From a911351f17cc946842f708b6b196e80b9a13f8f3 Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 13 Nov 2026 22:10:01 +0000
Subject: [PATCH] style and docs: run devtools::document() and style with
 styler or air

---
 DESCRIPTION                                  |   4 +-
 R/add_caption_alt_text.R                     |  24 +-
 R/conout_bam.R                               |  40 +--
 R/conout_rceattle.R                          |  68 ++--
 R/conout_ss3.R                               |  96 ++---
 R/convert_output.R                           |   9 +-
 R/data.R                                     |  12 +-
 R/extract_sis_data.R                         | 352 ++++++++++---------
 R/plot_abundance_at_age.R                    |  10 +-
 R/plot_biomass.R                             |  27 +-
 R/plot_biomass_at_age.R                      |  16 +-
 R/plot_catch_at_age.R                        |  10 +-
 R/plot_discard.R                             |  10 +-
 R/plot_fishing_mortality.R                   |  12 +-
 R/plot_landings.R                            |  14 +-
 R/plot_natural_mortality.R                   |   8 +-
 R/plot_recruitment.R                         |   8 +-
 R/plot_recruitment_deviations.R              |   4 +-
 R/plot_selectivity.R                         |  10 +-
 R/plot_spawning_biomass.R                    |  28 +-
 R/plot_spr.R                                 |  38 +-
 R/plot_stock_recruitment.R                   |  12 +-
 R/save_all_plots.R                           | 101 +++---
 R/table_biomass_abundance_catch.R            |  24 +-
 R/table_index.R                              |  22 +-
 R/table_landings.R                           |  19 +-
 R/table_projections.R                        |  32 +-
 R/table_total_catch.R                        |  20 +-
 R/utils_plot.R                               |  47 ++-
 R/utils_rda.R                                |  25 +-
 data-raw/DATASET_RCEATTLE.R                  |   5 +-
 man/save_all_plots.Rd                        |   2 +-
 man/table_landings.Rd                        |   3 +-
 man/table_projections.Rd                     |  12 +-
 tests/testthat/helper-test_functions.R       |  42 +--
 tests/testthat/test-check_data.R             |  12 +-
 tests/testthat/test-convert_output.R         |   4 +-
 tests/testthat/test-export_rda.R             |  84 ++---
 tests/testthat/test-extract_sis_data.R       |  40 ++-
 tests/testthat/test-plot_natural_mortality.R |   2 +-
 tests/testthat/test-plot_recruitment.R       |   1 -
 tests/testthat/test-plot_spr.R               |   4 +-
 tests/testthat/test-save_all_plots.R         | 188 +++++-----
 tests/testthat/test-table_landings.R         |   2 +-
 vignettes/extract-sis-data.Rmd               |   2 +-
 45 files changed, 770 insertions(+), 735 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ce341c63..b24a373e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -61,10 +61,10 @@ Suggests:
     r4ss,
     rmarkdown,
     testthat (>= 3.0.0)
-Remotes:
-    r4ss/r4ss
 VignetteBuilder: 
     knitr
+Remotes:
+    r4ss/r4ss
 Config/roxygen2/version: 8.1.1
 Config/testthat/edition: 3
 Config/testthat/parallel: true
diff --git a/R/add_caption_alt_text.R b/R/add_caption_alt_text.R
index 87def075..a2c1584d 100644
--- a/R/add_caption_alt_text.R
+++ b/R/add_caption_alt_text.R
@@ -4,25 +4,25 @@
 #' caption, and alt_text for a figure or table not present in stockplotr.
 #'
 #' @inheritParams create_rda
-#' 
-#' @param topic_label String. Figure/table label. For automated matching in 
+#'
+#' @param topic_label String. Figure/table label. For automated matching in
 #' asar-based report, it must match the label in your plot's chunk options, MINUS
-#' the "fig-" or "tab-". For example, the label "custom_table1" would match up 
+#' the "fig-" or "tab-". For example, the label "custom_table1" would match up
 #' properly with the "tbl-custom_table1" code chunk label.
-#' 
+#'
 #' @param caption String. Figure/table caption.
-#' 
+#'
 #' @param alt_text String. Figure alternative text. Unnecessary for text-based tables.
-#' 
+#'
 #' Default: ""
-#' 
+#'
 #' @param dir Path. Path to the existing captions_alt_text.csv file that will be
 #' updated with the new caption and alt text.
 #'
 #' Default: file.path(getwd(), "captions_alt_text.csv")
 #'
 #' @export
-#' 
+#'
 #' @examples \dontrun{
 #' add_caption_alt_text(
 #'   topic_label = "my_topic",
@@ -38,22 +38,22 @@ add_caption_alt_text <- function(topic_label,
                                  alt_text = "",
                                  dir = file.path(getwd(), "captions_alt_text.csv")) {
   captions_alt_text <- utils::read.csv(dir)
-  
+
   if (fig_or_table == tolower("figure") & alt_text == "") {
     cli::cli_alert_warning("No alt text provided for figure {topic_label}.")
     cli::cli_alert_warning("Figure alt text is necessary to pass asar report accessibility checks.")
     cli::cli_alert_info("Learn how to write descriptive alt text with the asar 'Increasing Report Accessibility' vignette: {.url https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#alternative-text}.")
   }
-  
+
   new_row <- data.frame(
     label = topic_label,
     type = fig_or_table,
     caption = caption,
     alt_text = alt_text
   )
-  
+
   captions_alt_text <- rbind(captions_alt_text, new_row)
-  
+
   utils::write.csv(
     captions_alt_text,
     file = dir,
diff --git a/R/conout_bam.R b/R/conout_bam.R
index 83215146..ed198d0d 100644
--- a/R/conout_bam.R
+++ b/R/conout_bam.R
@@ -1,5 +1,5 @@
 #' Code to convert BAM output to standard framework.
-#' 
+#'
 #' Does not change naming conventions.
 #'
 #' @inheritParams convert_output
@@ -8,13 +8,13 @@
 #'
 #' @returns Reshaped data frame.
 conout_bam <- function(
-    file,
-    out_new,
-    fleet_names = NULL
+  file,
+  out_new,
+  fleet_names = NULL
 ) {
   # Extract values from BAM output - model file after following ADMB2R
   dat <- dget(file)
-  
+
   # Find fleet names
   if (is.null(fleet_names)) {
     # Extract names from indices
@@ -24,13 +24,13 @@ conout_bam <- function(
     # Extract names from landings
     landings <- dat$t.series |>
       dplyr::select(dplyr::contains("L.") & dplyr::contains(".ob") |
-                      dplyr::contains("D.") & dplyr::contains(".ob"))
+        dplyr::contains("D.") & dplyr::contains(".ob"))
     fleets_land <- stringr::str_extract(as.vector(colnames(landings)), "(?<=L\\.)\\w+(?=\\.ob)")
     fleets_disc <- stringr::str_extract(as.vector(colnames(landings)), "(?<=D\\.)\\w+(?=\\.ob)")
     # Extract names from lof F dev
     parm <- dat$parm.tvec |>
       dplyr::select(dplyr::contains("log.F.dev.") |
-                      dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
+        dplyr::contains("log.F.dev.") & dplyr::contains(".D"))
     # fleets_parm_D <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+(?=\\.D)")
     fleets_parm <- stringr::str_extract(as.vector(colnames(parm)), "(?<=log\\.F\\.dev\\.)\\w+")
     fleets <- unique(tolower(c(fleets_ind, fleets_land, fleets_disc, fleets_parm)))
@@ -48,13 +48,13 @@ conout_bam <- function(
   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")
   # argument for function when model == BAM
   # fleet_names <- c("cl", "cL","cp","mrip","ct", "hb", "HB", "comm","Mbft","CVID")
-  
+
   ##### BAM loop ----
   # Extract data from list fit to output df
   # Loop over all items to output each object/transform
@@ -97,7 +97,7 @@ conout_bam <- function(
               df <- df |>
                 dplyr::rename_with(
                   ~ ifelse(max(as.numeric(df$year)) < 50,
-                           c("age_a"), c("year")
+                    c("age_a"), c("year")
                   ),
                   year
                 )
@@ -127,7 +127,7 @@ conout_bam <- function(
                     TRUE ~ names(extract[[1]][i])
                   )
                   # label_init = names(extract[[1]][i]),
-                  
+
                   # label = dplyr::case_when(
                   #   is.na(fleet) ~ names(extract[[1]][i]),
                   #   TRUE ~ stringr::str_replace(tolower(label), paste(".", fleet_names, sep = "", collapse = "|"), "")
@@ -505,7 +505,7 @@ conout_bam <- function(
       cli::cli_alert_warning(paste(names(extract), " not compatible.", sep = ""))
     } # close if statement
   } # close loop over objects listed in dat file
-  
+
   # Place out_list into a single data frame
   # VIRG, INIT, TIME, FORE
   out_new <- Reduce(rbind, out_list) |>
@@ -515,15 +515,15 @@ conout_bam <- function(
       label = tolower(label)
     )
   # if (model == "bam") {
-    out_new <- dplyr::mutate(
-      out_new,
-      era = dplyr::case_when(
-        year < dat$parms$styr ~ "init",
-        year >= dat$parms$styr & year <= dat$parms$endyr ~ "time",
-        year > dat$parms$endyr ~ "fore",
-        TRUE ~ NA
-      )
+  out_new <- dplyr::mutate(
+    out_new,
+    era = dplyr::case_when(
+      year < dat$parms$styr ~ "init",
+      year >= dat$parms$styr & year <= dat$parms$endyr ~ "time",
+      year > dat$parms$endyr ~ "fore",
+      TRUE ~ NA
     )
+  )
   # }
   return(out_new)
 }
diff --git a/R/conout_rceattle.R b/R/conout_rceattle.R
index 117fdae4..4289faa5 100644
--- a/R/conout_rceattle.R
+++ b/R/conout_rceattle.R
@@ -1,5 +1,5 @@
 #' Code to convert Rceattle output to standard framework.
-#' 
+#'
 #' Does not change naming conventions.
 #'
 #' @inheritParams convert_output
@@ -8,9 +8,9 @@
 #'
 #' @returns Reshaped data frame.
 conout_rceattle <- function(
-    file,
-    out_new,
-    fleet_names = NULL
+  file,
+  out_new,
+  fleet_names = NULL
 ) {
   # Want to extract and set values from:
   # quantities, sdrep, and estimated_params
@@ -28,7 +28,7 @@ conout_rceattle <- function(
   } else {
     dat <- file
   }
-  
+
   # The standardized output describes one stock and has no species dimension,
   # but CEATTLE is a multispecies model. A multispecies fit's `sdrep` holds
   # nspp * nyrs values per label, which fails the `n == length(styr:projyr)`
@@ -57,22 +57,22 @@ conout_rceattle <- function(
       i = "Subset the fit to a single species before converting."
     ))
   }
-  
+
   # Extract or use fleet names
   if (is.null(fleet_names)) {
     fleet_names <- names(dat$estimated_params$index_log_q)
   }
-  
+
   # Output fleet names in console
   cli::cli_alert_info("Identified fleet names:")
   cli::cli_alert_info("{fleet_names}")
   # Create list for morphed dfs to go into (for rbind later)
   out_list <- list()
-  
+
   factors <- c("year", "fleet", "fleet_name", "age", "sex", "area", "seas", "season", "time", "era", "subseas", "subseason", "platoon", "platoo", "growth_pattern", "gp", "nsim", "age_a")
   errors <- c("StdDev", "sd", "se", "SE", "cv", "CV", "stddev")
   # units <- c("mt", "lbs", "eggs")
-  
+
   ##### Loop ####
   # Select the modules by name rather than by position. An Rceattle fit's
   # element list depends on how it was fitted -- `phase = TRUE` adds
@@ -125,18 +125,18 @@ conout_rceattle <- function(
             dplyr::pull(label)
         ))
       )
-      
+
       df2 <- values |>
         dplyr::filter(n == length(dat[["data_list"]]$styr:dat[["data_list"]]$projyr)) |>
         dplyr::mutate(year = year_col)
-      
+
       df2 <- values |>
         dplyr::filter(
           n != length(dat[["data_list"]]$styr:dat[["data_list"]]$projyr)
         ) |>
         dplyr::mutate(year = NA) |>
         rbind(df2)
-      
+
       # Extract parameter values ts
       # The standard errors of the fixed effects are the square root of the
       # diagonal of cov.fixed, in the same order as par.fixed.
@@ -170,7 +170,7 @@ conout_rceattle <- function(
           par_fixes_count,
           by = "label"
         )
-      
+
       year_col_par_fix <- rep(
         dat[["data_list"]]$styr:dat[["data_list"]]$endyr,
         length(unique(
@@ -178,7 +178,7 @@ conout_rceattle <- function(
             dplyr::pull(label)
         ))
       )
-      
+
       df3 <- par_fixes |>
         dplyr::filter(n == length(dat[["data_list"]]$styr:dat[["data_list"]]$endyr)) |>
         dplyr::mutate(year = year_col_par_fix)
@@ -191,13 +191,13 @@ conout_rceattle <- function(
       # not sure how pop_scalar is indexed
       # not sure how log_index_hat is indexes
       # Did not use r_sd for the error in rec bc used it from the other element in the list
-      
+
       df4 <- rbind(df2, df3) |>
         dplyr::select(-n) |>
         dplyr::mutate(
           module_name = module_name
         )
-      
+
       df4[setdiff(tolower(names(out_new)), tolower(names(df4)))] <- NA
       out_list[[names(extract)]] <- df4
     } else if (module_name == "data_list") {
@@ -205,7 +205,7 @@ conout_rceattle <- function(
       # Only extract specific quantity needs
       # comp_data?, index_data, catch_data, weight, Ftarget, Flimit
       data_list_list <- list()
-      
+
       ####### Indices ####
       # Extract index_data
       df_index <- extract[[1]]$index_data |>
@@ -227,7 +227,7 @@ conout_rceattle <- function(
         # still needing to be dropped from an older one.
         dplyr::select(-dplyr::any_of(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$species)) > 1) {
         cli::cli_abort("Not currently compatible for multispecies.")
@@ -235,7 +235,7 @@ conout_rceattle <- function(
         df_index <- df_index |>
           dplyr::select(-species)
       }
-      
+
       # expand df long to have obs and pred in same column with label
       df_index_long <- df_index |>
         tidyr::pivot_longer(
@@ -252,10 +252,10 @@ conout_rceattle <- function(
           # )
           label = stringr::str_replace_all(label, "indices", "index")
         )
-      
+
       df_index_long[setdiff(tolower(names(out_new)), tolower(names(df_index_long)))] <- NA
       data_list_list[["index_data"]] <- df_index_long
-      
+
       ####### Catch indexing ####
       # Extract catch_data and align with log_index_hat and catch_h
       # Modify sdrep in outlist to include index
@@ -289,28 +289,28 @@ conout_rceattle <- function(
           values_to = "estimate"
         ) |>
         dplyr::select(-c(fleet_code, species))
-      
+
       # Remove fleet names if do not match object
       # if (unique(df_catch$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 = "index_observed"
         )
-      
+
       indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
-      
+
       # `age_hat` holds one row per row of `comp_data`, in the same order, so
       # it binds column-wise. cross_join() paired every observation with the
       # whole prediction matrix instead, which is a Cartesian product: on the
@@ -332,7 +332,7 @@ conout_rceattle <- function(
           # NOTE: the below age mutate slows down code
           age = stringr::str_replace(age, "agehat_", "")
         )
-      
+
       # Finish adjusting comp_obs
       # pivot obs data
       df_comp_obs <- df_comp_obs |>
@@ -347,7 +347,7 @@ conout_rceattle <- function(
           # NOTE: the below age mutate slows down code
           age = stringr::str_replace(age, "comp_", "")
         )
-      
+
       df_comp <- rbind(df_comp_obs, df_comp_pred) |>
         # Match the index and catch frames: the standard names the fleet
         # `fleet`, carries no `fleet_name` or `species`, and every row states
@@ -357,10 +357,10 @@ conout_rceattle <- function(
         dplyr::select(-dplyr::any_of("species")) |>
         # 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_comp[setdiff(tolower(names(out_new)), tolower(names(df_comp)))] <- NA
       data_list_list[["comp_data"]] <- df_comp
-      
+
       # final df for data_list module
       # rbind() rather than bind_rows(): every frame has already been padded
       # to the standard column set above, so rbind() succeeds and keeps the
@@ -379,7 +379,7 @@ conout_rceattle <- function(
       # Rceattle stores sex 1 as females, or both sexes when nsex = 1.
       sex_names <- if (nsex == 1) NA_character_ else c("female", "male")
       quantities_list <- list()
-      
+
       if ("sel_at_age" %in% names(extract[[1]])) {
         sel <- extract[[1]][["sel_at_age"]][, seq_len(nsex), seq_along(ages), , drop = FALSE]
         df_sel <- expand.grid(
@@ -396,7 +396,7 @@ conout_rceattle <- function(
         df_sel[setdiff(tolower(names(out_new)), tolower(names(df_sel)))] <- NA
         quantities_list[["sel_at_age"]] <- df_sel
       }
-      
+
       if ("M_at_age" %in% names(extract[[1]])) {
         m_at_age <- extract[[1]][["M_at_age"]][1, seq_len(nsex), seq_along(ages), , drop = FALSE]
         df_m <- expand.grid(
@@ -412,7 +412,7 @@ conout_rceattle <- function(
         df_m[setdiff(tolower(names(out_new)), tolower(names(df_m)))] <- NA
         quantities_list[["m_at_age"]] <- df_m
       }
-      
+
       if (length(quantities_list) > 0) {
         out_list[[names(extract)]] <- Reduce(rbind, quantities_list) |>
           dplyr::mutate(
@@ -441,7 +441,7 @@ conout_rceattle <- 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(
diff --git a/R/conout_ss3.R b/R/conout_ss3.R
index 6ca8ec69..95a6cd36 100644
--- a/R/conout_ss3.R
+++ b/R/conout_ss3.R
@@ -1,6 +1,6 @@
 #' Code to convert SS3 output to standard framework.
-#' 
-#' Does not change naming conventions. Contains code to work with SS3 Report.sso 
+#'
+#' Does not change naming conventions. Contains code to work with SS3 Report.sso
 #' file or returned object from `r4ss::ss_output()`.
 #'
 #' @inheritParams convert_output
@@ -9,9 +9,9 @@
 #'
 #' @returns Reshaped data frame.
 conout_ss3 <- function(
-    file,
-    out_new,
-    fleet_names = NULL
+  file,
+  out_new,
+  fleet_names = NULL
 ) {
   if (is.character(file)) {
     # report.sso file
@@ -31,7 +31,7 @@ conout_ss3 <- function(
     if (vers < 3.3) {
       cli::cli_abort("This function in its current state can not process the data.")
     }
-    
+
     # Extract fleet names
     if (is.null(fleet_names)) {
       fleet_names <- SS3_extract_fleet(dat, vers)
@@ -39,7 +39,7 @@ conout_ss3 <- function(
     # Output fleet names in console
     cli::cli_alert_info("Identified fleet names:")
     cli::cli_alert_info("{fleet_names}")
-    
+
     # Estimated and focal parameters to put into reformatted output df - naming conventions from SS3
     # Extract keywords from ss3 file
     # Find row where keywords start
@@ -59,7 +59,7 @@ conout_ss3 <- function(
     # identify first reported keyword
     keywords_end_row <- which(apply(dat, 1, function(row) any(grepl(keyword_1, row))))[2] - 12 # 12 rows behind is the last entry for keywords
     # always extract the second entry bc the first is just in the list of keywords
-    
+
     keywords <- dat[keywords_start_row:keywords_end_row, ][-c(1:3), c(1:3)] |>
       replace_empty_with_na_all()
     keywords <- Filter(function(x) !all(is.na(x)), keywords)
@@ -68,7 +68,7 @@ conout_ss3 <- function(
       dplyr::mutate(output_order = as.numeric(stringr::str_extract(output_order, "\\d+$"))) |>
       dplyr::filter(output == "Y") |>
       dplyr::pull(keyword)
-    
+
     # Group parameters base on table pattern
     std <- c(
       "DERIVED_QUANTITIES",
@@ -135,13 +135,13 @@ conout_ss3 <- function(
     # Output fleet names in console
     cli::cli_alert_info("Identified fleet names:")
     cli::cli_alert_info("{fleet_names}")
-    
+
     # Extract start year and end year
     start_year <- file$startyr
     end_year <- file$endyr
-    
+
     param_names <- names(dat)
-    
+
     std <- c(
       "recruit", # STD
       "exploitation", # STD
@@ -189,7 +189,7 @@ conout_ss3 <- function(
     cha <- c()
     info <- c()
   }
-  
+
   # Loop for all identified parameters to extract for plotting and use
   # Create list of parameters that were not found in the output file
   # 1,4,10,17,19,20,22,32,37
@@ -204,14 +204,14 @@ conout_ss3 <- function(
     "settlement", "birthseas", "count",
     "kind"
   )
-  
+
   errors <- c(
     "StdDev", "sd", "std", "stddev",
     "se", "SE",
     "cv", "CV"
     # "dev" # not included bc this is dev in model, not uncertainty of the value
   )
-  
+
   miss_parms <- c()
   out_list <- list()
   #### SS3 loop ####
@@ -225,7 +225,7 @@ conout_ss3 <- function(
       } else {
         extract <- file[[parm_sel]]
       }
-      
+
       if (!is.data.frame(extract)) {
         if (is.numeric(extract)) {
           df <- data.frame(
@@ -314,14 +314,14 @@ conout_ss3 <- function(
           } else if (any(colnames(df3) %in% c(factors, errors))) {
             # Keeping check here if case arises that there is a similar situation to the error
             # aka there are multiple columns containing the string and they are not selected properly
-            
+
             if ("sexes" %in% colnames(df3)) {
               df3 <- df3 |>
                 # add in case if sexes is present and add sex as na if so
                 dplyr::mutate(sex = if (any(grepl("^sexes$", colnames(df3)))) sexes else NA) |>
                 dplyr::select(-sexes)
             }
-            
+
             # Identify which errors were identified in a column & rename
             err_col_id <- colnames(df3)[grepl(paste0(errors, "$", collapse = "|"), colnames(df3))]
             # rename error column
@@ -395,7 +395,7 @@ conout_ss3 <- function(
                   )
                 }
               )
-            
+
             df4 <- df4 |>
               dplyr::mutate(
                 label = dplyr::case_when(
@@ -405,7 +405,7 @@ conout_ss3 <- function(
                   TRUE ~ stringr::str_extract(label, "^.*?(?=_\\d|_gp|_fem|_mal|_sx|:|$)")
                 )
               )
-            
+
             if (parm_sel == "DISCARD_OUTPUT") {
               df4 <- df4 |>
                 dplyr::mutate(label = glue::glue("discard_{label}"))
@@ -415,7 +415,7 @@ conout_ss3 <- function(
             cli::cli_alert_warning(glue::glue("Data frame not compatible in {parm_sel}."))
           }
           if (any(colnames(df4) %in% c("value"))) df4 <- dplyr::rename(df4, estimate = value)
-          
+
           # Check if error values are in the labels column and extract out
           if (any(sapply(paste0("(^|[_.])", errors, "($|[_.])"), function(x) grepl(x, unique(df4$label))))) {
             err_names <- unique(df4$label)[grepl(paste(paste0("(^|[_.])", errors, "($|[_.])"), collapse = "|"), unique(df4$label)) & !unique(df4$label) %in% errors]
@@ -494,7 +494,7 @@ conout_ss3 <- function(
               }
             }
           }
-          
+
           df5 <- df4 |>
             dplyr::select(tidyselect::any_of(c("label", "estimate", "year", factors, errors))) |>
             dplyr::mutate(
@@ -510,7 +510,7 @@ conout_ss3 <- function(
               # estimate
               # )
             )
-          
+
           if (any(colnames(df5) %in% errors)) {
             df5 <- df5 |>
               dplyr::mutate(uncertainty_label = intersect(names(df5), errors)) |>
@@ -525,11 +525,11 @@ conout_ss3 <- function(
             colnames(df5) <- tolower(names(df5))
           }
           if ("seas" %in% colnames(df5)) df5 <- dplyr::rename(df5, season = seas)
-          
+
           if ("subseas" %in% colnames(df5)) df5 <- dplyr::rename(df5, subseason = subseas)
-          
+
           if ("like" %in% colnames(df5)) df5 <- dplyr::rename(df5, likelihood = like)
-          
+
           df5[setdiff(tolower(names(out_new)), tolower(names(df5)))] <- NA
           if (ncol(out_new) < ncol(df5)) {
             diff <- setdiff(names(df5), names(out_new))
@@ -629,7 +629,7 @@ conout_ss3 <- function(
           # Add to new dataframe
           df5 <- Reduce(rbind, comps_list)
           out_list[[parm_sel]] <- df5
-          
+
           ##### cha ####
         } else if (parm_sel %in% cha) {
           # Only one keyword characterized as this
@@ -673,7 +673,7 @@ conout_ss3 <- function(
           # "SPAWN_RECR_CURVE"
           # "Biology_at_age_in_endyr"
           # "PARAMETERS"
-          
+
           if (parm_sel %in% c("SPAWN_RECR_CURVE", "SPAWN_RECRUIT_CURVE")) {
             # 32
             # TODO: add this to converter
@@ -749,7 +749,7 @@ conout_ss3 <- function(
                   # label = paste("estimate_", label, sep = ""),
                   morph = NA
                 )
-              
+
               sub_df2 <- df3[, c(1:2, (actual_col + 1):(moref_col - 1))] |>
                 tidyr::pivot_longer(
                   cols = -c(yr, era),
@@ -1049,7 +1049,7 @@ conout_ss3 <- function(
               row <- row[row != "XX"]
               df1 <- df1[, -loc_xx]
             }
-            
+
             # TODO: apply this next if statement to a general process so it's part of the standard cleaning
             # check if the headers make sense
             # this is a temporary fix to a specific bug
@@ -1063,10 +1063,10 @@ conout_ss3 <- function(
               df2 <- df1[stats::complete.cases(df1), ]
               row <- df2[1, ]
             }
-            
+
             # make row the header names for first df
             colnames(df1) <- row
-            
+
             # find row number that matches 'row'
             rownum <- row_match(row, df1)
             # Subset data frame
@@ -1098,20 +1098,20 @@ conout_ss3 <- function(
             (
               # add conditions for naming label from aa.al
               label <- switch(parm_sel,
-                              # "sizeselex" = "selectivity_length",
-                              "ageselex" = "selectivity_age",
-                              "Natural_Mortality" = "natural_mortality_age",
-                              "fatage" = "fishing_mortality_age",
-                              "natage" = "abundance_age",
-                              "batage" = "biomass_age",
-                              "natlen" = "abundance_length",
-                              "batlen" = "biomass_length",
-                              "discard_at_age" = "discard_age",
-                              "catage" = "catch_age",
-                              "Z_at_age" = "total_mortality_age",
-                              "M_at_age" = "natural_mortality_age",
-                              "Z_by_area" = "total_mortality",
-                              "M_by_area" = "natural_mortality"
+                # "sizeselex" = "selectivity_length",
+                "ageselex" = "selectivity_age",
+                "Natural_Mortality" = "natural_mortality_age",
+                "fatage" = "fishing_mortality_age",
+                "natage" = "abundance_age",
+                "batage" = "biomass_age",
+                "natlen" = "abundance_length",
+                "batlen" = "biomass_length",
+                "discard_at_age" = "discard_age",
+                "catage" = "catch_age",
+                "Z_at_age" = "total_mortality_age",
+                "M_at_age" = "natural_mortality_age",
+                "Z_by_area" = "total_mortality",
+                "M_by_area" = "natural_mortality"
               )
             )
           }
@@ -1124,10 +1124,10 @@ conout_ss3 <- function(
           } else {
             fac <- "age"
           }
-          
+
           # remove fac from label
           if (grepl(glue::glue("_{fac}"), label)) label <- stringr::str_remove(label, glue::glue("_{fac}"))
-          
+
           # Reformat dataframe
           if (any(colnames(df3) %in% c("Yr", "yr"))) {
             df3 <- df3 |>
diff --git a/R/convert_output.R b/R/convert_output.R
index d3b2ac99..111c63fd 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -63,18 +63,17 @@ convert_output <- function(
   save_dir = NULL,
   start_year = 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)) {
@@ -232,7 +231,7 @@ convert_output <- function(
     out_new <- conout_fims(file = file, out_new = out_new, start_year = start_year)
     #### Rceattle ####
   } else if (model == "rceattle") {
-   out_new <- conout_rceattle(file = file, out_new = out_new, fleet_names = fleet_names)
+    out_new <- conout_rceattle(file = file, out_new = out_new, fleet_names = fleet_names)
   } else {
     cli::cli_abort(c(
       message = "Output file not compatible.",
diff --git a/R/data.R b/R/data.R
index ec214e56..95263d2d 100644
--- a/R/data.R
+++ b/R/data.R
@@ -44,7 +44,7 @@
 
 #' 2018 Gulf of Alaska Pollock stock assessment output
 #'
-#' Output of the 2018 Gulf of Alaska Pollock stock assessment produced from Rceattle, standardized 
+#' Output of the 2018 Gulf of Alaska Pollock stock assessment produced from Rceattle, standardized
 #' using `stockplotr::convert_output()`. The example can be found and run from the Rceattle repository.
 #'
 #' @docType data
@@ -103,7 +103,7 @@
 
 #' SEDAR 55 South Atlantic Vermilion Snapper
 #'
-#' Standardized output of the 2018 South Atlantic Vermilion Snapper stock assessment 
+#' Standardized output of the 2018 South Atlantic Vermilion Snapper stock assessment
 #' produced from the Beaufort Assessment Model (BAM).
 #'
 #' @docType data
@@ -148,7 +148,7 @@
 #' }
 #'
 #' @keywords datasets
-#' 
+#'
 #' @references SEDAR (2018)
 #' (\url{https://sedarweb.org/documents/sedar-55-stock-assessment-report-south-atlantic-vermilion-snapper/})
 #'
@@ -160,9 +160,9 @@
 
 #' SS3 Simple stock assessment output
 #'
-#' Standardized output of a generic simple example of SS3 found from the `r4ss` 
-#' repository examples. The raw output is converted to an R readable object 
-#' using `r4ss::ss_output` then standardized using `stockplotr::convert_output()`. 
+#' Standardized output of a generic simple example of SS3 found from the `r4ss`
+#' repository examples. The raw output is converted to an R readable object
+#' using `r4ss::ss_output` then standardized using `stockplotr::convert_output()`.
 #'
 #' @docType data
 #'
diff --git a/R/extract_sis_data.R b/R/extract_sis_data.R
index 0e3e3999..5c59e650 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 <- utils::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 <- utils::read.csv(fs::path(key_quantities_dir,
-                           "key_quantities.csv"), 
-                  stringsAsFactors = FALSE)
+  if (file.exists(kqs_path)) {
+    kqs <- utils::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): ")
@@ -394,7 +408,7 @@ extract_sis_data <- function(sis_data_dir = getwd(),
     utils::write.csv(ts_dat_filled, ts_dat_path, row.names = FALSE)
     cli::cli_alert_success("Files saved successfully in {sis_data_dir}.")
   }
-  
+
   # remove global variables
   c("biomass", "spawning_biomass", "recruitment", "fishing_mortality", "index", "catch") |>
     purrr::walk(~ if (exists(.x, envir = .GlobalEnv)) rm(list = .x, envir = .GlobalEnv))
diff --git a/R/plot_abundance_at_age.R b/R/plot_abundance_at_age.R
index 22f7e7b7..480da3a1 100644
--- a/R/plot_abundance_at_age.R
+++ b/R/plot_abundance_at_age.R
@@ -112,7 +112,7 @@ plot_abundance_at_age <- function(
     unit_label = unit_label,
     scale_amount = scale_amount
   )
-  
+
   if (!is.null(facet) && facet == "none") {
     data <- b |>
       dplyr::group_by(year, age) |>
@@ -176,7 +176,7 @@ plot_abundance_at_age <- function(
       pop.naa.age.max,
       pop.naa.fish.min,
       pop.naa.fish.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -187,7 +187,7 @@ plot_abundance_at_age <- function(
       pop.naa.age.max,
       pop.naa.fish.min,
       pop.naa.fish.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -199,10 +199,10 @@ plot_abundance_at_age <- function(
       dat
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   plot
 }
diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index ac8570bc..211056d0 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -87,7 +87,7 @@ plot_biomass <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
-  
+
   if (is.null(unit_label)) {
     unit_label <- unique(prepared_data$unit)
     if (is.na(unit_label)) {
@@ -95,7 +95,7 @@ plot_biomass <- function(
       unit_label <- ""
     }
   }
-  
+
   biomass_label <- ifelse(
     relative,
     yes = "Relative biomass",
@@ -108,7 +108,7 @@ plot_biomass <- function(
       )
     }
   )
-  
+
   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'.")
@@ -190,10 +190,10 @@ plot_biomass <- function(
       )
 
       # calculate & export key quantities
-      export_kqs(rel.B.min, rel.B.max, dir=figures_dir)
+      export_kqs(rel.B.min, rel.B.max, dir = figures_dir)
 
       # Add key quantities to captions/alt text
-      insert_kqs(rel.B.min, rel.B.max, dir=figures_dir)
+      insert_kqs(rel.B.min, rel.B.max, dir = figures_dir)
     } else {
       B.min <- calc_kqs(
         returned_kq = "B.min",
@@ -204,8 +204,8 @@ plot_biomass <- function(
         prepared_data = prepared_data
       )
 
-      export_kqs(B.min, B.max, dir=figures_dir)
-      insert_kqs(B.min, B.max, dir=figures_dir)
+      export_kqs(B.min, B.max, dir = figures_dir)
+      insert_kqs(B.min, B.max, dir = figures_dir)
     }
 
     B.ref.pt <- as.character(ref_line)
@@ -292,8 +292,8 @@ plot_biomass <- function(
       B.msy,
       B.terminal.est,
       B.terminal.min,
-      B.terminal.max, 
-      dir=figures_dir
+      B.terminal.max,
+      dir = figures_dir
     )
 
     insert_kqs(
@@ -308,7 +308,7 @@ plot_biomass <- function(
       B.terminal.est,
       B.terminal.min,
       B.terminal.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     insert_kqs(
@@ -323,7 +323,7 @@ plot_biomass <- function(
       B.terminal.est,
       B.terminal.min,
       B.terminal.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -336,11 +336,10 @@ plot_biomass <- function(
       scale_amount = scale_amount
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
-  final
 
+  final
 }
diff --git a/R/plot_biomass_at_age.R b/R/plot_biomass_at_age.R
index 1b9cd130..f335ed19 100644
--- a/R/plot_biomass_at_age.R
+++ b/R/plot_biomass_at_age.R
@@ -64,7 +64,7 @@ plot_biomass_at_age <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
-  
+
   if (is.null(unit_label)) {
     unit_label <- unique(b$unit)
     if (is.na(unit_label)) {
@@ -72,14 +72,14 @@ plot_biomass_at_age <- function(
       unit_label <- ""
     }
   }
-  
+
   # Create label for abundance units in legend
   biomass_label <- label_magnitude(
     label = "Biomass",
     unit_label = unit_label,
     scale_amount = scale_amount
   )
-  
+
   if (!is.null(facet) && facet == "none") {
     data <- b |>
       dplyr::group_by(year, age) |>
@@ -142,7 +142,7 @@ plot_biomass_at_age <- function(
       pop.baa.age.max,
       pop.baa.fish.min,
       pop.baa.fish.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -153,7 +153,7 @@ plot_biomass_at_age <- function(
       pop.baa.age.max,
       pop.baa.fish.min,
       pop.baa.fish.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -161,14 +161,14 @@ plot_biomass_at_age <- function(
       # get name of function and remove "plot_" from it
       topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
       fig_or_table = "figure",
-      dir=figures_dir,
+      dir = figures_dir,
       dat
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   plot
 }
diff --git a/R/plot_catch_at_age.R b/R/plot_catch_at_age.R
index 4917c45d..78308e52 100644
--- a/R/plot_catch_at_age.R
+++ b/R/plot_catch_at_age.R
@@ -105,7 +105,7 @@ plot_catch_at_age <- function(
     scale_amount = scale_amount,
     legend = TRUE
   )
-  
+
   # Check for extracted data, if not return warning and empty plot
   if (nrow(catch) == 0) {
     cli::cli_alert_warning("No data found for catch at age. Please check the input data.")
@@ -164,7 +164,7 @@ plot_catch_at_age <- function(
       caa.age.max,
       tot.catch.min,
       tot.catch.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -175,7 +175,7 @@ plot_catch_at_age <- function(
       caa.age.max,
       tot.catch.min,
       tot.catch.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -187,10 +187,10 @@ plot_catch_at_age <- function(
       dat
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   plot
 }
diff --git a/R/plot_discard.R b/R/plot_discard.R
index 689bd45b..a547c266 100644
--- a/R/plot_discard.R
+++ b/R/plot_discard.R
@@ -58,7 +58,7 @@ plot_discard <- function(
     scale_amount = scale_amount,
     interactive = interactive
   )
-  
+
   # extract unit if unit_label is null and set lbs to F by default
   lbs <- FALSE
   if (is.null(unit_label)) {
@@ -139,7 +139,7 @@ plot_discard <- function(
       mod.fit.discards.end.year,
       fleet.or.survey.name,
       mod.fit.discards.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -150,7 +150,7 @@ plot_discard <- function(
       mod.fit.discards.end.year,
       fleet.or.survey.name,
       mod.fit.discards.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -162,10 +162,10 @@ plot_discard <- function(
       scale_amount = scale_amount
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index dfd5b141..ccbb73d7 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -111,8 +111,8 @@ plot_fishing_mortality <- function(
       prepared_data = prepared_data
     )
 
-    export_kqs(F.min, F.max, dir=figures_dir)
-    insert_kqs(F.min, F.max, dir=figures_dir)
+    export_kqs(F.min, F.max, dir = figures_dir)
+    insert_kqs(F.min, F.max, dir = figures_dir)
 
     F.ref.pt <- as.character(ref_line)
     F.start.year <- min(prepared_data$year)
@@ -173,7 +173,7 @@ plot_fishing_mortality <- function(
       F.MSY.terminal.max,
       F.MSY.terminal.min,
       F.MSY.terminal,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     insert_kqs(
@@ -189,7 +189,7 @@ plot_fishing_mortality <- function(
       F.MSY.terminal.max,
       F.MSY.terminal.min,
       F.MSY.terminal,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -202,10 +202,10 @@ plot_fishing_mortality <- function(
       scale_amount = 1
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/plot_landings.R b/R/plot_landings.R
index efd1b7bf..2021024c 100644
--- a/R/plot_landings.R
+++ b/R/plot_landings.R
@@ -59,7 +59,7 @@ plot_landings <- function(
   ) # |>
   # filter NA from year
   # dplyr::filter(!is.na(year))
-  
+
   # Process data
   processed_data <- process_data(
     dat = prepared_data,
@@ -77,7 +77,7 @@ plot_landings <- function(
       # always select the first label if TRUE
       dplyr::filter(label == unique(label)[1])
   }
-  
+
   # extract unit if unit_label is null and set lbs to F by default
   lbs <- FALSE
   if (is.null(unit_label)) {
@@ -93,7 +93,7 @@ plot_landings <- function(
   } else {
     if (grepl("lbs|pounds|lb", unit_label, ignore.case = TRUE)) lbs <- TRUE
   }
-  
+
   # Units
   landings_label <- label_magnitude(
     label = "Landings",
@@ -138,7 +138,7 @@ plot_landings <- function(
       landings.min,
       landings.max,
       landings.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -148,7 +148,7 @@ plot_landings <- function(
       landings.min,
       landings.max,
       landings.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -161,10 +161,10 @@ plot_landings <- function(
       scale_amount = scale_amount
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   plt
 }
diff --git a/R/plot_natural_mortality.R b/R/plot_natural_mortality.R
index e3c70b03..09d1c1e9 100644
--- a/R/plot_natural_mortality.R
+++ b/R/plot_natural_mortality.R
@@ -121,7 +121,7 @@ plot_natural_mortality <- function(
       M.age.max,
       M.rate.min,
       M.rate.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -130,7 +130,7 @@ plot_natural_mortality <- function(
       M.age.max,
       M.rate.min,
       M.rate.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -142,10 +142,10 @@ plot_natural_mortality <- function(
       dir = figures_dir
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/plot_recruitment.R b/R/plot_recruitment.R
index 95706a1c..5dbf3c9a 100644
--- a/R/plot_recruitment.R
+++ b/R/plot_recruitment.R
@@ -73,14 +73,14 @@ plot_recruitment <- function(
     unit_label <- unique(prepared_data$unit)
     if (is.na(unit_label) || is.null(unit_label)) cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
   }
-  
+
   recruitment_label <- label_magnitude(
     label = "Recruitment",
     unit_label = unit_label,
     scale_amount = scale_amount,
     legend = FALSE
   )
-  
+
   # Check if contains 'rec devs' and filter out
   if (any(grepl("recruitment_deviations", unique(recruitment$label)))) {
     if (length(unique(recruitment$label)) > 1) {
@@ -194,10 +194,10 @@ plot_recruitment <- function(
       dir = figures_dir
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/plot_recruitment_deviations.R b/R/plot_recruitment_deviations.R
index f00ae1af..f2ad753d 100644
--- a/R/plot_recruitment_deviations.R
+++ b/R/plot_recruitment_deviations.R
@@ -98,7 +98,7 @@ plot_recruitment_deviations <- function(
       recruit.dev.end.year,
       recruit.dev.min,
       recruit.dev.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -107,7 +107,7 @@ plot_recruitment_deviations <- function(
       recruit.dev.end.year,
       recruit.dev.min,
       recruit.dev.max,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
diff --git a/R/plot_selectivity.R b/R/plot_selectivity.R
index 2af46ca7..d4781ad4 100644
--- a/R/plot_selectivity.R
+++ b/R/plot_selectivity.R
@@ -54,7 +54,7 @@ plot_selectivity <- function(
     interactive = interactive,
     module = module
   )
-  
+
   if (is.null(unit_label)) {
     if (!any(grepl("length", prepared_data$label))) {
       unit_label <- "years"
@@ -167,7 +167,7 @@ plot_selectivity <- function(
       selectivity.x,
       selectivity.start.year,
       selectivity.end.year,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -179,7 +179,7 @@ plot_selectivity <- function(
       selectivity.x,
       selectivity.start.year,
       selectivity.end.year,
-      dir=figures_dir
+      dir = figures_dir
     )
 
 
@@ -192,10 +192,10 @@ plot_selectivity <- function(
       dir = figures_dir
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 91b3cb80..1047b598 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -40,9 +40,9 @@
 #'
 #' 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).
-#' @param unit_label String. Spawning biomass unit as indicated from the data. 
-#' When setting a unit of pounds please use one of the following keywords: 
-#' "lbs", "pounds", "lb". For example "1000s of lbs" would still be recognized 
+#' @param unit_label String. Spawning biomass unit as indicated from the data.
+#' When setting a unit of pounds please use one of the following keywords:
+#' "lbs", "pounds", "lb". For example "1000s of lbs" would still be recognized
 #' as pounds. Do not set unit_label to the desired order of magnitude, rather the
 #' unit label reflected in the data. Please refer to the argument `scale_amount`.
 #'
@@ -60,7 +60,7 @@
 #' If the interactive and >1 module_name is found, user will select the
 #' module_name in the console. @seealso [filter_data()]
 #' @param scale_amount Number. A number to scale the y-axis values. If > 1, the
-#'  magnitude of the scale amount will be added to the unit label 
+#'  magnitude of the scale amount will be added to the unit label
 #'  (e.g. scale_amount = 1000 with a unit label of "1000s of lbs" will result
 #'   in "thousands of 1000s of lbs")
 #'
@@ -166,7 +166,7 @@ plot_spawning_biomass <- function(
   } else {
     if (grepl("lbs|pounds|lb", unit_label, ignore.case = TRUE)) lbs <- TRUE
   }
-  
+
   spawning_biomass_label <- ifelse(
     relative,
     yes = "Relative spawning biomass",
@@ -179,7 +179,7 @@ plot_spawning_biomass <- function(
       )
     }
   )
-  
+
   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'.")
@@ -259,16 +259,16 @@ plot_spawning_biomass <- function(
       )
 
       # calculate & export key quantities
-      export_kqs(rel.ssb.min, rel.ssb.max, dir=figures_dir)
+      export_kqs(rel.ssb.min, rel.ssb.max, dir = figures_dir)
 
       # Add key quantities to captions/alt text
-      insert_kqs(rel.ssb.min, rel.ssb.max, dir=figures_dir)
+      insert_kqs(rel.ssb.min, rel.ssb.max, dir = figures_dir)
     } else {
       ssb.min <- min(plot_data$estimate) |> round(digits = 3)
       ssb.max <- max(plot_data$estimate) |> round(digits = 3)
 
-      export_kqs(ssb.min, ssb.max, dir=figures_dir)
-      insert_kqs(ssb.min, ssb.max, dir=figures_dir)
+      export_kqs(ssb.min, ssb.max, dir = figures_dir)
+      insert_kqs(ssb.min, ssb.max, dir = figures_dir)
     }
 
     # Obtain relevant key quantities for captions/alt text
@@ -283,7 +283,7 @@ plot_spawning_biomass <- function(
       ssb.units,
       ssb.start.year,
       ssb.end.year,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -292,7 +292,7 @@ plot_spawning_biomass <- function(
       ssb.units,
       ssb.start.year,
       ssb.end.year,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -305,11 +305,11 @@ plot_spawning_biomass <- function(
       scale_amount = scale_amount
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   # Output final plot
   final
 }
diff --git a/R/plot_spr.R b/R/plot_spr.R
index fada854f..dc000ab2 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).
@@ -48,13 +48,13 @@ plot_spr <- function(
   ...
 ) {
   check_data(dat)
-  
+
   # 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,
@@ -64,19 +64,19 @@ plot_spr <- 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]]
@@ -94,7 +94,7 @@ plot_spr <- function(
   if (!is.null(group)) {
     if (group %notin% colnames(prepared_data)) group <- NULL
   }
-  
+
   # inital base plot
   plt <- plot_timeseries(
     dat = prepared_data,
@@ -105,10 +105,14 @@ plot_spr <- 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,
@@ -116,7 +120,7 @@ plot_spr <- function(
       scale_amount = 1
     ) +
     theme_noaa()
-  
+
 
   if (length(unique(prepared_data$group_var)) == 1) {
     plt <- plt + ggplot2::theme(legend.position = "none")
@@ -126,20 +130,20 @@ plot_spr <- function(
   if (make_rda) {
     # TODO: Update caption, alt text, and quantities once plot is finalized
     # Obtain relevant key quantities for captions/alt text
-    
+
     spr.start.year <- min(prepared_data$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,
       spr.end.year,
       spr.min,
       spr.ref.pt,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -149,7 +153,7 @@ plot_spr <- function(
       spr.min,
       spr.max,
       spr.ref.pt,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
diff --git a/R/plot_stock_recruitment.R b/R/plot_stock_recruitment.R
index 514e8d1c..e0debed2 100644
--- a/R/plot_stock_recruitment.R
+++ b/R/plot_stock_recruitment.R
@@ -97,7 +97,7 @@ 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,
@@ -126,7 +126,7 @@ plot_stock_recruitment <- function(
   if (is.null(recruitment_label)) {
     recruitment_label <- unique(recruitment$unit)
     recruitment_label <- recruitment_label[!is.na(recruitment_label)]
-    if (is.na(recruitment_label) || is.null(recruitment_label))  {
+    if (is.na(recruitment_label) || is.null(recruitment_label)) {
       cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'recruitment_label' argument.")
       recruitment_label <- ""
     }
@@ -211,7 +211,7 @@ plot_stock_recruitment <- function(
       recruitment.min,
       recruitment.max,
       recruitment.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     # Add key quantities to captions/alt text
@@ -223,7 +223,7 @@ plot_stock_recruitment <- function(
       recruitment.min,
       recruitment.max,
       recruitment.units,
-      dir=figures_dir
+      dir = figures_dir
     )
 
     create_rda(
@@ -235,11 +235,11 @@ plot_stock_recruitment <- function(
       dir = figures_dir
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final +
     ggplot2::scale_x_continuous(
       labels = scales::label_comma()
diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index c530b094..0c7b1ac3 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -1,8 +1,8 @@
 #' Export all figures and tables
 #'
 #' Export all figures and tables to Rda files within one function.
-#' This primary purpose of this function is to quickly export all 
-#' available figures and tables. We recommend running individual 
+#' This primary purpose of this function is to quickly export all
+#' available figures and tables. We recommend running individual
 #' plotting functions for greater customization of figures and tables.
 #'
 #' @inheritParams plot_spawning_biomass
@@ -11,32 +11,32 @@
 #'
 #' Default: the working directory (`getwd()`)
 #'
-#' @param plot_recruitment_options List. List object of parameter values to pass 
+#' @param plot_recruitment_options List. List object of parameter values to pass
 #' directly to the `plot_recruitment` function. All default parameters for the
-#' `plot_recruitment` function, except for `dat`, can be overridden with this list 
-#' object. 
-#' 
+#' `plot_recruitment` function, except for `dat`, can be overridden with this list
+#' object.
+#'
 #' Default: list(module = "TIME_SERIES")
 #'
-#' @param plot_natural_mortality_options List. List object of parameter values to pass 
+#' @param plot_natural_mortality_options List. List object of parameter values to pass
 #' directly to the `plot_natural_mortality_options` function. All default parameters for the
-#' `plot_natural_mortality_options` function, except for `dat`, can be overridden with this list 
-#' object. 
-#' 
+#' `plot_natural_mortality_options` function, except for `dat`, can be overridden with this list
+#' object.
+#'
 #' Default: list(module = "Natural_Mortality")
-#' 
-#' @param table_total_catch_options List. List object of parameter values to pass 
+#'
+#' @param table_total_catch_options List. List object of parameter values to pass
 #' directly to the `table_total_catch_options` function. All default parameters for the
-#' `table_total_catch_options` function, except for `dat`, can be overridden with this list 
-#' object. 
-#' 
+#' `table_total_catch_options` function, except for `dat`, can be overridden with this list
+#' object.
+#'
 #' Default: list(module = "TIME_SERIES")
-#' 
+#'
 #' ... Additional list objects of parameter values to pass directly to corresponding
 #' plot or table functions. Parameter names should follow the naming convention
-#' `{function_name}_options`. All default parameters, except for `dat`, of this function 
+#' `{function_name}_options`. All default parameters, except for `dat`, of this function
 #' can be overridden with this list object. See example.
-#' 
+#'
 #' @returns Rda files for each figure/table.
 #'
 #' @seealso [convert_output()], [create_rda()]
@@ -73,7 +73,7 @@
 #'    ),
 #'    plot_abundance_at_age_options = list(
 #'      scale_amount = 1,         # custom scale for abundance-at-age plot
-#'      proportional = FALSE      # don't proportionalize abundance-at-age 
+#'      proportional = FALSE      # don't proportionalize abundance-at-age
 #'    ),
 #'    plot_spr_options = list(
 #'      ylab = "Fishing Intensity (1-SPR)/(1-SPR_ref)" # custom Y label for SPR plot
@@ -92,16 +92,16 @@ save_all_plots <- function(
   # no standard default modules
   plot_recruitment_options = list(module = "TIME_SERIES"),
   plot_natural_mortality_options = list(module = "Natural_Mortality"),
-  table_total_catch_options = list( module = "TIME_SERIES"),
+  table_total_catch_options = list(module = "TIME_SERIES"),
   # All other functions can be modified with appropriate *_options
   # parameter lists.
   ...
 ) {
   check_data(dat)
 
-  all_params <- as.list(environment(), all=TRUE)
+  all_params <- as.list(environment(), all = TRUE)
   make_rda <- TRUE
-  
+
   cli::cli_h1("Starting export of figures and tables")
 
   # These arguments are used by every plot and table
@@ -123,38 +123,39 @@ save_all_plots <- function(
   # plottab_functions <- sub("\\.[^\\.]*$", "", plottab_function_files)
   all_functions <- ls(getNamespace("stockplotr"))
   all_plottab_functions <- all_functions[grepl("plot_|table_", all_functions)]
-  plottab_functions <- all_plottab_functions[!(grepl(paste0(helper_functions, collapse="|"), all_plottab_functions))]
+  plottab_functions <- all_plottab_functions[!(grepl(paste0(helper_functions, collapse = "|"), all_plottab_functions))]
 
-  for(i in seq_along(plottab_functions)){
-      func_name <- plottab_functions[i]
-      func_specific_args <- all_params[paste0(func_name,"_options")][[1]]
+  for (i in seq_along(plottab_functions)) {
+    func_name <- plottab_functions[i]
+    func_specific_args <- all_params[paste0(func_name, "_options")][[1]]
 
-      func_pars <- default_args
-      if(!is.null(func_specific_args))
-        func_pars <- c(default_args, func_specific_args)
+    func_pars <- default_args
+    if (!is.null(func_specific_args)) {
+      func_pars <- c(default_args, func_specific_args)
+    }
 
-      # switch from "figures_dir" to "tables_dir" dynamically
-      if(grepl("table",func_name)){
-        names(func_pars)[which(names(func_pars)=="figures_dir")] <- "tables_dir"
-      }
+    # switch from "figures_dir" to "tables_dir" dynamically
+    if (grepl("table", func_name)) {
+      names(func_pars)[which(names(func_pars) == "figures_dir")] <- "tables_dir"
+    }
 
-      cli::cli_alert_info("Exporting: {func_name} figure")
-      tryCatch(
-        {
-          suppressMessages(
-              do.call(func_name, func_pars) # Execute plotting/table function
-          )
-        },
-        error = function(e) {
-            cli::cli_alert_danger("Failed to execute: {func_name}.")
-            cli::cli_alert("Tip: check that your arguments are correct.")
-            for(a in seq_along(func_specific_args)){
-              arg_name = names(func_specific_args)[a]
-              arg_value = as.character(func_specific_args[a])
-              cli::cli_li("{arg_name} = {arg_value}")
-            }
-            print(e)
+    cli::cli_alert_info("Exporting: {func_name} figure")
+    tryCatch(
+      {
+        suppressMessages(
+          do.call(func_name, func_pars) # Execute plotting/table function
+        )
+      },
+      error = function(e) {
+        cli::cli_alert_danger("Failed to execute: {func_name}.")
+        cli::cli_alert("Tip: check that your arguments are correct.")
+        for (a in seq_along(func_specific_args)) {
+          arg_name <- names(func_specific_args)[a]
+          arg_value <- as.character(func_specific_args[a])
+          cli::cli_li("{arg_name} = {arg_value}")
         }
-      )   
+        print(e)
+      }
+    )
   }
 }
diff --git a/R/table_biomass_abundance_catch.R b/R/table_biomass_abundance_catch.R
index 1b7a9f8c..a29ddfa3 100644
--- a/R/table_biomass_abundance_catch.R
+++ b/R/table_biomass_abundance_catch.R
@@ -77,7 +77,7 @@ table_biomass_abundance_catch <- function(
     "^abundance" = "abundance",
     "catch$|landings_observed" = "catch"
   )
-  
+
   biomass_abundance_catch.biomass.units <- NA
   biomass_abundance_catch.abundance.units <- NA
   biomass_abundance_catch.catch.units <- NA
@@ -97,7 +97,7 @@ table_biomass_abundance_catch <- function(
         module = module,
         scale_amount = 1,
         interactive = interactive
-      ) 
+      )
 
       uncertainty_label <- ifelse(
         is.na(unique(filtered_data$uncertainty_label)),
@@ -156,14 +156,16 @@ table_biomass_abundance_catch <- function(
 
       data <- processed_data[[1]]
       group <- processed_data[[2]]
-      
+
       # Labs
       # get unit label for biomass, abundance, and catch if not NULL
       unit_name <- named_vec[grep(x, names(named_vec), fixed = TRUE)][[1]]
       if (is.null(get(paste0(unit_name, "_label")))) {
         unit_label <- filtered_data |>
-          dplyr::filter(grepl(x, unit_name),
-                        !is.na(.data$unit)) |>
+          dplyr::filter(
+            grepl(x, unit_name),
+            !is.na(.data$unit)
+          ) |>
           dplyr::pull("unit") |>
           unique()
         if (is.na(unit_label) || length(unit_label) == 0) {
@@ -173,7 +175,7 @@ table_biomass_abundance_catch <- function(
       } else {
         unit_label <- get(paste0(unit_name, "_label"))
       }
-      
+
       # Obtain relevant key quantities for captions/alt text
       idx <- match(x, names(named_vec)[1:3])
       if (identical(idx, 1L)) biomass_abundance_catch.biomass.units <<- unit_label
@@ -198,7 +200,7 @@ table_biomass_abundance_catch <- function(
     gt::gt()
 
   final <- theme_table(combine_data)
-  
+
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
     # calculate & export key quantities
@@ -206,7 +208,7 @@ table_biomass_abundance_catch <- function(
       biomass_abundance_catch.biomass.units,
       biomass_abundance_catch.abundance.units,
       biomass_abundance_catch.catch.units,
-      dir=tables_dir
+      dir = tables_dir
     )
 
     # Add key quantities to captions/alt text
@@ -214,7 +216,7 @@ table_biomass_abundance_catch <- function(
       biomass_abundance_catch.biomass.units,
       biomass_abundance_catch.abundance.units,
       biomass_abundance_catch.catch.units,
-      dir=tables_dir
+      dir = tables_dir
     )
 
     create_rda(
@@ -230,10 +232,10 @@ table_biomass_abundance_catch <- function(
   }
 
   rm(biomass_abundance_catch.biomass.units, biomass_abundance_catch.abundance.units, biomass_abundance_catch.catch.units)
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/table_index.R b/R/table_index.R
index 5c21a8ac..9e41058c 100644
--- a/R/table_index.R
+++ b/R/table_index.R
@@ -150,17 +150,17 @@ table_index <- function(
       )
     }
 
-      create_rda(
-        object = final,
-        # get name of function and remove "table_" from it
-        topic_label = gsub("table_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
-        fig_or_table = "table",
-        dat = dat,
-        dir = tables_dir,
-        scale_amount = 1,
-        table_df = final
-      )
+    create_rda(
+      object = final,
+      # get name of function and remove "table_" from it
+      topic_label = gsub("table_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
+      fig_or_table = "table",
+      dat = dat,
+      dir = tables_dir,
+      scale_amount = 1,
+      table_df = final
+    )
   }
-  
+
   final
 }
diff --git a/R/table_landings.R b/R/table_landings.R
index 7f711c9a..cf776486 100644
--- a/R/table_landings.R
+++ b/R/table_landings.R
@@ -43,7 +43,8 @@
 #'
 #' @examples
 #' table_landings(stockplotr::example_data,
-#'   interactive = FALSE)
+#'   interactive = FALSE
+#' )
 #'
 #' table_landings(
 #'   stockplotr::example_data,
@@ -118,7 +119,7 @@ table_landings <- function(
   table_data <- table_data_info[[1]]
   indexed_vars <- table_data_info[[2]]
   id_col_vals <- table_data_info[[3]]
-  
+
   if (is.null(unit_label)) {
     # remove fleet names from table_data colnames
     fleet_pattern <- paste0("_(", paste(fleets, collapse = "|"), ")$")
@@ -133,7 +134,7 @@ table_landings <- function(
       unit_label <- ""
     }
   }
-  
+
   # set unit label if scaled
   landings_label <- label_magnitude(
     label = "",
@@ -141,7 +142,7 @@ table_landings <- function(
     scale_amount = scale_amount
   )
 
-    # TODO: add check if there is a landings column for every error column -- if not remove the error (can keep landings)
+  # TODO: add check if there is a landings column for every error column -- if not remove the error (can keep landings)
 
   # merge error and landings columns and rename
   final_tab <- merge_error(
@@ -159,13 +160,13 @@ table_landings <- function(
   if (make_rda == TRUE) {
     # Obtain relevant key quantities for captions/alt text
     landings.units <- unit_label
-    
+
     # calculate & export key quantities
     export_kqs(landings.units, dir = tables_dir)
-    
+
     # Add key quantities to captions/alt text
     insert_kqs(landings.units, dir = tables_dir)
-    
+
     create_rda(
       object = final,
       # get name of function and remove "table_" from it
@@ -177,10 +178,10 @@ table_landings <- function(
       table_df = final
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
diff --git a/R/table_projections.R b/R/table_projections.R
index 37e0a299..b18c429a 100644
--- a/R/table_projections.R
+++ b/R/table_projections.R
@@ -23,14 +23,14 @@
 #'   interactive = FALSE,
 #'   module = "DERIVED_QUANTITIES"
 #' )
-#' 
+#'
 #' table_projections(
-#'  dat = stockplotr::example_data,
-#'  interactive = FALSE,
-#'  catch_label = "kg",
-#'  spawning_biomass_label = "kg",
-#'  module = c(NULL, "DERIVED_QUANTITIES", "DERIVED_QUANTITIES")
-#'  )
+#'   dat = stockplotr::example_data,
+#'   interactive = FALSE,
+#'   catch_label = "kg",
+#'   spawning_biomass_label = "kg",
+#'   module = c(NULL, "DERIVED_QUANTITIES", "DERIVED_QUANTITIES")
+#' )
 table_projections <- function(
   dat,
   catch_label = NULL,
@@ -52,13 +52,13 @@ table_projections <- function(
   # if ("landings" %notin% names(catch_lab)) {
   #   catch_label <- c(catch_label, "landings_weight" = catch_label[["catch"]])
   # }
-  
+
   named_vec <- c(
     "catch" = catch_lab,
     "spawning_biomass" = "spawning_biomass",
     "fishing_mortality" = "fishing_mortality"
   )
-  
+
   # iterate through 3 label names
   lab_list <- purrr::map(
     names(named_vec),
@@ -98,15 +98,17 @@ table_projections <- function(
       # Labs
       # get unit labels if not NULL
       unit_name <- named_vec[grep(x, names(named_vec), fixed = TRUE)][[1]]
-      
+
       if (x == "fishing_mortality") {
         fishing_mortality_label <- ""
         unit_label <- fishing_mortality_label
         unit_name <- "fishing_mortality"
       } else if (is.null(get(paste0(unit_name, "_label")))) {
         unit_label <- filtered_data |>
-          dplyr::filter(grepl(x, unit_name),
-                        !is.na(unit)) |>
+          dplyr::filter(
+            grepl(x, unit_name),
+            !is.na(unit)
+          ) |>
           dplyr::pull(unit) |>
           unique()
         if (is.na(unit_label) || length(unit_label) == 0) {
@@ -116,7 +118,7 @@ table_projections <- function(
       } else {
         unit_label <- get(paste0(unit_name, "_label"))
       }
-      
+
       # merge data with uncertainty and unit labels
       merge_error(
         table_data = data,
@@ -131,7 +133,7 @@ table_projections <- function(
     purrr::compact(lab_list),
     dplyr::full_join,
     by = c("Year")
-    ) |>
+  ) |>
     gt::gt()
 
   final <- theme_table(combine_data)
@@ -165,7 +167,7 @@ table_projections <- function(
       table_df = final$`_data`
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
diff --git a/R/table_total_catch.R b/R/table_total_catch.R
index c9779324..7965aa7a 100644
--- a/R/table_total_catch.R
+++ b/R/table_total_catch.R
@@ -50,13 +50,15 @@ table_total_catch <- function(
   tables_dir = getwd()
 ) {
   check_data(dat)
-  
+
   # Filter data for catch
   prepared_data <- filter_data(
     dat = dat |>
-      dplyr::filter(!is.na(year),
-                    !is.na(estimate),
-                    label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")),
+      dplyr::filter(
+        !is.na(year),
+        !is.na(estimate),
+        label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")
+      ),
     label_name = "^catch",
     geom = "line",
     era = era,
@@ -69,17 +71,17 @@ table_total_catch <- function(
   if (nrow(prepared_data) == 0 | unique(stringr::str_detect(prepared_data$label, "catchability"))) {
     cli::cli_abort("No catch data found.")
   }
-  
+
   # Labs
   if (is.null(unit_label)) {
     unit_label <- unique(prepared_data$unit)
     unit_label <- unit_label[!is.na(unit_label)]
-    if (is.na(unit_label) || is.null(unit_label) || length(unit_label) == 0)  {
+    if (is.na(unit_label) || is.null(unit_label) || length(unit_label) == 0) {
       cli::cli_alert_warning("No unit label found in the data. Please provide a unit label using the 'unit_label' argument.")
       unit_label <- ""
     }
   }
-  
+
   # set unit label if scaled
   catch_label <- label_magnitude(
     label = "",
@@ -196,10 +198,10 @@ table_total_catch <- function(
       table_df = final
     )
   }
-  
+
   if (exists("selected_module")) {
     rm(selected_module, envir = .GlobalEnv)
   }
-  
+
   final
 }
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/R/utils_rda.R b/R/utils_rda.R
index 8ece629c..cd15e956 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -376,9 +376,9 @@ fill_in_kqs <- function(df, ...) {
 #'
 #' @param ... Key quantities whose values should be added to the
 #' exported "key_quantities.csv"
-#' 
+#'
 #' @param dir String directory to write "key_quantities.csv" to.
-#' 
+#'
 #' DEFAULT: getwd()
 #'
 #' @returns Exports a file based on key quantities template, with values
@@ -391,21 +391,22 @@ fill_in_kqs <- function(df, ...) {
 #'   F.min,
 #'   F.max,
 #' )
-#' 
+#'
 #' export_kqs(
 #'   F.min,
 #'   F.max,
 #'   dir = fs::path(getwd(), "plots")
 #' )
 #' }
-export_kqs <- function(..., dir=getwd()) {
+export_kqs <- function(..., dir = getwd()) {
   # Open new or existing key quantities csv
   if (file.exists(fs::path(dir, "key_quantities.csv"))) {
     cli::cli_alert_info("Key quantities text file (key_quantities.csv) exists. Newly calculated key quantities will be added to it.", wrap = TRUE)
     kqs <- utils::read.csv(file.path(dir, "key_quantities.csv"))
   } else {
-    if(!dir.exists(dir))
+    if (!dir.exists(dir)) {
       dir.create(dir)
+    }
 
     kqs <- utils::read.csv(
       system.file("resources", "key_quantity_template.csv", package = "stockplotr")
@@ -429,9 +430,9 @@ export_kqs <- function(..., dir=getwd()) {
 #'
 #' @param ... Key quantities whose values should be added to the
 #' exported "captions_alt_text.csv"
-#' 
+#'
 #' @param dir String directory to write "captions_alt_text.csv" to.
-#' 
+#'
 #' DEFAULT: getwd()
 #'
 #' @returns Exports a file ("captions_alt_text.csv") containing captions
@@ -445,14 +446,14 @@ export_kqs <- function(..., dir=getwd()) {
 #'   F.max
 #' )
 #' }
-insert_kqs <- function(..., dir=getwd()) {
+insert_kqs <- function(..., dir = getwd()) {
   if (file.exists(fs::path(dir, "captions_alt_text.csv"))) {
     cli::cli_alert_info("Captions/alternative text file (captions_alt_text.csv) exists. Newly calculated key quantities will be added to it.", wrap = TRUE)
     caps_alttext <- utils::read.csv(fs::path(dir, "captions_alt_text.csv"))
   } else {
-    
-    if(!dir.exists(dir))
+    if (!dir.exists(dir)) {
       dir.create(dir)
+    }
 
     caps_alttext <- utils::read.csv(
       system.file("resources", "captions_alt_text_template.csv", package = "stockplotr")
@@ -540,9 +541,9 @@ insert_kqs <- function(..., dir=getwd()) {
 #' @param object Object. Table or plot object
 #' @param topic_label String. Name of the object
 #' @param fig_or_table String. Indicates whether the object is a "table" or "figure"
-#' 
+#'
 #' Options: "figure" or "table"
-#' 
+#'
 #' @param dat Data frame. Data which will fill in captions and
 #' alternative text for the object
 #' @param dir Path. Directory to where the rda will be saved
diff --git a/data-raw/DATASET_RCEATTLE.R b/data-raw/DATASET_RCEATTLE.R
index 7e1fada2..ba88dbca 100644
--- a/data-raw/DATASET_RCEATTLE.R
+++ b/data-raw/DATASET_RCEATTLE.R
@@ -5,7 +5,7 @@ remotes::install_github("afsc-assessments/Rceattle")
 # library(Rceattle)
 # library(readxl)
 GOApollock <- Rceattle::GOApollock
-GOApollock$styr = 1977 # The SAFE model starts at 1970, so change styr to 1970 to run the full time series model (data is in there). I start them all at 1977 because thats the years with overlap.
+GOApollock$styr <- 1977 # The SAFE model starts at 1970, so change styr to 1970 to run the full time series model (data is in there). I start them all at 1977 because thats the years with overlap.
 pollock_model <- Rceattle::fit_mod(
   data_list = GOApollock,
   inits = NULL, # Initial parameters = 0
@@ -14,7 +14,8 @@ pollock_model <- Rceattle::fit_mod(
   random_rec = FALSE, # No random recruitment
   msmMode = 0, # 0 = Single species mode, 1 = MSVPA multi-species mode
   verbose = 1, # Silence optimization output
-  phase = TRUE) # Use default phasing
+  phase = TRUE
+) # Use default phasing
 # Install stockplotr
 pak::local_install(".")
 # Convert output
diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd
index ef04c037..b577e9c7 100644
--- a/man/save_all_plots.Rd
+++ b/man/save_all_plots.Rd
@@ -97,7 +97,7 @@ save_all_plots(
    ),
    plot_abundance_at_age_options = list(
      scale_amount = 1,         # custom scale for abundance-at-age plot
-     proportional = FALSE      # don't proportionalize abundance-at-age 
+     proportional = FALSE      # don't proportionalize abundance-at-age
    ),
    plot_spr_options = list(
      ylab = "Fishing Intensity (1-SPR)/(1-SPR_ref)" # custom Y label for SPR plot
diff --git a/man/table_landings.Rd b/man/table_landings.Rd
index 309b4161..1b78e1f8 100644
--- a/man/table_landings.Rd
+++ b/man/table_landings.Rd
@@ -106,7 +106,8 @@ containing a gt-based table, caption, and LaTeX-based table.
 }
 \examples{
 table_landings(stockplotr::example_data,
-  interactive = FALSE)
+  interactive = FALSE
+)
 
 table_landings(
   stockplotr::example_data,
diff --git a/man/table_projections.Rd b/man/table_projections.Rd
index 6a4c4fc5..b3e3e049 100644
--- a/man/table_projections.Rd
+++ b/man/table_projections.Rd
@@ -70,10 +70,10 @@ table_projections(
 )
 
 table_projections(
- dat = stockplotr::example_data,
- interactive = FALSE,
- catch_label = "kg",
- spawning_biomass_label = "kg",
- module = c(NULL, "DERIVED_QUANTITIES", "DERIVED_QUANTITIES")
- )
+  dat = stockplotr::example_data,
+  interactive = FALSE,
+  catch_label = "kg",
+  spawning_biomass_label = "kg",
+  module = c(NULL, "DERIVED_QUANTITIES", "DERIVED_QUANTITIES")
+)
 }
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-check_data.R b/tests/testthat/test-check_data.R
index 8884b3c3..16060d09 100644
--- a/tests/testthat/test-check_data.R
+++ b/tests/testthat/test-check_data.R
@@ -28,8 +28,10 @@ test_that("check_data rejects lists containing invalid elements", {
     "biomass",
     list(label = "biomass", estimate = 1),
     list(dat),
-    matrix(c("biomass", "1"), nrow = 1,
-           dimnames = list(NULL, c("label", "estimate"))),
+    matrix(c("biomass", "1"),
+      nrow = 1,
+      dimnames = list(NULL, c("label", "estimate"))
+    ),
     data.frame(),
     data.frame(label = "biomass"),
     data.frame(estimate = 1)
@@ -53,8 +55,10 @@ test_that("check_data rejects objects without the required structure", {
     1,
     "biomass",
     list(label = "biomass", estimate = 1),
-    matrix(c("biomass", "1"), nrow = 1,
-           dimnames = list(NULL, c("label", "estimate"))),
+    matrix(c("biomass", "1"),
+      nrow = 1,
+      dimnames = list(NULL, c("label", "estimate"))
+    ),
     data.frame(),
     data.frame(label = "biomass"),
     data.frame(estimate = 1)
diff --git a/tests/testthat/test-convert_output.R b/tests/testthat/test-convert_output.R
index 51d111c5..20ea9aaf 100644
--- a/tests/testthat/test-convert_output.R
+++ b/tests/testthat/test-convert_output.R
@@ -14,13 +14,13 @@ 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)) {
     # Ensure no errors occur while converting SS3 output
     expect_no_error(result <- convert_output(
-      file = r4ss::SS_output(file.path(models_to_test[i]))#file.path(models_to_test[i], "Report.sso")
+      file = r4ss::SS_output(file.path(models_to_test[i])) # file.path(models_to_test[i], "Report.sso")
     ))
 
     # Check that the result has exactly 35 columns
diff --git a/tests/testthat/test-export_rda.R b/tests/testthat/test-export_rda.R
index 8f2481dc..1bd0ae7b 100644
--- a/tests/testthat/test-export_rda.R
+++ b/tests/testthat/test-export_rda.R
@@ -85,46 +85,46 @@ test_that("export_rda works for tables", {
 
 
 test_that("export_rda to custom directory location", {
-    topic_label <- "biomass"
-    fig_or_table <- "figure"
-
-    B.min <- 100
-    B.max <- 200
-
-    custom_dir <- fs::path(getwd(), "tests-export_rda")
-
-    # add KQs to caps/alt text csv
-    insert_kqs(B.min, B.max, dir=custom_dir)
-
-    # extract this plot's caption and alt text
-    caps_alttext <- extract_caps_alttext(
-      topic_label = topic_label,
-      fig_or_table = fig_or_table,
-      dir = custom_dir
-    )
-
-    # make a simple plot
-    # library(ggplot2)
-    final <- ggplot2::ggplot(Orange, ggplot2::aes(circumference, age)) +
-      ggplot2::geom_point()
-
-    # export rda
-    export_rda(
-      object = final,
-      caps_alttext = caps_alttext,
-      figures_tables_dir = custom_dir,
-      topic_label = topic_label,
-      fig_or_table = fig_or_table
-    )
-
-    # expect that both figures dir and the biomass_figure.rda file exist
-    expect_true(dir.exists(fs::path(custom_dir, "figures")))
-    expect_true(file.exists(fs::path(
-      custom_dir, "figures", "biomass_figure.rda"
-    )))
-
-    # erase temporary testing files
-    file.remove(fs::path(custom_dir, "captions_alt_text.csv"))
-    # file.remove(fs::path(getwd(), "key_quantities.csv")) # file is not made in this test
-    unlink(fs::path(custom_dir, "figures"), recursive = T)
+  topic_label <- "biomass"
+  fig_or_table <- "figure"
+
+  B.min <- 100
+  B.max <- 200
+
+  custom_dir <- fs::path(getwd(), "tests-export_rda")
+
+  # add KQs to caps/alt text csv
+  insert_kqs(B.min, B.max, dir = custom_dir)
+
+  # extract this plot's caption and alt text
+  caps_alttext <- extract_caps_alttext(
+    topic_label = topic_label,
+    fig_or_table = fig_or_table,
+    dir = custom_dir
+  )
+
+  # make a simple plot
+  # library(ggplot2)
+  final <- ggplot2::ggplot(Orange, ggplot2::aes(circumference, age)) +
+    ggplot2::geom_point()
+
+  # export rda
+  export_rda(
+    object = final,
+    caps_alttext = caps_alttext,
+    figures_tables_dir = custom_dir,
+    topic_label = topic_label,
+    fig_or_table = fig_or_table
+  )
+
+  # expect that both figures dir and the biomass_figure.rda file exist
+  expect_true(dir.exists(fs::path(custom_dir, "figures")))
+  expect_true(file.exists(fs::path(
+    custom_dir, "figures", "biomass_figure.rda"
+  )))
+
+  # erase temporary testing files
+  file.remove(fs::path(custom_dir, "captions_alt_text.csv"))
+  # file.remove(fs::path(getwd(), "key_quantities.csv")) # file is not made in this test
+  unlink(fs::path(custom_dir, "figures"), recursive = T)
 })
diff --git a/tests/testthat/test-extract_sis_data.R b/tests/testthat/test-extract_sis_data.R
index 45641925..08238009 100644
--- a/tests/testthat/test-extract_sis_data.R
+++ b/tests/testthat/test-extract_sis_data.R
@@ -1,40 +1,43 @@
 test_that("extract_sis_data() runs with all possible rdas present", {
-
   savedir <- fs::path(getwd(), "test-extract_sis_data")
-  if(!dir.exists(savedir))
+  if (!dir.exists(savedir)) {
     dir.create(savedir)
+  }
 
-  save_all_plots(stockplotr::example_data, figures_tables_dir=savedir)
+  save_all_plots(stockplotr::example_data, figures_tables_dir = savedir)
   # table_total_catch(stockplotr::example_data,
   #                   module = "TIME_SERIES",
   #                   interactive = FALSE,
   #                   make_rda = TRUE)
 
   files <- c(
-    fs::path(savedir, "figures",
-             c("biomass_figure.rda", "spawning_biomass_figure.rda", "abundance_at_age_figure.rda", "fishing_mortality_figure.rda",  "index_figure.rda")
-             ),
-    fs::path(savedir, "tables",
-             "total_catch_table.rda")
+    fs::path(
+      savedir, "figures",
+      c("biomass_figure.rda", "spawning_biomass_figure.rda", "abundance_at_age_figure.rda", "fishing_mortality_figure.rda", "index_figure.rda")
+    ),
+    fs::path(
+      savedir, "tables",
+      "total_catch_table.rda"
+    )
   )
 
   expect_true(all(file.exists(files)))
 
-  extract_sis_data(sis_data_dir=savedir, key_quantities_dir=savedir, figures_tables_dir=savedir)
+  extract_sis_data(sis_data_dir = savedir, key_quantities_dir = savedir, figures_tables_dir = savedir)
 
   # erase temporary testing files
-  unlink(fs::path(savedir), recursive=TRUE)
+  unlink(fs::path(savedir), recursive = TRUE)
 })
 
 test_that("extract_sis_data() runs with some of all possible rdas present", {
-
   savedir <- fs::path(getwd(), "test-extract_sis_data")
-  if(!dir.exists(savedir))
+  if (!dir.exists(savedir)) {
     dir.create(savedir)
+  }
 
-  plot_biomass(stockplotr::example_data, module = "TIME_SERIES", interactive = FALSE, make_rda = TRUE, figures_dir=savedir)
-  plot_fishing_mortality(stockplotr::example_data, interactive = FALSE, make_rda = TRUE, figures_dir=savedir)
-  expect_no_error(extract_sis_data(sis_data_dir=savedir, key_quantities_dir=savedir, figures_tables_dir=savedir))
+  plot_biomass(stockplotr::example_data, module = "TIME_SERIES", interactive = FALSE, make_rda = TRUE, figures_dir = savedir)
+  plot_fishing_mortality(stockplotr::example_data, interactive = FALSE, make_rda = TRUE, figures_dir = savedir)
+  expect_no_error(extract_sis_data(sis_data_dir = savedir, key_quantities_dir = savedir, figures_tables_dir = savedir))
 
   # test that extract_sis_data() exports csvs
   expect_true(file.exists(fs::path(savedir, "sis_assmt_template.csv")))
@@ -46,10 +49,11 @@ test_that("extract_sis_data() runs with some of all possible rdas present", {
 
 test_that("extract_sis_data() fails with no rdas present", {
   savedir <- fs::path(getwd(), "test-extract_sis_data")
-  if(!dir.exists(savedir))
+  if (!dir.exists(savedir)) {
     dir.create(savedir)
-    
-  expect_error(extract_sis_data(sis_data_dir=savedir, key_quantities_dir=savedir, figures_tables_dir=savedir))
+  }
+
+  expect_error(extract_sis_data(sis_data_dir = savedir, key_quantities_dir = savedir, figures_tables_dir = savedir))
 
   # erase temporary testing files
   unlink(fs::path(savedir), recursive = TRUE)
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_recruitment.R b/tests/testthat/test-plot_recruitment.R
index 1cd652e4..979f26fb 100644
--- a/tests/testthat/test-plot_recruitment.R
+++ b/tests/testthat/test-plot_recruitment.R
@@ -53,4 +53,3 @@ test_that("plot_recruitment generates plots without errors", {
     "gg"
   )
 })
-
diff --git a/tests/testthat/test-plot_spr.R b/tests/testthat/test-plot_spr.R
index dffac3d3..5c4d984f 100644
--- a/tests/testthat/test-plot_spr.R
+++ b/tests/testthat/test-plot_spr.R
@@ -3,7 +3,7 @@ test_that("plot_spr generates plots without errors", {
   expect_no_error(
     plot_spr(stockplotr::example_data, interactive = FALSE)
   )
-  
+
   # expect error-free plot with many arguments
   expect_no_error(
     plot_spr(
@@ -14,7 +14,7 @@ test_that("plot_spr generates plots without errors", {
     )
   )
 
-  
+
   # expect ggplot object is returned
   expect_s3_class(
     plot_spr(
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index 4ddc4e3e..cd1b773c 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -26,10 +26,10 @@ tab_base_temp_files <- c(
 )
 
 test_that("save_all_plots works when all figures/tables are plotted", {
-
   savedir <- fs::path(getwd(), "test-save_all_plots")
-  if(!dir.exists(savedir))
+  if (!dir.exists(savedir)) {
     dir.create(savedir)
+  }
 
   save_all_plots(
     stockplotr::example_data,
@@ -53,125 +53,125 @@ test_that("save_all_plots works when all figures/tables are plotted", {
   )
 
   # erase temporary testing files
-  unlink(fs::path(savedir), recursive=TRUE)
-  
+  unlink(fs::path(savedir), recursive = TRUE)
 })
 
 test_that("save_all_plots with custom plot options", {
-    
-    savedir <- fs::path(getwd(), "test-save_all_plots")
-    if(!dir.exists(savedir))
-      dir.create(savedir)
+  savedir <- fs::path(getwd(), "test-save_all_plots")
+  if (!dir.exists(savedir)) {
+    dir.create(savedir)
+  }
 
-    
-    save_all_plots(
-      stockplotr::example_data,
-      figures_tables_dir = savedir,
-      interactive = FALSE,
-      plot_spawning_biomass_options = list(
-        ref_line = "target"
-      ),
-      plot_abundance_at_age_options = list(
-        scale_amount = 1000
-      )
+
+  save_all_plots(
+    stockplotr::example_data,
+    figures_tables_dir = savedir,
+    interactive = FALSE,
+    plot_spawning_biomass_options = list(
+      ref_line = "target"
+    ),
+    plot_abundance_at_age_options = list(
+      scale_amount = 1000
     )
+  )
 
-    # expect that the figures and tables dirs exist
-    expect_true(dir.exists(fs::path(savedir, "figures")))
-    expect_true(dir.exists(fs::path(savedir, "tables")))
+  # expect that the figures and tables dirs exist
+  expect_true(dir.exists(fs::path(savedir, "figures")))
+  expect_true(dir.exists(fs::path(savedir, "tables")))
 
-    # expect that the figures are all created with expected names
-    
-    expect_equal(
-      sort(list.files(fs::path(savedir, "figures"))),
-      sort(fig_base_temp_files)
-    )
+  # expect that the figures are all created with expected names
 
-    # expect that the tables are all created with expected names
-    expect_equal(
-      sort(list.files(fs::path(savedir, "tables"))),
-      sort(tab_base_temp_files)
-    )
+  expect_equal(
+    sort(list.files(fs::path(savedir, "figures"))),
+    sort(fig_base_temp_files)
+  )
+
+  # expect that the tables are all created with expected names
+  expect_equal(
+    sort(list.files(fs::path(savedir, "tables"))),
+    sort(tab_base_temp_files)
+  )
 
-    # erase temporary testing files
-    unlink(fs::path(savedir), recursive=TRUE)
+  # erase temporary testing files
+  unlink(fs::path(savedir), recursive = TRUE)
 })
 
 test_that("save_all_plots returns error when plot not made", {
+  savedir <- fs::path(getwd(), "test-save_all_plots")
+  if (!dir.exists(savedir)) {
+    dir.create(savedir)
+  }
 
-    savedir <- fs::path(getwd(), "test-save_all_plots")
-    if(!dir.exists(savedir))
-      dir.create(savedir)
-
-    save_all_plots(
-      stockplotr::example_data,
-      figures_tables_dir = savedir,
-      interactive = FALSE,
-      plot_natural_mortality_options = list(
-        module = NULL
-      )
+  save_all_plots(
+    stockplotr::example_data,
+    figures_tables_dir = savedir,
+    interactive = FALSE,
+    plot_natural_mortality_options = list(
+      module = NULL
     )
+  )
 
-    # expect that the figures and tables dirs exist
-    expect_true(dir.exists(fs::path(savedir, "figures")))
-    expect_true(dir.exists(fs::path(savedir, "tables")))
+  # expect that the figures and tables dirs exist
+  expect_true(dir.exists(fs::path(savedir, "figures")))
+  expect_true(dir.exists(fs::path(savedir, "tables")))
 
-    # expect that the figures are all created with expected names
-    # no natural_mortality_figure.rda as that throws and error
-    # and is not generated in this test.
-    expect_equal(
-      sort(list.files(fs::path(savedir, "figures"))),
-      sort(fig_base_temp_files[which(!grepl("natural_mortality", fig_base_temp_files))])
-    )
+  # expect that the figures are all created with expected names
+  # no natural_mortality_figure.rda as that throws and error
+  # and is not generated in this test.
+  expect_equal(
+    sort(list.files(fs::path(savedir, "figures"))),
+    sort(fig_base_temp_files[which(!grepl("natural_mortality", fig_base_temp_files))])
+  )
 
-    # expect that the tables are all created with expected names
-    expect_equal(
-      sort(list.files(fs::path(savedir, "tables"))),
-      sort(tab_base_temp_files)
-    )
+  # expect that the tables are all created with expected names
+  expect_equal(
+    sort(list.files(fs::path(savedir, "tables"))),
+    sort(tab_base_temp_files)
+  )
 
-    # erase temporary testing files
-    unlink(fs::path(savedir), recursive=TRUE)
+  # erase temporary testing files
+  unlink(fs::path(savedir), recursive = TRUE)
 })
 
 test_that("save_all_plots returns error when dat is not valid", {
-    savedir <- fs::path(getwd(), "test-save_all_plots")
-    if(!dir.exists(savedir))
-      dir.create(savedir)
-
-    expect_error(
-      save_all_plots(
-        r4ss::SS_output(file.path(test_path("fixtures", "ss3_models"), "models", "Hake_2018", "Report.sso")),
-        figures_tables_dir = savedir,
-        interactive = FALSE,
-        plot_natural_mortality_options = list(
-          module = NULL
-        )
+  savedir <- fs::path(getwd(), "test-save_all_plots")
+  if (!dir.exists(savedir)) {
+    dir.create(savedir)
+  }
+
+  expect_error(
+    save_all_plots(
+      r4ss::SS_output(file.path(test_path("fixtures", "ss3_models"), "models", "Hake_2018", "Report.sso")),
+      figures_tables_dir = savedir,
+      interactive = FALSE,
+      plot_natural_mortality_options = list(
+        module = NULL
       )
     )
+  )
 
-    expect_error(
-      save_all_plots(
-        data.frame(),
-        figures_tables_dir = savedir,
-        interactive = FALSE,
-        plot_natural_mortality_options = list(
-          module = NULL
-        )
+  expect_error(
+    save_all_plots(
+      data.frame(),
+      figures_tables_dir = savedir,
+      interactive = FALSE,
+      plot_natural_mortality_options = list(
+        module = NULL
       )
     )
+  )
 
-    expect_error(
-      save_all_plots(
-        data.frame(label="label"),
-        figures_tables_dir = savedir,
-        interactive = FALSE,
-        plot_natural_mortality_options = list(
-          module = NULL
-        )
+  expect_error(
+    save_all_plots(
+      data.frame(label = "label"),
+      figures_tables_dir = savedir,
+      interactive = FALSE,
+      plot_natural_mortality_options = list(
+        module = NULL
       )
     )
-    
-    # erase temporary testing files
-    unlink(fs::path(savedir), recursive=TRUE)
+  )
+
+  # erase temporary testing files
+  unlink(fs::path(savedir), recursive = TRUE)
 })
diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index 0db427d4..b0067d98 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -51,4 +51,4 @@ test_that("table_landings generates error with incorrect module", {
       tables_dir = getwd()
     )
   )
-})
\ No newline at end of file
+})
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).