From 84f91eca85299d7a9942f665b3af188def4391c5 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Tue, 18 Aug 2026 16:57:41 -0400
Subject: [PATCH 1/6] Draft Exec Summary catch table

---
 NAMESPACE          |   1 +
 R/table_catch.R    | 147 +++++++++++++++++++++++++++++++++++++++++++++
 man/table_catch.Rd |  90 +++++++++++++++++++++++++++
 3 files changed, 238 insertions(+)
 create mode 100644 R/table_catch.R
 create mode 100644 man/table_catch.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 9645f508..16189ec1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,6 +27,7 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
+export(table_catch)
 export(table_index)
 export(table_landings)
 export(table_projections)
diff --git a/R/table_catch.R b/R/table_catch.R
new file mode 100644
index 00000000..08093f5e
--- /dev/null
+++ b/R/table_catch.R
@@ -0,0 +1,147 @@
+#' Catch (table) by fleet, gear type, sector
+#'
+#' @inheritParams plot_recruitment
+#' @param unit_label String. Abbreviated catch units
+#'
+#' Default: "mt"
+#' 
+#' @param digits Number. Numeric value indicating the number of digits catch values in the
+#' table will be rounded to.
+#'
+#' Default: 2
+#' 
+#' @param tables_dir Path. The location of the folder containing the generated table
+#' rda files ("tables") that will be created if the argument `make_rda` = TRUE.
+#'
+#' Default: the working directory (`getwd()`)
+#'
+#' @returns A table ready of landed catch by fleet and year.
+#'
+#' @details The input is from an assessment model output file
+#' translated to a standardized output (\link[stockplotr]{convert_output}).
+#' There are options to return a [gt::gt()] object or export an rda object
+#' containing a gt-based table, caption, and LaTeX-based table.
+#'
+#' @seealso [convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()]
+#' @export
+#'
+#' @examples
+#' table_catch(stockplotr::example_data)
+#'
+#' table_catch(
+#'   stockplotr::example_data,
+#'   unit_label = "lbs"
+#' )
+table_catch <- function(
+  dat,
+  unit_label = "mt",
+  era = NULL,
+  interactive = TRUE,
+  module = NULL,
+  scale_amount = 1,
+  digits = 2,
+  make_rda = FALSE,
+  tables_dir = getwd()
+) {
+  # set unit label if scaled
+  unit_label <- label_magnitude(
+    label = "",
+    unit_label = unit_label,
+    scale_amount = scale_amount
+  )
+
+  # Filter data for catch
+  prepared_data <- filter_data(
+    dat = dat,
+    label_name = "catch",
+    geom = "line",
+    era = era,
+    module = module,
+    scale_amount = scale_amount,
+    interactive = interactive
+  )
+
+  # Check if there is any data and if all labels contain "catchability", not "catch"
+  if (nrow(prepared_data) == 0 | unique(stringr::str_detect(prepared_data$label, "catchability"))) {
+    cli::cli_abort("No catch data found.")
+  }
+  
+  catch <- prepared_data |>
+    dplyr::filter(label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")) |>
+    dplyr::filter(!is.na(year)) |>
+    dplyr::filter(!is.na(estimate)) |>
+    dplyr::group_by(year, fleet, sex, area, season, type) |>
+    dplyr::summarise(total_catch = sum(estimate)) |>
+    dplyr::mutate(total_catch = round(total_catch, digits = digits)) |>
+    dplyr::ungroup()
+  
+  # filter out columns if there is only one unique value
+  cols_to_remove <- c()
+  for (i in 1:ncol(catch)){
+    if (length(unique(catch[[i]])) == 1) {
+      cols_to_remove <- c(cols_to_remove,
+                          colnames(catch[i]))
+    }
+  }
+  
+  catch <- catch |>
+    dplyr::select(-cols_to_remove)
+  
+  names(catch) <- stringr::str_to_title(names(catch))
+  
+  if ("Fleet" %in% colnames(catch)){
+    catch <- catch |>
+      tidyr::pivot_wider(names_from = Fleet,
+                         names_glue = "Fleet {Fleet} {unit_label}",
+                         values_from = Total_catch)
+  } else {
+    catch <- catch |>
+      dplyr::rename_with(~ paste0("Catch", unit_label), .cols = Total_catch)
+  }
+  
+  # transform dfs into tables
+  final <- catch |>
+      gt::gt() |>
+      theme_table()
+
+  # export figure to rda if argument = T
+  if (make_rda == TRUE) {
+    if (length(df_list) == 1) {
+      # Obtain relevant key quantities for captions/alt text
+      catch.units <- unit_label
+
+      # calculate & export key quantities
+      export_kqs(catch.units)
+
+      # Add key quantities to captions/alt text
+      insert_kqs(catch.units)
+
+      create_rda(
+        object = final[[1]],
+        # 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,
+        unit_label = unit_label,
+        table_df = final
+      )
+    }
+  } else {
+    cli::cli_alert_warning("Multiple tables cannot be exported at this time.")
+    cli::cli_alert_info("We are currently developing this feature.")
+  }
+
+  # Send table(s) to viewer
+  if (!is.data.frame(table_data)) {
+    for (t in final) {
+      print(t)
+    }
+    # Return table list invisibly
+    return(invisible(final))
+  } else {
+    # Return finished table (when only one table)
+    return(final)
+  }
+}
diff --git a/man/table_catch.Rd b/man/table_catch.Rd
new file mode 100644
index 00000000..2fb98914
--- /dev/null
+++ b/man/table_catch.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/table_catch.R
+\name{table_catch}
+\alias{table_catch}
+\title{Catch (table) by fleet, gear type, sector}
+\usage{
+table_catch(
+  dat,
+  unit_label = "mt",
+  era = NULL,
+  interactive = TRUE,
+  module = NULL,
+  scale_amount = 1,
+  digits = 2,
+  make_rda = FALSE,
+  tables_dir = getwd()
+)
+}
+\arguments{
+\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`)
+returned from \link[stockplotr]{convert_output}.
+
+If inputting a list of tibbles, the first tibble's reference point defined
+in `ref_line` is used to plot a reference line or calculate relative spawning biomass.}
+
+\item{unit_label}{String. Abbreviated catch units
+
+Default: "mt"}
+
+\item{era}{String. Era of data.
+
+Default: "time"
+
+Options: "early", "time", "fore" (forecast), or NULL (all data)}
+
+\item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive.
+
+Default: `FALSE`}
+
+\item{module}{Character vector. (Optional) Module name found in `dat$module_name`.
+If selecting >1 module, place them in a vector like c("module1", "module2").
+
+Default: NULL
+
+If the interactive and >1 module_name is found, user will select the
+module_name in the console. @seealso [filter_data()]}
+
+\item{scale_amount}{Number. A number to scale the y-axis values.
+
+Default: 1}
+
+\item{digits}{Number. Numeric value indicating the number of digits catch values in the
+table will be rounded to.
+
+Default: 2}
+
+\item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and
+make an automated caption and alternative text in the form of an `rda` object. If TRUE,
+the rda will be exported to the folder indicated in the argument "figures_dir".
+
+Default: `FALSE`.}
+
+\item{tables_dir}{Path. The location of the folder containing the generated table
+rda files ("tables") that will be created if the argument `make_rda` = TRUE.
+
+Default: the working directory (`getwd()`)}
+}
+\value{
+A table ready of landed catch by fleet and year.
+}
+\description{
+Catch (table) by fleet, gear type, sector
+}
+\details{
+The input is from an assessment model output file
+translated to a standardized output (\link[stockplotr]{convert_output}).
+There are options to return a [gt::gt()] object or export an rda object
+containing a gt-based table, caption, and LaTeX-based table.
+}
+\examples{
+table_catch(stockplotr::example_data)
+
+table_catch(
+  stockplotr::example_data,
+  unit_label = "lbs"
+)
+}
+\seealso{
+[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()]
+}

From 21a442fc7ff91b2d45141dca359bd76f432e0279 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Wed, 19 Aug 2026 11:53:50 -0400
Subject: [PATCH 2/6] Update table_catch() key quantity pipeline

---
 R/table_catch.R                               | 25 ++++++-------------
 inst/resources/captions_alt_text_template.csv |  2 +-
 inst/resources/key_quantity_template.csv      |  1 +
 3 files changed, 9 insertions(+), 19 deletions(-)

diff --git a/R/table_catch.R b/R/table_catch.R
index 08093f5e..29d37eb5 100644
--- a/R/table_catch.R
+++ b/R/table_catch.R
@@ -92,7 +92,7 @@ table_catch <- function(
   if ("Fleet" %in% colnames(catch)){
     catch <- catch |>
       tidyr::pivot_wider(names_from = Fleet,
-                         names_glue = "Fleet {Fleet} {unit_label}",
+                         names_glue = stringr::str_glue("Fleet {{Fleet}}{unit_label}"),
                          values_from = Total_catch)
   } else {
     catch <- catch |>
@@ -106,18 +106,17 @@ table_catch <- function(
 
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
-    if (length(df_list) == 1) {
       # Obtain relevant key quantities for captions/alt text
-      catch.units <- unit_label
+      tot.catch.units <- unit_label
 
       # calculate & export key quantities
-      export_kqs(catch.units)
+      export_kqs(tot.catch.units)
 
       # Add key quantities to captions/alt text
-      insert_kqs(catch.units)
+      insert_kqs(tot.catch.units)
 
       create_rda(
-        object = final[[1]],
+        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",
@@ -127,21 +126,11 @@ table_catch <- function(
         unit_label = unit_label,
         table_df = final
       )
-    }
-  } else {
+
     cli::cli_alert_warning("Multiple tables cannot be exported at this time.")
     cli::cli_alert_info("We are currently developing this feature.")
   }
 
   # Send table(s) to viewer
-  if (!is.data.frame(table_data)) {
-    for (t in final) {
-      print(t)
-    }
-    # Return table list invisibly
-    return(invisible(final))
-  } else {
-    # Return finished table (when only one table)
-    return(final)
-  }
+  final
 }
diff --git a/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv
index 42c0db88..17db477d 100644
--- a/inst/resources/captions_alt_text_template.csv
+++ b/inst/resources/captions_alt_text_template.csv
@@ -32,7 +32,7 @@ proj.catch,figure,Forecasted catch in proj.catch.units over future years for dif
 proj.biomass,table,Forecasted biomass over future years for different fishing mortality scenarios.,
 report.version.model.changes,table,Document version history briefly describing when major changes or updates are made to each version of the report.,
 projections,table,"Forecasted catch, spawning biomass, and fishing mortality over future years. ",
-catch,table,Observed (points) and model estimated (line) catch over time for fleet catch.fleet.,
+catch,table,Total catch over time.,
 life.history.params,table,Life history parameters used in the stock assessment model. The last column of the table indicates whether the parameters were estimated by the model or fixed.,
 landings,table,Landed catch by fleet and year in landings.units.,
 discards,table,Discarded catch by fleet and year in discards.tbl.units.,
diff --git a/inst/resources/key_quantity_template.csv b/inst/resources/key_quantity_template.csv
index e074e83f..540c4f91 100644
--- a/inst/resources/key_quantity_template.csv
+++ b/inst/resources/key_quantity_template.csv
@@ -131,6 +131,7 @@ ssb.start.year,,start year of the SSB time series,,,,
 ssb.units,,units for spawning biomass,,,,
 tot.catch.max,,maximum total catch,,,,
 tot.catch.min,,minimum total catch,,,,
+tot.catch.units,,units for total catch,,,,
 total.length.max,,maximum total length,,,,
 total.length.min,,minimum total length,,,,
 total.length.units,,units for total length,,,,

From 1c6e56b25f9e45a1789482649fa47e6a8e749377 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Wed, 19 Aug 2026 16:02:41 -0400
Subject: [PATCH 3/6] Add uncertainty to catch table; update examples

---
 R/table_catch.R    | 109 ++++++++++++++++++++++++++++++++-------------
 man/table_catch.Rd |   5 ++-
 2 files changed, 82 insertions(+), 32 deletions(-)

diff --git a/R/table_catch.R b/R/table_catch.R
index 29d37eb5..dfdae862 100644
--- a/R/table_catch.R
+++ b/R/table_catch.R
@@ -30,7 +30,10 @@
 #'
 #' table_catch(
 #'   stockplotr::example_data,
-#'   unit_label = "lbs"
+#'   unit_label = "lbs",
+#'   module = "TIME_SERIES",
+#'   digits = 4,
+#'   scale_amount = 100
 #' )
 table_catch <- function(
   dat,
@@ -59,26 +62,48 @@ table_catch <- function(
     module = module,
     scale_amount = scale_amount,
     interactive = interactive
-  )
+  ) |>
+    dplyr::filter(label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")) |>
+    dplyr::filter(!is.na(year)) |>
+    dplyr::filter(!is.na(estimate))
 
   # Check if there is any data and if all labels contain "catchability", not "catch"
   if (nrow(prepared_data) == 0 | unique(stringr::str_detect(prepared_data$label, "catchability"))) {
     cli::cli_abort("No catch data found.")
   }
   
+  # get uncertainty label by model
+  uncert_lab <- prepared_data |>
+    dplyr::filter(!is.na(uncertainty_label)) |>
+    dplyr::group_by(model) |>
+    dplyr::reframe(unique_uncert = unique(uncertainty_label)) # changed to reframe -- may cause errors
+  uncert_lab <- stats::setNames(uncert_lab$unique_uncert, uncert_lab$model)
+  # if (length(unique(uncert_lab)) == 1) uncert_lab <- unique(uncert_lab) # might need this line
+  
+  # This needs to be adjusted when comparing different models and diff error
+  if (length(uncert_lab) > 1 & length(unique(uncert_lab)) == 1 | length(names(uncert_lab)) == 1) { # prepared_data$model
+    # cli::cli_alert_warning("More than one value for uncertainty exists: {uncert_lab}")
+    uncert_lab <- uncert_lab[[1]]
+    # cli::cli_alert_warning("The first value ({uncert_lab}) will be chosen.")
+  }
+  
+  if (length(uncert_lab) == 0 || is.na(uncert_lab)) uncert_lab <- "uncertainty"
+
   catch <- prepared_data |>
-    dplyr::filter(label %in% c("catch_retained", "catch_dead", "catch_selected", "catch")) |>
-    dplyr::filter(!is.na(year)) |>
-    dplyr::filter(!is.na(estimate)) |>
-    dplyr::group_by(year, fleet, sex, area, season, type) |>
+    dplyr::group_by(year, fleet, sex, area, season, type, uncertainty) |>
     dplyr::summarise(total_catch = sum(estimate)) |>
     dplyr::mutate(total_catch = round(total_catch, digits = digits)) |>
+    dplyr::mutate(total_catch = format(total_catch, big.mark = ",")) |>
     dplyr::ungroup()
   
   # filter out columns if there is only one unique value
   cols_to_remove <- c()
   for (i in 1:ncol(catch)){
-    if (length(unique(catch[[i]])) == 1) {
+    if (length(unique(catch[[i]])) == 1 & names(catch[i]) != "uncertainty") {
+      cols_to_remove <- c(cols_to_remove,
+                        colnames(catch[i]))
+    }
+    if (names(catch[i]) == "uncertainty" && is.na(unique(catch[[i]]))) {
       cols_to_remove <- c(cols_to_remove,
                           colnames(catch[i]))
     }
@@ -87,17 +112,39 @@ table_catch <- function(
   catch <- catch |>
     dplyr::select(-cols_to_remove)
   
+  if ("uncertainty" %in% colnames(catch)) {
+    catch <- catch |>
+      dplyr::mutate(total_catch = paste0(total_catch, " (", uncertainty, ")")) |>
+      dplyr::rename_with(~ paste0("total_catch (", uncert_lab, ")"), .cols = total_catch)  |>   
+      dplyr::select(-uncertainty)
+  }
+  
   names(catch) <- stringr::str_to_title(names(catch))
   
+  if (uncert_lab %in% cols_to_remove){
+    uncert_lab <- ""
+  }
+  
   if ("Fleet" %in% colnames(catch)){
-    catch <- catch |>
-      tidyr::pivot_wider(names_from = Fleet,
-                         names_glue = stringr::str_glue("Fleet {{Fleet}}{unit_label}"),
-                         values_from = Total_catch)
+    if (uncert_lab != ""){
+      catch <- catch |>
+        tidyr::pivot_wider(names_from = Fleet,
+                           names_glue = stringr::str_glue("Fleet {{Fleet}}{unit_label} ({uncert_lab})"),
+                           values_from = dplyr::starts_with("Total_catch"))
+    } else {
+      catch <- catch |>
+        tidyr::pivot_wider(names_from = Fleet,
+                           names_glue = stringr::str_glue("Fleet {{Fleet}}{unit_label}"),
+                           values_from = dplyr::starts_with("Total_catch"))
+    }
   } else {
-    catch <- catch |>
-      dplyr::rename_with(~ paste0("Catch", unit_label), .cols = Total_catch)
-  }
+    if (uncert_lab != ""){
+      catch <- catch |>
+        dplyr::rename_with(~ paste0("Catch", unit_label, " (", uncert_lab, ")"), .cols = dplyr::starts_with("Total_catch"))
+      } else {
+      catch <- catch |>
+        dplyr::rename_with(~ paste0("Catch", unit_label), .cols = dplyr::starts_with("Total_catch"))}
+    }
   
   # transform dfs into tables
   final <- catch |>
@@ -106,26 +153,26 @@ table_catch <- function(
 
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
-      # Obtain relevant key quantities for captions/alt text
-      tot.catch.units <- unit_label
+    # Obtain relevant key quantities for captions/alt text
+    tot.catch.units <- unit_label
 
-      # calculate & export key quantities
-      export_kqs(tot.catch.units)
+    # calculate & export key quantities
+    export_kqs(tot.catch.units)
 
-      # Add key quantities to captions/alt text
-      insert_kqs(tot.catch.units)
+    # Add key quantities to captions/alt text
+    insert_kqs(tot.catch.units)
 
-      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,
-        unit_label = unit_label,
-        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,
+      unit_label = unit_label,
+      table_df = final
+    )
 
     cli::cli_alert_warning("Multiple tables cannot be exported at this time.")
     cli::cli_alert_info("We are currently developing this feature.")
diff --git a/man/table_catch.Rd b/man/table_catch.Rd
index 2fb98914..47ce5ebc 100644
--- a/man/table_catch.Rd
+++ b/man/table_catch.Rd
@@ -82,7 +82,10 @@ table_catch(stockplotr::example_data)
 
 table_catch(
   stockplotr::example_data,
-  unit_label = "lbs"
+  unit_label = "lbs",
+  module = "TIME_SERIES",
+  digits = 4,
+  scale_amount = 100
 )
 }
 \seealso{

From 9c7fa0129c68ba7daacf948ac7aab98c49b3407f Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Wed, 19 Aug 2026 16:03:02 -0400
Subject: [PATCH 4/6] Add tests (and fix/consolidate other table tests)

---
 tests/testthat/test-table_catch.R    | 126 +++++++++++++++++++++++++++
 tests/testthat/test-table_index.R    |   4 +-
 tests/testthat/test-table_landings.R |   3 -
 3 files changed, 127 insertions(+), 6 deletions(-)
 create mode 100644 tests/testthat/test-table_catch.R

diff --git a/tests/testthat/test-table_catch.R b/tests/testthat/test-table_catch.R
new file mode 100644
index 00000000..bb718472
--- /dev/null
+++ b/tests/testthat/test-table_catch.R
@@ -0,0 +1,126 @@
+test_that("table_catch generates plots without errors", {
+  # expect error-free plot with minimal arguments
+  expect_no_error(
+    table_catch(
+      stockplotr::example_data,
+      interactive = FALSE,
+      module = "TIME_SERIES"
+    )
+  )
+
+  # expect error-free plot with many arguments
+  expect_no_error(
+    table_catch(
+      dat = stockplotr::example_data,
+      unit_label = "mt",
+      interactive = FALSE,
+      module = "TIME_SERIES",
+      make_rda = FALSE,
+      tables_dir = getwd()
+    )
+  )
+
+
+  # expect gt object is returned
+  # adjust this test to work for multiple output tables
+  # expect_s3_class(
+  #   table_catch(
+  #     dat = stockplotr::example_data,
+  #     unit_label = "mt",
+  #     era = NULL,
+  #     interactive = FALSE,
+  #     module = "TIME_SERIES",
+  #     make_rda = FALSE,
+  #     tables_dir = getwd()
+  #   ),
+  #   "gt_tbl"
+  # )
+})
+
+test_that("rda file made when indicated", {
+  # export rda
+  table_catch(
+    dat = stockplotr::example_data,
+    unit_label = "mt",
+    era = NULL,
+    interactive = FALSE,
+    module = "TIME_SERIES",
+    make_rda = TRUE,
+    tables_dir = getwd()
+  )
+
+  # expect that both tables dir and the catch_table.rda file exist
+  expect_true(dir.exists(fs::path(getwd(), "tables")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "catch_table.rda")))
+
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+})
+
+test_that("table_catch generates error with incorrect module", {
+  # expect error
+  # Need to test this -- not exactly the right test/result
+  expect_error(
+    table_catch(
+      dat = stockplotr::example_data,
+      unit_label = "mt",
+      era = NULL,
+      interactive = FALSE,
+      module = "SPR_SERIES",
+      make_rda = FALSE,
+      tables_dir = getwd()
+    )
+  )
+})
+
+
+test_that("rda file made when indicated", {
+  # export rda
+  table_catch(
+    dat = stockplotr::example_data,
+    module = "TIME_SERIES",
+    make_rda = TRUE,
+    tables_dir = getwd()
+  )
+  
+  # expect that both tables dir and the catch_table.rda file exist
+  expect_true(dir.exists(fs::path(getwd(), "tables")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "catch_table.rda")))
+  
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+
+  
+  # export rda
+  table_catch(
+    dat = stockplotr::example_data,
+    module = "TIME_SERIES",
+    make_rda = TRUE,
+    tables_dir = getwd()
+  )
+  
+  # load the rda file and check that it contains the expected object
+  load(fs::path(getwd(), "tables", "catch_table.rda"))
+  # expect rda contains three objects: table, caption, and latex table
+  expect_false(
+    is.null(rda$table)
+  )
+  expect_false(
+    is.null(rda$caption)
+  )
+  expect_false(
+    is.null(rda$latex_table)
+  )
+  
+  expect_true(rda$caption == "Total catch over time.")
+  
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  file.remove(fs::path(getwd(), "key_quantities.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+})
+
diff --git a/tests/testthat/test-table_index.R b/tests/testthat/test-table_index.R
index 43869f99..088eca87 100644
--- a/tests/testthat/test-table_index.R
+++ b/tests/testthat/test-table_index.R
@@ -48,10 +48,8 @@ test_that("rda file made when indicated", {
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
   unlink(fs::path(getwd(), "tables"), recursive = T)
-})
-
 
-test_that("rda file made when indicated", {
+  
   # export rda
   table_index(
     dat = stockplotr::example_data,
diff --git a/tests/testthat/test-table_landings.R b/tests/testthat/test-table_landings.R
index a177a4d6..8a1ccb4b 100644
--- a/tests/testthat/test-table_landings.R
+++ b/tests/testthat/test-table_landings.R
@@ -92,10 +92,7 @@ test_that("rda file made when indicated", {
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
   file.remove(fs::path(getwd(), "key_quantities.csv"))
   unlink(fs::path(getwd(), "tables"), recursive = T)
-})
-
 
-test_that("rda file made when indicated", {
   # export rda
   table_landings(
     dat = stockplotr::example_data,

From 3d2646ccf1ed5835bfe9c30f62b4bf477c2d109a Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Wed, 19 Aug 2026 16:37:28 -0400
Subject: [PATCH 5/6] Update save_all_plots() and test for catch table

---
 R/save_all_plots.R                   | 28 +++++++++++++++++++++-------
 man/save_all_plots.Rd                |  6 ------
 tests/testthat/test-save_all_plots.R |  7 ++++---
 3 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index 75c19584..228319eb 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -105,12 +105,6 @@
 #'
 #' Default: c("catch" = "mt", "spawning_biomass" = "mt", 
 #' "fishing_mortality" = "")
-#' 
-#' @param projections_uncert_label Abbreviated uncertainty label for
-#' each quantity
-#' 
-#' Default: c("catch" = "stddev", "spawning_biomass" = "stddev",
-#' "fishing_mortality" = "stddev")
 #'
 #' @param proportional Logical. TRUE/FALSE; scale size of bubble plots
 #'
@@ -493,6 +487,26 @@ save_all_plots <- function(
   #   }
   # )
 
+  tryCatch(
+    {
+      cli::cli_h2("table_catch")
+      table_catch(
+        dat,
+        unit_label = catch_unit_label,
+        interactive = interactive,
+        make_rda = TRUE,
+        tables_dir = figures_tables_dir
+      ) # |>
+      # suppressWarnings() |>
+      # invisible()
+    },
+    error = function(e) {
+      cli::cli_alert_danger("table_catch failed to run.")
+      cli::cli_alert("Tip: check that your arguments are correct.")
+      print(e)
+    }
+  )
+  
   tryCatch(
     {
       cli::cli_h2("table_index")
@@ -549,7 +563,7 @@ save_all_plots <- function(
       cli::cli_alert_danger("table_projections failed to run.")
       cli::cli_alert("Tip: check that your arguments are correct.")
       cli::cli_li("projections_unit_label = {projections_unit_label}")
-      cli::cli_li("projections_uncert_label = {projections_uncert_label}")
+      # cli::cli_li("projections_uncert_label = {projections_uncert_label}")
       print(e)
     }
   )
diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd
index b8532563..f173a562 100644
--- a/man/save_all_plots.Rd
+++ b/man/save_all_plots.Rd
@@ -144,12 +144,6 @@ Default: 1}
 
 Default: c("catch" = "mt", "spawning_biomass" = "mt", 
 "fishing_mortality" = "")}
-
-\item{projections_uncert_label}{Abbreviated uncertainty label for
-each quantity
-
-Default: c("catch" = "stddev", "spawning_biomass" = "stddev",
-"fishing_mortality" = "stddev")}
 }
 \value{
 Rda files for each figure/table.
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index db97bed0..b021b587 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -16,17 +16,17 @@ test_that("save_all_plots works when all figures/tables are plotted", {
 
   # expect that the figures are all created with expected names
   fig_base_temp_files <- c(
+    "abundance_at_age_figure.rda",
     "biomass_figure.rda",
-    "index_figure.rda",
     "fishing_mortality_figure.rda",
+    "index_figure.rda",
     "landings_figure.rda",
     "natural_mortality_figure.rda",
     # "biomass_at_age_figure.rda", # comment out bc as is this needs to be interactive to select correct module -- TODO: release fix to filter BAA plot data for non-NAs in age
     # "catch_comp_figure.rda", # same TODO as above
-    "abundance_at_age_figure.rda",
+    "recruitment_deviations_figure.rda",
     "recruitment_figure.rda",
     "selectivity_figure.rda",
-    "recruitment_deviations_figure.rda",
     "spawning_biomass_figure.rda",
     "stock_recruitment_figure.rda"
   )
@@ -38,6 +38,7 @@ test_that("save_all_plots works when all figures/tables are plotted", {
   # expect that the tables are all created with expected names
   tab_base_temp_files <- c(
     # "bnc_table.rda",
+    # "catch_table.rda", # comment out bc as is this needs to be interactive to select correct module
     "index_table.rda",
     "landings_table.rda",
     "projections_table.rda"

From 764bf05f1d11675abef0e8c0776465ff8f307a6b Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Thu, 20 Aug 2026 10:10:31 -0400
Subject: [PATCH 6/6] Add values to global variables; update table_catch()
 example

---
 R/stockplotr-package.R | 1 +
 R/table_catch.R        | 3 ++-
 man/table_catch.Rd     | 3 ++-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/stockplotr-package.R b/R/stockplotr-package.R
index f11bf767..177d517b 100644
--- a/R/stockplotr-package.R
+++ b/R/stockplotr-package.R
@@ -19,6 +19,7 @@ globvar <- c(
   "like", "match_key", "morph", "nsim", "output", "output_order", "parm_stdev", "seas",
   "sexes", "subseas", "unique_count", "value", "yr", "fleet_names", "across",
   "everything", "fleet_name", "name", "value_new", "y", ".", "x",
+  "Fleet", "length_bins", "month", "na.omit", "rp_dat", "selected_module",
   # Rceattle conout terms
   "n", "observation", "selectivity_block", "log_sd", "fleet_code",
   "q_block", "species", "indices_observed", "indices_predicted",
diff --git a/R/table_catch.R b/R/table_catch.R
index dfdae862..fcb35bed 100644
--- a/R/table_catch.R
+++ b/R/table_catch.R
@@ -26,7 +26,8 @@
 #' @export
 #'
 #' @examples
-#' table_catch(stockplotr::example_data)
+#' table_catch(stockplotr::example_data,
+#' module = "TIME_SERIES")
 #'
 #' table_catch(
 #'   stockplotr::example_data,
diff --git a/man/table_catch.Rd b/man/table_catch.Rd
index 47ce5ebc..08ae9dae 100644
--- a/man/table_catch.Rd
+++ b/man/table_catch.Rd
@@ -78,7 +78,8 @@ There are options to return a [gt::gt()] object or export an rda object
 containing a gt-based table, caption, and LaTeX-based table.
 }
 \examples{
-table_catch(stockplotr::example_data)
+table_catch(stockplotr::example_data,
+module = "TIME_SERIES")
 
 table_catch(
   stockplotr::example_data,