 man/convert_output.Rd                       |   4 +-
 man/example_data.Rd                         |   2 +-
 man/plot_landings.Rd                        |   2 +-
 man/plot_spawning_biomass.Rd                |   2 +-
 man/process_data.Rd                         |   2 +-
 man/reference_line.Rd                       |   2 +-
 man/stockplotr-package.Rd                   |   1 +
 tests/testthat/test-plot_biomass.R          |   2 +-
 tests/testthat/test-plot_spawning_biomass.R |   1 -
 tests/testthat/test-save_all_plots.R        |  16 +-
 31 files changed, 197 insertions(+), 201 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 57273285..7ff57014 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -65,9 +65,9 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
+Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.3.3
diff --git a/R/convert_output.R b/R/convert_output.R
index 92aff989..15b8fca9 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -14,11 +14,11 @@
 #'
 #' @returns A reformatted and standardized version of assessment model results
 #'         for application in building a stock assessment reports and to easily
-#'         adapt results among regional assessments. 
-#' @details The resulting object is simply a transformed and machine readable 
-#' version of a model output file. Converted data frame is always returned. 
+#'         adapt results among regional assessments.
+#' @details The resulting object is simply a transformed and machine readable
+#' version of a model output file. Converted data frame is always returned.
 #' It will also be saved if save_dir is not NULL.
-#' 
+#'
 #'
 #' @export
 #'
@@ -118,28 +118,27 @@ convert_output <- function(
   if (is.character(file)) {
     if (is.null(model)) {
       model <- switch(stringr::str_extract(file, "\\.([^.]+)$"),
-                      ".sso" = {
-                        cli::cli_alert_info("Processing Stock Synthesis output file...")
-                        "ss3"
-                      },
-                      ".rdat" = {
-                        cli::cli_alert_info("Processing BAM output file...")
-                        "bam"
-                      },
-                      ".rds" = {
-                        cli::cli_alert_info("Processing WHAM output file...")
-                        "wham"
-                      },
-                      ".RDS" = {
-                        cli::cli_alert_info("Processing FIMS output file...")
-                        "fims"
-                      },
-                      
-                      cli::cli_abort("Unknown file type. Please indicate model.")
+        ".sso" = {
+          cli::cli_alert_info("Processing Stock Synthesis output file...")
+          "ss3"
+        },
+        ".rdat" = {
+          cli::cli_alert_info("Processing BAM output file...")
+          "bam"
+        },
+        ".rds" = {
+          cli::cli_alert_info("Processing WHAM output file...")
+          "wham"
+        },
+        ".RDS" = {
+          cli::cli_alert_info("Processing FIMS output file...")
+          "fims"
+        },
+        cli::cli_abort("Unknown file type. Please indicate model.")
       )
     }
   } else {
-    model <- switch (class(file)[1],
+    model <- switch(class(file)[1],
       "fims" = {
         cli::cli_alert_info("Processing FIMS output file...")
         "fims"
@@ -151,7 +150,7 @@ convert_output <- function(
       cli::cli_abort("Unknown file type. Please indicate model.")
     )
   }
-  
+
 
   #### SS3 ####
   # Convert SS3 output Report.sso file
@@ -1798,26 +1797,26 @@ convert_output <- function(
     } else {
       dat <- file
     }
-    
+
     # Extract or use fleet names
     if (is.null(fleet_names)) {
       fleet_names <- names(dat$estimated_params$index_ln_q)
     }
-    
+
     # Output fleet names in console
     cli::cli_alert_info("Identified fleet names:")
     cli::cli_alert_info("{fleet_names}")
     # Create list for morphed dfs to go into (for rbind later)
     out_list <- list()
-    
+
     factors <- c("year", "fleet", "fleet_name", "age", "sex", "area", "seas", "season", "time", "era", "subseas", "subseason", "platoon", "platoo", "growth_pattern", "gp", "nsim", "age_a")
     errors <- c("StdDev", "sd", "se", "SE", "cv", "CV", "stddev")
     # units <- c("mt", "lbs", "eggs")
-    
+
     ##### Loop ####
     for (p in (2:length(dat))[-c(6, 9, 10)]) {
       extract <- dat[p]
-      module_name <- names(extract) 
+      module_name <- names(extract)
       cli::cli_alert_info("Processing {module_name}")
       if (module_name == "sdrep") {
         ##### sdrep ####
@@ -1836,30 +1835,32 @@ convert_output <- function(
         values <- values |>
           dplyr::left_join(
             {
-              values |> dplyr::group_by(label) |> dplyr::count() 
+              values |>
+                dplyr::group_by(label) |>
+                dplyr::count()
             },
             by = "label"
-          ) 
+          )
         # make year column
         year_col <- rep(
           file[["data_list"]]$styr:file[["data_list"]]$projyr,
           length(unique(
-            dplyr::filter(values_count, n == length(file[["data_list"]]$styr:file[["data_list"]]$projyr)) |> 
+            dplyr::filter(values_count, n == length(file[["data_list"]]$styr:file[["data_list"]]$projyr)) |>
               dplyr::pull(label)
           ))
         )
-      
+
         df2 <- values |>
           dplyr::filter(n == length(file[["data_list"]]$styr:file[["data_list"]]$projyr)) |>
           dplyr::mutate(year = year_col)
-          
-        df2 <- values |> 
-                dplyr::filter(
-                  n != length(file[["data_list"]]$styr:file[["data_list"]]$projyr)
-                ) |>
-                dplyr::mutate(year = NA) |>
+
+        df2 <- values |>
+          dplyr::filter(
+            n != length(file[["data_list"]]$styr:file[["data_list"]]$projyr)
+          ) |>
+          dplyr::mutate(year = NA) |>
           rbind(df2)
-        
+
         # Extract parameter values ts
         par_fixes <- data.frame(
           label = names(extract[[1]]$par.fixed),
@@ -1872,23 +1873,23 @@ convert_output <- function(
           dplyr::left_join(
             par_fixes_count,
             by = "label"
-          ) 
-        
+          )
+
         year_col_par_fix <- rep(
           file[["data_list"]]$styr:file[["data_list"]]$endyr,
           length(unique(
-            dplyr::filter(par_fixes_count, n == length(file[["data_list"]]$styr:file[["data_list"]]$endyr)) |> 
+            dplyr::filter(par_fixes_count, n == length(file[["data_list"]]$styr:file[["data_list"]]$endyr)) |>
               dplyr::pull(label)
           ))
         )
-        
+
         df3 <- par_fixes |>
           dplyr::filter(n == length(file[["data_list"]]$styr:file[["data_list"]]$endyr)) |>
           dplyr::mutate(year = year_col_par_fix)
-        df3 <- par_fixes |> 
+        df3 <- par_fixes |>
           dplyr::filter(
             n != length(file[["data_list"]]$styr:file[["data_list"]]$endyr)
-            ) |>
+          ) |>
           dplyr::mutate(year = NA) |>
           rbind(df3) |>
           dplyr::mutate(
@@ -1898,13 +1899,13 @@ convert_output <- function(
         # not sure how pop_scalar is indexed
         # not sure how log_index_hat is indexes
         # Did not use r_sd for the error in rec bc used it from the other element in the list
-        
+
         df4 <- rbind(df2, df3) |>
           dplyr::select(-n) |>
           dplyr::mutate(
             module_name = module_name
           )
-        
+
         df4[setdiff(tolower(names(out_new)), tolower(names(df4)))] <- NA
         out_list[[names(extract)]] <- df4
       } else if (module_name == "data_list") {
@@ -1912,9 +1913,9 @@ convert_output <- function(
         # Only extract specific quantity needs
         # comp_data?, index_data, catch_data, weight, Ftarget, Flimit
         data_list_list <- list()
-        
+
         ####### Indices ####
-        # Extract index_data 
+        # Extract index_data
         df_index <- extract[[1]]$index_data |>
           # rename all columns to lower case to match standard
           dplyr::rename_with(tolower) |>
@@ -1931,7 +1932,7 @@ convert_output <- function(
           ) |>
           dplyr::select(-c(fleet_code, q_block))
         cli::cli_alert_info("'Selectivity_block' values located in 'block' columns.")
-        
+
         # check if species > 1
         if (length(unique(df_index$species)) > 1) {
           cli::cli_abort("Not currently compatible for multispecies.")
@@ -1939,7 +1940,7 @@ convert_output <- function(
           df_index <- df_index |>
             dplyr::select(-species)
         }
-        
+
         # expand df long to have obs and pred in same column with label
         df_index_long <- df_index |>
           tidyr::pivot_longer(
@@ -1948,19 +1949,19 @@ convert_output <- function(
             values_to = "estimate"
           ) |>
           dplyr::mutate(
-            module_name = names(extract)#,
+            module_name = names(extract) # ,
             # era = dplyr::if_else(
             #   year > dat$data_list$endyr,
             #   "fore",
             #   NA_character_
             # )
           )
-        
+
         df_index_long[setdiff(tolower(names(out_new)), tolower(names(df_index_long)))] <- NA
         data_list_list[["index_data"]] <- df_index_long
-        
+
         ####### Catch indexing ####
-        # Extract catch_data and align with log_index_hat and catch_h 
+        # Extract catch_data and align with log_index_hat and catch_h
         # Modify sdrep in outlist to include index
         df_catch <- extract[[1]]$catch_data |>
           # dplyr::filter(!is.na(Catch)) |>
@@ -1988,28 +1989,28 @@ convert_output <- function(
             values_to = "estimate"
           ) |>
           dplyr::select(-c(fleet_code, species))
-        
+
         # Remove fleet names if do not match object
         # if (unique(df_catch$fleet) %notin% fleet_names) {
         #   df_catch <- df_catch |>
         #     dplyr::mutate(fleet = NA)
         # }
-        
+
         if (length(unique(df_catch$month)) == 1) {
           df_catch$month <- NA
         }
         df_catch[setdiff(tolower(names(out_new)), tolower(names(df_catch)))] <- NA
         data_list_list[["catch_data"]] <- df_catch
-        
+
         ####### Comp indexing ####
         df_comp_obs <- dat$data_list$comp_data |>
           dplyr::rename_with(tolower) |>
           dplyr::mutate(
             label = "indices_observed"
           )
-        
-        indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))] 
-        
+
+        indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
+
         df_comp_pred <- dplyr::select(df_comp_obs, dplyr::all_of(indexing_vars_cols)) |>
           dplyr::cross_join(as.data.frame(dat$quantities$age_hat)) |>
           tidyr::pivot_longer(
@@ -2022,9 +2023,9 @@ convert_output <- function(
           dplyr::mutate(
             label = "composition_predicted",
             # NOTE: the below age mutate slows down code
-            age = stringr::str_replace(age, "V","")
+            age = stringr::str_replace(age, "V", "")
           )
-        
+
         # Finish adjusting comp_obs
         # pivot obs data
         df_comp_obs <- df_comp_obs |>
@@ -2037,32 +2038,31 @@ convert_output <- function(
           dplyr::mutate(
             label = "composition_observed",
             # NOTE: the below age mutate slows down code
-            age = stringr::str_replace(age, "comp_","")
+            age = stringr::str_replace(age, "comp_", "")
           )
-          
+
         df_comp <- rbind(df_comp_obs, df_comp_pred) |>
           # TODO: do I need to filter sample size by <3 for confidentiality or does this not apply?
           dplyr::select(-c(age0_length1, fleet_code, sample_size))
-        
+
         df_catch[setdiff(tolower(names(out_new)), tolower(names(df_catch)))] <- NA
         data_list_list[["comp_data"]] <- df_catch
-        
+
         # final df for data_list module
         new_df <- Reduce(rbind, data_list_list)
         out_list[[names(extract)]] <- new_df
-        
       } else if (is.list(extract[[1]])) { # indicates vector and list
         ##### remaining lmnts ####
         if (any(vapply(extract[[1]], is.matrix, FUN.VALUE = logical(1)))) {
-                ##############################################################
+          ##############################################################
           df <- extract[[1]] |>
             expand_element(fleet_names = fleet_names) |>
             dplyr::mutate(
               module_name = module_name
-            ) |> suppressWarnings()
+            ) |>
+            suppressWarnings()
           df[setdiff(tolower(names(out_new)), tolower(names(df)))] <- NA
           out_list[[names(extract)]] <- df
-          
         } else if (any(vapply(extract[[1]], is.vector, FUN.VALUE = logical(1)))) { # all must be a vector to work - so there must be conditions for dfs with a mix
           extract_list <- list()
           # mod_name1 <- names(extract)
@@ -2072,7 +2072,7 @@ convert_output <- function(
               # mod_name2 <- glue::glue("{module_name}_{names(extract[[1]][i])}")
               # comment out message once finished development
               cli::cli_alert_info("Processing {names(extract[[1]][i])}")
-              
+
               df <- extract[[1]][i][[1]] |>
                 expand_element(fleet_names = fleet_names) |>
                 dplyr::mutate(
@@ -2102,12 +2102,12 @@ convert_output <- function(
       } else {
         cli::cli_alert_warning("Not compatible yet.")
       }
-    # } else if (is.list(extract[[1]])) { # list only
-    # } else if (is.matrix(extract[[1]])) { # matrix only
-    # } else {
-    #   cli::cli_alert_warning(paste(names(extract), " not compatible.", sep = ""))
-    # } # close if statement
-  } # close loop over objects listed in dat file
+      # } else if (is.list(extract[[1]])) { # list only
+      # } else if (is.matrix(extract[[1]])) { # matrix only
+      # } else {
+      #   cli::cli_alert_warning(paste(names(extract), " not compatible.", sep = ""))
+      # } # close if statement
+    } # close loop over objects listed in dat file
     # Finish out df
     out_new <- Reduce(rbind, out_list) |>
       # Add era as factor into BAM conout
@@ -2116,12 +2116,11 @@ convert_output <- function(
         label = tolower(label),
         # set era
         era = dplyr::if_else(
-          year > dat$data_list$endyr, 
+          year > dat$data_list$endyr,
           "fore",
           "time"
         )
       )
-    
   } else {
     cli::cli_abort(c(
       message = "Output file not compatible.",
@@ -2177,13 +2176,13 @@ convert_output <- function(
   #   con_file <- system.file("resources", "rceattle_var_names.csv", package = "stockplotr", mustWork = TRUE)
   #   var_names_sheet <- utils::read.csv(con_file, na.strings = "")
   # }
-  
+
   # 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)
   # 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 (file.exists(con_file)) {
     # Remove 'X' column if it exists
     var_names_sheet <- var_names_sheet |>
diff --git a/R/data.R b/R/data.R
index 3f758d14..ffc31b2c 100644
--- a/R/data.R
+++ b/R/data.R
@@ -1,6 +1,6 @@
 #' SS3 Example data
 #'
-#' Included data set that represents a Report.sso file converted using 
+#' Included data set that represents a Report.sso file converted using
 #' convert_output(). This example is from the 2022 Petrale sole stock assessment.
 #'
 #' @format A tibble with 591109 rows and 33 variables:
@@ -39,5 +39,5 @@
 #'   \item{count}{indexing column of data}
 #'   \item{block}{indexing column of data}
 #' }
-#' 
-"example_data"
\ No newline at end of file
+#'
+"example_data"
diff --git a/R/html_all_figs_tables.R b/R/html_all_figs_tables.R
index 9c0fddae..983ad392 100644
--- a/R/html_all_figs_tables.R
+++ b/R/html_all_figs_tables.R
@@ -7,11 +7,11 @@
 #'
 #' @returns A folder ("all_tables_figures") in your working directory containing
 #' html and qmd files that show all tables and figures.
-#' 
+#'
 #' @seealso
 #' \code{\link[asar:create_figures_doc]{asar::create_figures_doc()}},
 #' \code{\link[asar:create_tables_doc]{asar::create_tables_doc()}}
-#' 
+#'
 #'
 #' @export
 #'
diff --git a/R/plot_abundance_at_age.R b/R/plot_abundance_at_age.R
index 91714d58..71c6967f 100644
--- a/R/plot_abundance_at_age.R
+++ b/R/plot_abundance_at_age.R
@@ -22,14 +22,14 @@
 #' ("rda_files") that will be created if the argument `make_rda` = TRUE.
 #' Default is the working directory.
 #' @returns A plot showing total abundance (or numbers) at age.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_aa()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index 8c41ba6e..e2b94bdb 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -11,14 +11,14 @@
 #'   regardless of how it is specified in `dat`. Other possibilities may include
 #'   "target", "MSY", and "unfished".
 #' @returns A plot showing total biomass.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -108,7 +108,7 @@ plot_biomass <- function(
         )
     }
   }
-    
+
   # Process data for indexing/grouping
   # TODO: check and add into process_data step to summarize when theres >1 label
   processing <- process_data(
@@ -116,12 +116,12 @@ plot_biomass <- function(
     group,
     facet
   )
-  
+
   # variable <- processing[[1]]
   prepared_data <- processing[[1]]
   group <- processing[[2]]
   if (!is.null(processing[[3]])) facet <- processing[[3]]
-  
+
 
   plt <- plot_timeseries(
     dat = prepared_data,
diff --git a/R/plot_biomass_at_age.R b/R/plot_biomass_at_age.R
index 54e7ccac..d10e605d 100644
--- a/R/plot_biomass_at_age.R
+++ b/R/plot_biomass_at_age.R
@@ -8,16 +8,16 @@
 #' @param interactive TRUE/FALSE; indicate whether the environment in which the
 #' function is operating  is interactive. This bypasses some options for
 #' filtering when preparing data for the plot. Default is FALSE.
-#' 
+#'
 #' @returns A plot showing total biomass at age.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_aa()], [export_kqs()], [insert_kqs()], [create_rda()]
-#'  
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/plot_catch_comp.R b/R/plot_catch_comp.R
index 560aec60..9b092aa0 100644
--- a/R/plot_catch_comp.R
+++ b/R/plot_catch_comp.R
@@ -19,7 +19,7 @@
 #' will select the most relevant module if more than 1 exists.
 #'
 #' @returns A plot showing catch or landings composition.
-#' 
+#'
 #' @details This plot is made only when catch or landings are explicitly named
 #' in the output file. The current plot function does not combine all sources of
 #' catch.
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index 7bf802ed..c301478c 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -3,14 +3,14 @@
 #' @inheritParams plot_spawning_biomass
 #'
 #' @returns A plot showing fishing mortality over time.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [reference_line()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -85,13 +85,12 @@ plot_fishing_mortality <- function(
 
   ### Make RDA ----
   if (make_rda) {
-    
     F.min <- min(prepared_data$estimate) |> round(digits = 3)
     F.max <- max(prepared_data$estimate) |> round(digits = 3)
-    
+
     export_kqs(F.min, F.max)
     insert_kqs(F.min, F.max)
-    
+
     F.ref.pt <- as.character(ref_line)
     F.start.year <- min(prepared_data$year)
     F.end.year <- max(prepared_data$year)
diff --git a/R/plot_indices.R b/R/plot_indices.R
index fa9fbb90..92bb5670 100644
--- a/R/plot_indices.R
+++ b/R/plot_indices.R
@@ -8,14 +8,14 @@
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
 #' @returns A plot showing the expected and predicted indices.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_obsvpred()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -70,7 +70,7 @@ plot_indices <- function(
     prepared_data <- prepared_data |>
       dplyr::filter(fleet %in% focus)
   }
-  
+
   processed_data <- process_data(
     dat = prepared_data,
     group = group,
@@ -116,7 +116,7 @@ plot_indices <- function(
     facet_formula <- stats::reformulate(facet)
     plt <- plt + ggplot2::facet_wrap(facet_formula, scales = "free")
   }
-  
+
   ### Make RDA ----
   if (make_rda) {
     # Obtain relevant key quantities for captions/alt text
diff --git a/R/plot_landings.R b/R/plot_landings.R
index d1967521..ffe7876f 100644
--- a/R/plot_landings.R
+++ b/R/plot_landings.R
@@ -3,14 +3,14 @@
 #' @inheritParams plot_spawning_biomass
 #'
 #' @returns A plot showing cumulative landings over time.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -48,7 +48,7 @@ plot_landings <- function(
     cli::cli_alert_info("Unit label was not changed. Setting unit_label to 'lbs'.")
     unit_label <- "lbs"
   }
-  
+
   # Units
   landings_label <- label_magnitude(
     label = "Landings",
diff --git a/R/plot_natural_mortality.R b/R/plot_natural_mortality.R
index 6bb1e6af..de85727c 100644
--- a/R/plot_natural_mortality.R
+++ b/R/plot_natural_mortality.R
@@ -3,14 +3,14 @@
 #' @inheritParams plot_spawning_biomass
 #'
 #' @returns A plot showing natural mortality at age.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/plot_recruitment.R b/R/plot_recruitment.R
index c8cbef99..cedae3f0 100644
--- a/R/plot_recruitment.R
+++ b/R/plot_recruitment.R
@@ -4,14 +4,14 @@
 #' @param unit_label units for recruitment
 #'
 #' @returns A plot showing recruitment over time.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
-#' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] 
-#' 
+#'
+#' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()]
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 176f0cd0..acf4d586 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -38,7 +38,7 @@
 #' Default: "metric tons"
 #' @param lbs A logical value indicating whether to convert the y-axis values from
 #' kilograms to pounds. The default units match the default in the
-#' unit_label argument - 'metric tons'. 
+#' unit_label argument - 'metric tons'.
 #'
 #' Default: `FALSE`
 #' @param module (Optional) A string indicating the module_name found in `dat`.
@@ -68,14 +68,14 @@
 #'
 #' Default: `FALSE`
 #' @param ... Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}
-#' 
+#'
 #' @return A plot showing spawning biomass over time.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @note
 #' All plotting functions automatically recognize indexing variables and will
 #' use them in groupings and/or facetting. @seealso [process_data()].
@@ -123,7 +123,7 @@ plot_spawning_biomass <- function(
     cli::cli_alert_info("Unit label was not changed. Setting unit_label to 'lbs'.")
     unit_label <- "lbs"
   }
-  
+
   # TODO: Fix the unit label if scaling. Maybe this is up to the user to do if
   #       they want something scaled then they have to supply a better unit name
   #       or we create a helper function to do this.
@@ -135,10 +135,10 @@ plot_spawning_biomass <- function(
         label = "Spawning Biomass",
         unit_label = unit_label,
         scale_amount = dplyr::if_else(
-          lbs, 
-          ifelse(unit_label %in% c("mt", "mts", "metric tons", "metric ton"), 1000, 1) * scale_amount, 
+          lbs,
+          ifelse(unit_label %in% c("mt", "mts", "metric tons", "metric ton"), 1000, 1) * scale_amount,
           scale_amount
-          ),
+        ),
         legend = TRUE
       )
     }
@@ -157,24 +157,24 @@ plot_spawning_biomass <- function(
 
   # Filter data for spawning biomass
   prepared_data <- filter_data(
-      dat = dat,
-      label_name = ifelse(relative, glue::glue("spawning_biomass_spawning_biomass_{ref_line}|spawning_biomass_ratio"), "^spawning_biomass$"),
-      geom = geom,
-      era = era,
-      group = group,
-      facet = facet,
-      module = module,
-      scale_amount = scale_amount,
-      interactive = interactive
-    )
-  
+    dat = dat,
+    label_name = ifelse(relative, glue::glue("spawning_biomass_spawning_biomass_{ref_line}|spawning_biomass_ratio"), "^spawning_biomass$"),
+    geom = geom,
+    era = era,
+    group = group,
+    facet = facet,
+    module = module,
+    scale_amount = scale_amount,
+    interactive = interactive
+  )
+
   if (relative) {
     if (nrow(prepared_data) == 0) {
       cli::cli_abort("No data found for relative biomass. Please check that your data contains a label for 'biomass_biomass_unfished'.")
       stop()
     }
-  }  
-  
+  }
+
   # process the data for grouping
   processing <- process_data(
     dat = prepared_data,
@@ -187,7 +187,7 @@ plot_spawning_biomass <- function(
   plot_data <- processing[[1]]
   group <- processing[[2]]
   if (!is.null(processing[[3]])) facet <- processing[[3]]
-  
+
   # Override grouping variable when there is only NA's
   if (!is.null(group)) {
     if (group %notin% colnames(plot_data)) group <- NULL
diff --git a/R/plot_stock_recruitment.R b/R/plot_stock_recruitment.R
index 673841d9..ff3ba387 100644
--- a/R/plot_stock_recruitment.R
+++ b/R/plot_stock_recruitment.R
@@ -9,15 +9,15 @@
 #' @param recruitment_label units for recruitment
 #'
 #' @returns A plot showing the stock recruitment relationship.
-#' 
+#'
 #' @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 `ggplot2` object or export an .rda object
 #' containing associated caption and alternative text for the figure.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()]
-#' 
-#' 
+#'
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/process_data.R b/R/process_data.R
index 08559c48..3200b409 100644
--- a/R/process_data.R
+++ b/R/process_data.R
@@ -12,7 +12,7 @@
 #' variable(s) of the data.
 #' @param lbs A logical value indicating whether to convert the y-axis values from
 #' kilograms to pounds. The default units match the default in the
-#' unit_label argument - 'metric tons'. 
+#' unit_label argument - 'metric tons'.
 #'
 #' Default: `FALSE`
 #' @param method A string describing the method of summarizing data when group
@@ -27,11 +27,11 @@
 #' \item{facet}{A string or vector of strings identifying the faceting
 #' variable(s) of the data. If NULL, no faceting variable is identified. Any
 #' identified indexed variables found in this function will be added to facet.}
-#' 
+#'
 #' @details Automatically detects potential grouping and faceting data from a
 #' dataframe output from \link[stockplotr]{filter_data}.
-#' 
-#' 
+#'
+#'
 #' @export
 #'
 #' @examples {
@@ -314,7 +314,7 @@ process_data <- function(
       group <- NULL
     }
   }
-  
+
   # Ensure that index_variables -- group or facets are non-numeric to be plotted accurately
   data <- data |>
     dplyr::mutate(
@@ -323,14 +323,14 @@ process_data <- function(
         as.character
       )
     )
-  
+
   if (lbs) {
     data <- data |>
       dplyr::mutate(
         # multiple by conversion from kg to lbs -- default then becomes thousands of lbs
         estimate = (estimate * 2.20462),
-        estimate_lower = NA_real_, #(estimate_lower * 2.20462),
-        estimate_upper = NA_real_, #(estimate_upper * 2.20462)
+        estimate_lower = NA_real_, # (estimate_lower * 2.20462),
+        estimate_upper = NA_real_, # (estimate_upper * 2.20462)
       )
   }
 
@@ -352,7 +352,7 @@ process_data <- function(
 #'
 #' @returns A dataframe of processed data ready for formatting into a table.
 #' @details Input is an object created with \link[stockplotr]{filter_data}.
-#' 
+#'
 #' @export
 #'
 #' @examples {
diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index 84030372..9d9132b8 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -43,9 +43,9 @@
 #' @param proportional T/F to scale size of bubble plots
 #'
 #' @returns Rda files for each figure/table.
-#' 
+#'
 #' @seealso [convert_output()], [create_rda()]
-#' 
+#'
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
 #'
diff --git a/R/table_landings.R b/R/table_landings.R
index 52d14eac..46028440 100644
--- a/R/table_landings.R
+++ b/R/table_landings.R
@@ -14,15 +14,15 @@
 #' "landings_predicted", "landings".
 #'
 #' @returns A table ready of landed catch by fleet and year.
-#' 
+#'
 #' @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 [gt::gt()] object or export an rda object
 #' containing a gt-based table, caption, and LaTeX-based table.
-#' 
+#'
 #' @seealso [convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()]
 #' @export
-#' 
+#'
 #' @examples
 #' table_landings(stockplotr::example_data)
 #'
diff --git a/R/utils.R b/R/utils.R
index 6ba1da95..08cb3b82 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -198,14 +198,14 @@ SS3_extract_fleet <- function(dat, vers) {
 # input_list = unlisted object from model output
 
 expand_element <- function(input_list, fleet_names = "Pollock") {
-  
   # Use map_dfr to iterate over each element of the list
   # .id = "origin_var" keeps track of which list element the data came from
   purrr::imap_dfr(input_list, function(x, name) {
-    
     # Skip empty/null elements immediately
-    if (length(x) == 0 || is.null(x)) return(NULL)
-    
+    if (length(x) == 0 || is.null(x)) {
+      return(NULL)
+    }
+
     # Standardize current element 'x' to a Long Data Frame
     if (!is.null(dim(x)) && length(dim(x)) > 1) {
       # Handles Arrays/Matrices
@@ -225,25 +225,25 @@ expand_element <- function(input_list, fleet_names = "Pollock") {
         )) |>
         dplyr::select(-dim_info)
     }
-    
+
     # Process the labels
     df |>
       dplyr::mutate(
         label_init = as.character(label_init),
-        
+
         # Pull parameter name
         label = dplyr::case_when(
           stringr::str_extract(label_init, "^[^\\.]+") == "rec_pars" ~ stringr::str_extract(label_init, "[^\\.]+$"),
           TRUE ~ stringr::str_extract(label_init, "^[^\\.]+")
-          ),
-        
+        ),
+
         # Extract Age
         age = dplyr::case_when(
-          grepl("age", label_init, ignore.case = TRUE) ~ 
+          grepl("age", label_init, ignore.case = TRUE) ~
             as.numeric(stringr::str_extract(label_init, "(?<=\\.[Aa]ge)[0-9]+(?=\\.|$)")),
           TRUE ~ NA_real_
         ),
-        
+
         # Extract Sex
         sex = dplyr::case_when(
           grepl("Sex.combined|combined", label_init, ignore.case = TRUE) ~ "combined",
@@ -251,16 +251,16 @@ expand_element <- function(input_list, fleet_names = "Pollock") {
           grepl("male", label_init, ignore.case = TRUE) ~ "male", # check havent seen example of this!
           TRUE ~ NA_character_
         ),
-        
+
         # Extract Year (4 digits)
         year = dplyr::case_when(
           grepl("[0-9]{4}", label_init) ~ as.numeric(stringr::str_extract(label_init, "[0-9]{4}")),
           TRUE ~ NA_real_
         ),
-        
+
         # Extract Fleet
         fleet = dplyr::case_when(
-          grepl(paste0(fleet_names, collapse = "|"), label_init) ~ 
+          grepl(paste0(fleet_names, collapse = "|"), label_init) ~
             stringr::str_extract(label_init, paste0(fleet_names, collapse = "|")),
           TRUE ~ NA_character_
         )
@@ -270,4 +270,3 @@ expand_element <- function(input_list, fleet_names = "Pollock") {
       dplyr::select(-label_init)
   })
 }
-
diff --git a/R/utils_plot.R b/R/utils_plot.R
index e294167d..7f76b890 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -26,7 +26,7 @@
 #' @details The user can create a line, point, or area plot, where the x-axis is
 #' year and y can vary for any time series quantity. Currently, grouping is
 #' restricted to one group where faceting can be any number of facets.
-#' 
+#'
 #' @export
 #'
 #' @examples
@@ -952,7 +952,6 @@ calculate_reference_point <- function(
   } else {
     ref_line_val
   }
-  
 }
 
 #------------------------------------------------------------------------------
diff --git a/R/utils_rda.R b/R/utils_rda.R
index abe31d1f..b22ebaa6 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -56,7 +56,7 @@ fill_in_kqs <- function(df, ...) {
 #' added next to the names of the key quantities specified as ellipsis
 #' arguments. File is saved as "key_quantities.csv" to the working directory.
 #' @seealso [fill_in_kqs()], [insert_kqs()]
-#' 
+#'
 #' @examples \dontrun{
 #' export_kqs(
 #'   F.min,
@@ -96,7 +96,7 @@ export_kqs <- function(...) {
 #' and alternative text for figures and tables, with key quantities inserted
 #' into the "captions_alt_text_template.csv" template's placeholders.
 #' @seealso [fill_in_kqs()], [export_kqs()]
-#' 
+#'
 #' @examples \dontrun{
 #' insert_kqs(
 #'   F.min,
@@ -582,7 +582,7 @@ extract_caps_alttext <- function(topic_label = NULL,
 #' @returns An rda file with a figure's ggplot, caption, and alternative text, or
 #' a table's gt-based table, caption, and LaTeX-based table.
 #' @seealso [create_rda()], [extract_caps_alttext()]
-#' 
+#'
 #' @export
 #'
 #' @examples
diff --git a/man/convert_output.Rd b/man/convert_output.Rd
index 5dad2c6e..2d238a1a 100644
--- a/man/convert_output.Rd
+++ b/man/convert_output.Rd
@@ -27,8 +27,8 @@ A reformatted and standardized version of assessment model results
 Format stock assessment output files to a standardized format.
 }
 \details{
-The resulting object is simply a transformed and machine readable 
-version of a model output file. Converted data frame is always returned. 
+The resulting object is simply a transformed and machine readable
+version of a model output file. Converted data frame is always returned.
 It will also be saved if save_dir is not NULL.
 }
 \examples{
diff --git a/man/example_data.Rd b/man/example_data.Rd
index 90e120b4..3cbf0892 100644
--- a/man/example_data.Rd
+++ b/man/example_data.Rd
@@ -46,7 +46,7 @@ A tibble with 591109 rows and 33 variables:
 example_data
 }
 \description{
-Included data set that represents a Report.sso file converted using 
+Included data set that represents a Report.sso file converted using
 convert_output(). This example is from the 2022 Petrale sole stock assessment.
 }
 \keyword{datasets}
diff --git a/man/plot_landings.Rd b/man/plot_landings.Rd
index 534fde54..a2419108 100644
--- a/man/plot_landings.Rd
+++ b/man/plot_landings.Rd
@@ -50,7 +50,7 @@ Default: NULL}
 
 \item{lbs}{A logical value indicating whether to convert the y-axis values from
 kilograms to pounds. The default units match the default in the
-unit_label argument - 'metric tons'. 
+unit_label argument - 'metric tons'.
 
 Default: `FALSE`}
 
diff --git a/man/plot_spawning_biomass.Rd b/man/plot_spawning_biomass.Rd
index fff4f851..595807d4 100644
--- a/man/plot_spawning_biomass.Rd
+++ b/man/plot_spawning_biomass.Rd
@@ -65,7 +65,7 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)}
 
 \item{lbs}{A logical value indicating whether to convert the y-axis values from
 kilograms to pounds. The default units match the default in the
-unit_label argument - 'metric tons'. 
+unit_label argument - 'metric tons'.
 
 Default: `FALSE`}
 
diff --git a/man/process_data.Rd b/man/process_data.Rd
index ce7bb7cb..e4e2b6b2 100644
--- a/man/process_data.Rd
+++ b/man/process_data.Rd
@@ -18,7 +18,7 @@ variable(s) of the data.}
 
 \item{lbs}{A logical value indicating whether to convert the y-axis values from
 kilograms to pounds. The default units match the default in the
-unit_label argument - 'metric tons'. 
+unit_label argument - 'metric tons'.
 
 Default: `FALSE`}
 
diff --git a/man/reference_line.Rd b/man/reference_line.Rd
index fc8fade9..5005a441 100644
--- a/man/reference_line.Rd
+++ b/man/reference_line.Rd
@@ -23,7 +23,7 @@ Default: 1}
 
 \item{lbs}{A logical value indicating whether to convert the y-axis values from
 kilograms to pounds. The default units match the default in the
-unit_label argument - 'metric tons'. 
+unit_label argument - 'metric tons'.
 
 Default: `FALSE`}
 }
diff --git a/man/stockplotr-package.Rd b/man/stockplotr-package.Rd
index ce67c60e..0dcd782c 100644
--- a/man/stockplotr-package.Rd
+++ b/man/stockplotr-package.Rd
@@ -22,6 +22,7 @@ Useful links:
 
 Authors:
 \itemize{
+  \item Samantha Schiano \email{samantha.schiano@noaa.gov} (\href{https://orcid.org/0009-0003-3744-6428}{ORCID})
   \item Sophie Breitbart \email{sophie.breitbart@noaa.gov} (\href{https://orcid.org/0000-0001-9641-9786}{ORCID}) [contributor]
   \item Steve Saul \email{steven.saul@noaa.gov}
 }
diff --git a/tests/testthat/test-plot_biomass.R b/tests/testthat/test-plot_biomass.R
index b9e87194..f9b40089 100644
--- a/tests/testthat/test-plot_biomass.R
+++ b/tests/testthat/test-plot_biomass.R
@@ -7,7 +7,7 @@ load(file.path(
 # Below is now moot bc relative is coming from model results
 # Make another sample dataset for testing relative
 # n <- 448
-# 
+#
 # sim_df <- data.frame(
 #   label = "biomass",
 #   estimate = rlnorm(n, meanlog = 6.2, sdlog = 1.6),
diff --git a/tests/testthat/test-plot_spawning_biomass.R b/tests/testthat/test-plot_spawning_biomass.R
index 8dc1d811..267c2094 100644
--- a/tests/testthat/test-plot_spawning_biomass.R
+++ b/tests/testthat/test-plot_spawning_biomass.R
@@ -59,4 +59,3 @@ test_that("rda file made when indicated", {
   file.remove(fs::path(getwd(), "key_quantities.csv"))
   unlink(fs::path(getwd(), "figures"), recursive = T)
 })
-
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index ee5bc68c..1b268f39 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -41,15 +41,15 @@ test_that("save_all_plots works when all figures/tables are plotted", {
   )
 
   # expect that the tables are all created with expected names
-   tab_base_temp_files <- c(
+  tab_base_temp_files <- c(
     # "bnc_table.rda",
-   #  "indices.abundance_table.rda",
-     "landings_table.rda"
-   )
-   expect_equal(
-     list.files(fs::path(getwd(), "tables")),
-     tab_base_temp_files
-   )
+    #  "indices.abundance_table.rda",
+    "landings_table.rda"
+  )
+  expect_equal(
+    list.files(fs::path(getwd(), "tables")),
+    tab_base_temp_files
+  )
 
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))