From 118fba915404646240e6ec568399b0cc7126e23c Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Tue, 2 Jun 2026 15:53:41 -0400
Subject: [PATCH 01/10] Update indices table as per
 https://github.com/nmfs-ost/stockplotr/issues/273

---
 NAMESPACE                                     |   1 +
 R/table_indices.R                             | 359 +++++++++---------
 inst/resources/captions_alt_text_template.csv |   2 +-
 man/table_indices.Rd                          | 108 ++++++
 tests/testthat/test-table_indices.R           | 122 +++---
 5 files changed, 353 insertions(+), 239 deletions(-)
 create mode 100644 man/table_indices.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 19b69c0f..a2cbce9b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,5 +27,6 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
+export(table_indices)
 export(table_landings)
 export(theme_noaa)
diff --git a/R/table_indices.R b/R/table_indices.R
index 90b20992..db7c1e30 100644
--- a/R/table_indices.R
+++ b/R/table_indices.R
@@ -1,173 +1,186 @@
-# #' Create Indices of Abundance Table
-# #'
-# #' @inheritParams plot_recruitment
-# #' @param tables_dir 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 of observed annual indices of abundance plus error
-# #' stratified by fleet.
-# #' @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
-# #' \dontrun{
-# #' table_indices(dat)
-# #'
-# #' table_indices(
-# #'   dat,
-# #'   end_year = 2024,
-# #'   make_rda = TRUE,
-# #'   tables_dir = getwd()
-# #' )
-# #' }
-# table_indices <- function(
-#     dat,
-#     end_year = format(Sys.Date(), "%Y"),
-#     make_rda = FALSE,
-#     tables_dir = getwd()) {
-#   # create plot-specific variables to use throughout fxn for naming and IDing
-#   topic_label <- "indices.abundance"
-
-#   # identify output
-#   fig_or_table <- "table"
-
-#   # check year isn't past end_year if not projections plot
-#   check_year(
-#     end_year = end_year,
-#     fig_or_table = fig_or_table,
-#     topic = topic_label
-#   )
-
-#   # Load data
-#   output <- dat |>
-#     dplyr::filter(module_name == "INDEX_2" | module_name == "t.series") |>
-#     dplyr::filter(year <= end_year)
-#   # Check for U
-#   if (any(unique(output$module_name == "INDEX_2"))) {
-#     output <- output |>
-#       dplyr::filter(
-#         grepl("expected_indices", label) | grepl("indices_predicted", label)
-#       ) # grepl("input_indices", label) |
-#   } else if (any(unique(output$module_name == "t.series"))) {
-#     output <- output |>
-#       dplyr::filter(grepl("cpue", label))
-#   }
-
-#   # Extract fleet names
-#   fleet_names <- unique(as.character(output$fleet))
-#   factors <- c("year", "fleet", "fleet_name", "age", "sex", "area", "seas", "season", "time", "era", "subseas", "subseason", "platoon", "platoo", "growth_pattern", "gp")
-#   # re-structure df for table
-#   indices <- output |>
-#     tidyr::pivot_wider(
-#       # id_cols = c(year, uncertainty, uncertainty_label),
-#       names_from = label,
-#       values_from = estimate
-#     ) |>
-#     dplyr::select(year, fleet, unique(output$label), uncertainty, uncertainty_label) # |>
-
-#   # na.omit()
-#   # check if uncertainty is a measure in the df
-#   if (all(is.na(indices$uncertainty))) {
-#     indices <- indices |>
-#       dplyr::select(-c(uncertainty_label, uncertainty))
-#   } else {
-#     uncertainty_col <- paste("uncertainty_", unique(indices$uncertainty_label), sep = "")
-#     colnames(indices) <- stringr::str_replace(colnames(indices), "^uncertainty$", uncertainty_col)
-#     indices <- dplyr::select(indices, -uncertainty_label)
-#   }
-
-#   # Check if observed/inital values are in the df
-#   if (any(grepl("observed", colnames(indices)))) {
-#     indices <- indices |>
-#       dplyr::select(-colnames(indices)[grep(c("observed"), colnames(indices))])
-#   }
-
-#   # rename columns to remove cpue/effort
-#   if (any(grep("_indices", colnames(indices)))) {
-#     colnames(indices) <- stringr::str_replace_all(colnames(indices), "_indices", "")
-#   } else if (any(grep("indices_", colnames(indices)))) {
-#     colnames(indices) <- stringr::str_replace_all(colnames(indices), "indices_", "")
-#   } else {
-#     colnames(indices) <- stringr::str_replace_all(colnames(indices), "cpue_", "")
-#   }
-
-#   # Check for which column is U and filter out na values
-#   if (any(grep("predicted", colnames(indices)))) {
-#     indices <- indices |>
-#       dplyr::filter(!is.na(predicted))
-#   }
-#   if (any(grep("expected", colnames(indices)))) {
-#     indices <- indices |>
-#       dplyr::filter(!is.na(expected))
-#   }
-
-#   # move fleet data into own columns
-#   indices2 <- indices |>
-#     tidyr::pivot_wider(
-#       names_from = fleet,
-#       values_from = colnames(indices)[!colnames(indices) %in% c("year", "fleet")]
-#     ) |>
-#     dplyr::select(year, dplyr::ends_with(fleet_names))
-
-#   fleet_col_names <- stringr::str_extract(colnames(indices2)[colnames(indices2) != "year"], "[^_]+$")
-#   if (any(grepl("[0-9]+", fleet_col_names))) {
-#     fleet_header_lab <- ""
-#     fleet_col_names <- paste("Fleet ", fleet_col_names)
-#   } else {
-#     fleet_header_lab <- "Fleet"
-#   }
-
-#   tab <- indices2 |>
-#     dplyr::mutate(dplyr::across(where(is.numeric), ~ round(.x, 2)),
-#       year = as.character(year)
-#     ) |>
-#     flextable::flextable() |>
-#     flextable::set_header_labels(
-#       # TODO: set uncertainty to the actual value instead of word uncertainty
-#       values = c("Year", rep(c("Estimated CPUE", "Uncertainty"), (ncol(indices2) - 1) / 2))
-#     ) |>
-#     flextable::add_header_row(
-#       values = c(fleet_header_lab, fleet_col_names)
-#     ) |>
-#     flextable::merge_h(part = "header") |>
-#     flextable::align(part = "header")
-
-#   final <- suppressWarnings(add_theme(tab))
-
-#   # export table to rda if argument = T
-#   if (make_rda) {
-#     # run write_captions.R if its output doesn't exist
-#     if (!file.exists(
-#       fs::path(getwd(), "captions_alt_text.csv")
-#     )
-#     ) {
-#       stockplotr::write_captions(
-#         dat = dat,
-#         dir = tables_dir,
-#         year = end_year
-#       )
-#     }
-
-#     # extract this plot's caption and alt text
-#     caps_alttext <- extract_caps_alttext(
-#       topic_label = topic_label,
-#       fig_or_table = fig_or_table,
-#       dir = tables_dir
-#     )
-
-
-# export_rda(
-#   object = final,
-#   caps_alttext = caps_alttext,
-#   figures_tables_dir = tables_dir,
-#   # get name of function and remove "table_" from it
-#   topic_label = gsub("table_", "", as.character(sys.call()[[1]])),
-#   fig_or_table = fig_or_table
-# )
-#   }
-#   final
-# }
+#' Indices of abundance table
+#'
+#' @inheritParams plot_recruitment
+#' @param group A string of a single column that groups the data.
+#'
+#' Set group = "none" to summarize data over all indexing values.
+#'
+#' Default: NULL
+#' Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL
+#' @param method A string describing the method of summarizing data when group
+#' is set to "none".
+#'
+#' Default: "sum"
+#'
+#' Options: "sum" or "mean"
+#' @param digits Numeric value indicating the number of digits values in the
+#' table will be rounded to.
+#'
+#' Default: 2
+#' @param tables_dir 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()`)
+#' @param label The label that will be chosen from the input file. If unspecified,
+#' the function will search the "label" column and use the first matching label
+#' in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
+#' "indices_predicted", "indices".
+#'
+#' Default: NULL
+#'
+#' @returns A table of observed annual indices of abundance plus error,
+#' stratified by fleet.
+#' @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
+#' \dontrun{
+#' table_indices(dat)
+#'
+#' table_indices(
+#'   dat,
+#'   make_rda = TRUE,
+#'   tables_dir = getwd()
+#' )
+#' }
+table_indices <- function(
+    dat,
+    era = NULL,
+    interactive = TRUE,
+    group = NULL,
+    method = "sum",
+    module = NULL,
+    label = NULL,
+    digits = 2,
+    make_rda = FALSE,
+    tables_dir = getwd()
+    ) {
+  
+  # TODO: do group and facet need to be uncommented and updated?
+  # Filter data for landings
+  prepared_data <- filter_data(
+    dat = dat,
+    label_name = "indices",
+    geom = "line",
+    era = era,
+    module = module,
+    scale_amount = 1,
+    interactive = interactive
+  ) |>
+    dplyr::mutate(estimate = round(as.numeric(estimate), digits = digits)) |>
+    dplyr::mutate(uncertainty = round(as.numeric(uncertainty), digits = digits))
+  
+  # Add check if there is any data
+  if (nrow(prepared_data) == 0) {
+    cli::cli_abort("No indices 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$model
+    # cli::cli_alert_warning("More than one value for uncertainty exists: {uncert_lab}")
+    uncert_lab <- uncert_lab[[1]]
+    # cli::cli_alert_warning("The first value ({uncert_lab}) will be chosen.")
+  }
+  
+  if (is.na(uncert_lab)) uncert_lab <- "uncertainty"
+  
+  # get fleet names
+  # TODO: change from fleets to id_group AFTER the process data step and adjust throughout the table based on indexing
+  fleets <- unique(prepared_data$fleet) |>
+    # sort numerically even if fleets are 100% characters
+    stringr::str_sort(numeric = TRUE)
+  
+  # TODO: fix this so that fleet names aren't removed if, e.g., group = "fleet"
+  table_data_info <- process_table(
+    dat = prepared_data,
+    # group = group,
+    method = method,
+    label = label,
+    digits = digits
+  )
+  table_data <- table_data_info[[1]]
+  indexed_vars <- table_data_info[[2]]
+  id_col_vals <- table_data_info[[3]]
+  
+  # id_group_vals <- sapply(id_cols, function(x) unique(prepared_data[[x]]), simplify = FALSE)
+  # TODO: add check if there is a indices column for every error column -- if not remove the error (can keep indices)
+  
+  # merge error and indices columns and rename
+  df_list <- merge_error(
+    table_data,
+    uncert_lab,
+    fleets,
+    label = "indices",
+    unit_label = "" # should this be CPUE?
+  )
+  
+  # transform dfs into tables
+  final <- lapply(df_list, function(df) {
+    df |>
+      gt::gt() |>
+      add_theme()
+  })
+  
+  # export figure to rda if argument = T
+  if (make_rda == TRUE) {
+    
+    # Caption contains no key quantities for indices table
+    # So, export captions/alt text csv if absent
+    if (!file.exists(fs::path(getwd(), "captions_alt_text.csv"))) {
+      caps_alttext <- utils::read.csv(
+        system.file("resources", "captions_alt_text_template.csv", package = "stockplotr")
+      )
+    # export df with captions and alt text to csv
+    utils::write.csv(
+      x = caps_alttext,
+      file = fs::path(getwd(), "captions_alt_text.csv"),
+      row.names = FALSE
+      )    
+    }
+ 
+
+
+        
+    if (length(df_list) == 1) {
+      
+      create_rda(
+        object = final$label,
+        # get name of function and remove "table_" from it
+        topic_label = gsub("table_", "", as.character(sys.call()[[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/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv
index 07e829c0..517017da 100644
--- a/inst/resources/captions_alt_text_template.csv
+++ b/inst/resources/captions_alt_text_template.csv
@@ -37,7 +37,7 @@ life.history.params,table,Life history parameters used in the stock assessment m
 landings,table,Landed catch by fleet and year in landings.units.,
 discards,table,Discarded catch by fleet and year in discards.tbl.units.,
 age.length.key,table,Age-length key: the proportion of fish for each age that belong to a particular length group. ,
-indices,table,Calculated indices of abundance and their corresponding CVs for the fleets and surveys identified in the column headers. ,
+indices,table,Calculated indices of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
 model.runs,table,"The base configuration and alternative sensitivity analysis configurations of the stock assessment model, in which parameters and/or data input streams are changed from one configuration to another.",
 derived.quantities,table,Derived quantities calculated by the base configuration of the stock assessment model.,
 est.params,table,Parameters used in the base stock assessment model and whether the parameter was estimated by the model or fixed (i.e. not allowed to be estimated or changed by the model). CVs for estimated models are provided.,
diff --git a/man/table_indices.Rd b/man/table_indices.Rd
new file mode 100644
index 00000000..9eaedaec
--- /dev/null
+++ b/man/table_indices.Rd
@@ -0,0 +1,108 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/table_indices.R
+\name{table_indices}
+\alias{table_indices}
+\title{Indices of abundance table}
+\usage{
+table_indices(
+  dat,
+  era = NULL,
+  interactive = TRUE,
+  group = NULL,
+  method = "sum",
+  module = NULL,
+  label = NULL,
+  digits = 2,
+  make_rda = FALSE,
+  tables_dir = getwd()
+)
+}
+\arguments{
+\item{dat}{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{era}{A string naming the era of data.
+
+Default: "time"
+
+Options: "early", "time", "fore" (forecast), or NULL (all data)}
+
+\item{interactive}{A logical value indicating if the environment is interactive.
+
+Default: `FALSE`}
+
+\item{group}{A string of a single column that groups the data.
+
+Set group = "none" to summarize data over all indexing values.
+
+Default: NULL
+Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL}
+
+\item{method}{A string describing the method of summarizing data when group
+is set to "none".
+
+Default: "sum"
+
+Options: "sum" or "mean"}
+
+\item{module}{(Optional) A string indicating the module_name found in `dat`.
+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{label}{The label that will be chosen from the input file. If unspecified,
+the function will search the "label" column and use the first matching label
+in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
+"indices_predicted", "indices".
+
+Default: NULL}
+
+\item{digits}{Numeric value indicating the number of digits values in the
+table will be rounded to.
+
+Default: 2}
+
+\item{make_rda}{A logical value indicating 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}{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 of observed annual indices of abundance plus error,
+stratified by fleet.
+}
+\description{
+Indices of abundance table
+}
+\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{
+\dontrun{
+table_indices(dat)
+
+table_indices(
+  dat,
+  make_rda = TRUE,
+  tables_dir = getwd()
+)
+}
+}
+\seealso{
+[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()]
+}
diff --git a/tests/testthat/test-table_indices.R b/tests/testthat/test-table_indices.R
index 50081a07..17a2fe4a 100644
--- a/tests/testthat/test-table_indices.R
+++ b/tests/testthat/test-table_indices.R
@@ -1,65 +1,57 @@
-# # load sample dataset
-# load(file.path(
-#   "fixtures", "ss3_models_converted", "Hake_2018",
-#   "std_output.rda"
-# ))
-
-# test_that("table_indices generates plots without errors", {
-#   # expect error-free plot with minimal arguments
-#   expect_no_error(
-#     stockplotr::table_indices(out_new)
-#   )
-
-#   # expect error-free plot with many arguments
-#   expect_no_error(
-#     stockplotr::table_indices(
-#       out_new,
-#       end_year = 2024,
-#       make_rda = FALSE,
-#       tables_dir = getwd()
-#     )
-#   )
-
-
-#   # expect flextable object is returned
-#   expect_s3_class(
-#     stockplotr::table_indices(
-#       out_new,
-#       make_rda = FALSE,
-#       tables_dir = getwd()
-#     ),
-#     "flextable"
-#   )
-# })
-
-# test_that("rda file made when indicated", {
-#   # export rda
-#   table_indices(
-#     out_new,
-#     end_year = 2024,
-#     make_rda = TRUE,
-#     tables_dir = getwd()
-#   )
-
-#   # expect that both tables dir and the indices.abundance_table.rda file exist
-#   expect_true(dir.exists(fs::path(getwd(), "tables")))
-#   expect_true(file.exists(fs::path(getwd(), "tables", "indices.abundance_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_indices generates error with future end_year", {
-#   # expect error
-#   expect_error(
-#     stockplotr::table_indices(
-#       out_new,
-#       end_year = 2035,
-#       make_rda = TRUE,
-#       tables_dir = getwd()
-#     )
-#   )
-# })
+# load sample dataset
+load(file.path(
+  "fixtures", "ss3_models_converted", "Hake_2018",
+  "std_output.rda"
+))
+
+test_that("table_indices generates plots without errors", {
+  # expect error-free plot with minimal arguments
+  expect_no_error(
+    table_indices(
+      out_new,
+      interactive = FALSE
+    )
+  )
+  
+  # expect error-free plot with many arguments
+  expect_no_error(
+    table_indices(
+      dat = out_new,
+      make_rda = FALSE,
+      tables_dir = getwd()
+    )
+  )
+  
+  
+  # expect gt object is returned
+  # adjust this test to work for multiple output tables
+  # expect_s3_class(
+  #   table_indices(
+  #     dat = out_new,
+  #     unit_label = "mt",
+  #     era = NULL,
+  #     interactive = FALSE,
+  #     module = "CATCH",
+  #     make_rda = FALSE,
+  #     tables_dir = getwd()
+  #   ),
+  #   "gt_tbl"
+  # )
+})
+
+test_that("rda file made when indicated", {
+  # export rda
+  table_indices(
+    dat = out_new,
+    make_rda = TRUE,
+    tables_dir = getwd()
+  )
+  
+  # expect that both tables dir and the indices_table.rda file exist
+  expect_true(dir.exists(fs::path(getwd(), "tables")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "indices_table.rda")))
+  
+  # erase temporary testing files
+  file.remove(fs::path(getwd(), "captions_alt_text.csv"))
+  unlink(fs::path(getwd(), "tables"), recursive = T)
+})

From a3fc8dcc3210a49da2ab987dd31a3e2190c186de Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Wed, 3 Jun 2026 15:07:39 -0400
Subject: [PATCH 02/10] Add commas to large numbers in tables

---
 R/process_data.R  |  4 ++--
 R/table_indices.R | 10 +++-------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/R/process_data.R b/R/process_data.R
index 11ce6e7d..09c4bd59 100644
--- a/R/process_data.R
+++ b/R/process_data.R
@@ -532,8 +532,8 @@ process_table <- function(
       dplyr::rename(
         !!mod_uncert_lab := uncertainty
       ) |>
-      # set values to strings to include training zeros from rounding
-      dplyr::mutate(estimate = sprintf(glue::glue("%.{digits}f"), estimate)) |>
+    # set values to strings to include trailing zeros from rounding and     # format large estimate values with commas
+      dplyr::mutate(estimate = formatC(estimate, format = "f", digits = digits, big.mark = ",")) |>
       tidyr::pivot_wider(
         id_cols = dplyr::all_of(c(stringr::str_to_title(mod_cols))),
         values_from = dplyr::all_of(c("estimate", mod_uncert_lab)),
diff --git a/R/table_indices.R b/R/table_indices.R
index db7c1e30..bcf19f70 100644
--- a/R/table_indices.R
+++ b/R/table_indices.R
@@ -71,8 +71,8 @@ table_indices <- function(
     scale_amount = 1,
     interactive = interactive
   ) |>
-    dplyr::mutate(estimate = round(as.numeric(estimate), digits = digits)) |>
-    dplyr::mutate(uncertainty = round(as.numeric(uncertainty), digits = digits))
+    dplyr::mutate(estimate = round(as.numeric(estimate), digits = digits),
+                  uncertainty = round(as.numeric(uncertainty), digits = digits))
   
   # Add check if there is any data
   if (nrow(prepared_data) == 0) {
@@ -149,12 +149,8 @@ table_indices <- function(
       row.names = FALSE
       )    
     }
- 
-
-
-        
+  
     if (length(df_list) == 1) {
-      
       create_rda(
         object = final$label,
         # get name of function and remove "table_" from it

From 2646b7d6eb86b2c20d6b5ca9d4d7b0b45a0dfbe5 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Thu, 4 Jun 2026 14:06:58 -0400
Subject: [PATCH 03/10] update converter indices names for BAM

---
 inst/resources/bam_var_names.csv | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/inst/resources/bam_var_names.csv b/inst/resources/bam_var_names.csv
index 2f788ed7..a9678ffd 100644
--- a/inst/resources/bam_var_names.csv
+++ b/inst/resources/bam_var_names.csv
@@ -212,6 +212,9 @@ t.series,total.D.knum,discards_numbers
 t.series,U.ob,indices_expected
 t.series,U.pr,indices_predicted
 t.series,cv.U,indices_cv
+t.series,u.ob,indices_expected
+t.series,u.pr,indices_predicted
+t.series,cv.u,indices_cv
 t.series,q.rate.mult,catchability_rate
 t.series,q.DD.mult,q_DD_mult
 t.series,q.DD.B.4plus,q_DD_B_4plus

From 41331d71bd252c937c098750f4e23d0741a07703 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Thu, 4 Jun 2026 15:42:42 -0400
Subject: [PATCH 04/10] fix bam naming conventions from expected to observed

---
 inst/resources/bam_var_names.csv | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/inst/resources/bam_var_names.csv b/inst/resources/bam_var_names.csv
index a9678ffd..e919aa30 100644
--- a/inst/resources/bam_var_names.csv
+++ b/inst/resources/bam_var_names.csv
@@ -182,13 +182,13 @@ sel.age,sel.v,sel_v
 sel.age,sel.v.Mcvt,sel_v_Mcvt
 ,sel.m,sel_m
 ,sel.m.D,sel_m_D
-comp.mats,lcomp.ob,length_composition_expected
+comp.mats,lcomp.ob,length_composition_observed
 ,lcomp.pr,length_composition_predicted
-,lcomp.D.ob,length_composition_discard_expected
+,lcomp.D.ob,length_composition_discard_observed
 ,lcomp.D.pr,length_composition_discard_predicted
-,acomp.ob,age_composition_expected
+,acomp.ob,age_composition_observed
 ,acomp.pr,age_composition_predicted
-,acomp.Mcvt.ob,age_composition_expected
+,acomp.Mcvt.ob,age_composition_observed
 ,acomp.Mcvt.pr,age_composition_predicted
 sdnr,sdnr.U,sdnr_U
 t.series,F.Fmsy,F_F_msy
@@ -209,20 +209,20 @@ t.series,total.L.klb,landings_weight
 t.series,total.L.knum,landings_numbers
 t.series,total.D.klb,discards_weight
 t.series,total.D.knum,discards_numbers
-t.series,U.ob,indices_expected
+t.series,U.ob,indices_observed
 t.series,U.pr,indices_predicted
 t.series,cv.U,indices_cv
-t.series,u.ob,indices_expected
+t.series,u.ob,indices_observed
 t.series,u.pr,indices_predicted
 t.series,cv.u,indices_cv
 t.series,q.rate.mult,catchability_rate
 t.series,q.DD.mult,q_DD_mult
 t.series,q.DD.B.4plus,q_DD_B_4plus
 t.series,q.RW.log.dev,q_RW_log_dev
-t.series,L.ob,landings_expected
+t.series,L.ob,landings_observed
 t.series,L.pr,landings_predicted
 t.series,cv.L,landings_cv
-t.series,D.ob,discard_expected
+t.series,D.ob,discard_observed
 t.series,D.pr,discard_predicted
 t.series,cv.D,discard_cv
 t.series,cl.D.release,cl_D_release

From 3b8d9cc70d3c918ecfd125fe96b9c0f2cc0c4bfc Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Thu, 4 Jun 2026 16:54:32 -0400
Subject: [PATCH 05/10] convert "indices" to "index"

---
 NAMESPACE                                     |  4 +--
 R/convert_output.R                            | 18 ++++++-------
 R/{plot_indices.R => plot_index.R}            | 14 +++++-----
 R/save_all_plots.R                            | 26 +++++++++----------
 R/stockplotr-package.R                        |  2 +-
 R/table_afsc_tier.R                           |  2 +-
 R/table_harvest_projection.R                  |  2 +-
 R/{table_indices.R => table_index.R}          | 26 +++++++++----------
 R/utils.R                                     |  2 +-
 R/utils_rda.R                                 |  6 ++---
 inst/resources/bam_var_names.csv              | 12 ++++-----
 inst/resources/captions_alt_text_template.csv |  4 +--
 inst/resources/fims_var_names.csv             | 14 +++++-----
 inst/resources/ss3_var_names.csv              |  4 +--
 man/{plot_indices.Rd => plot_index.Rd}        | 12 ++++-----
 man/save_all_plots.Rd                         |  6 ++---
 man/{table_indices.Rd => table_index.Rd}      | 22 ++++++++--------
 tests/testthat/test-html_all_figs_tables.R    |  6 ++---
 tests/testthat/test-plot_indices.R            | 12 ++++-----
 tests/testthat/test-save_all_plots.R          |  5 ++--
 tests/testthat/test-table_indices.R           | 14 +++++-----
 vignettes/convert_output_details.Rmd          |  2 +-
 vignettes/faqs.Rmd                            |  2 +-
 23 files changed, 108 insertions(+), 109 deletions(-)
 rename R/{plot_indices.R => plot_index.R} (93%)
 rename R/{table_indices.R => table_index.R} (89%)
 rename man/{plot_indices.Rd => plot_index.Rd} (94%)
 rename man/{table_indices.Rd => table_index.Rd} (87%)

diff --git a/NAMESPACE b/NAMESPACE
index a2cbce9b..e5c39491 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,7 +14,7 @@ export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
 export(plot_fishing_mortality)
-export(plot_indices)
+export(plot_index)
 export(plot_landings)
 export(plot_natural_mortality)
 export(plot_obsvpred)
@@ -27,6 +27,6 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
-export(table_indices)
+export(table_index)
 export(table_landings)
 export(theme_noaa)
diff --git a/R/convert_output.R b/R/convert_output.R
index 78ebad67..5e37dd59 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -1262,10 +1262,10 @@ convert_output <- function(
 
     # Find fleet names
     if (is.null(fleet_names)) {
-      # Extract names from indices
-      indices <- dat$t.series |>
+      # Extract names from index
+      index <- dat$t.series |>
         dplyr::select(dplyr::contains("U.") & dplyr::contains(".ob"))
-      fleets_ind <- stringr::str_extract(as.vector(colnames(indices)), "(?<=U\\.)\\w+(?=\\.ob)")
+      fleets_ind <- stringr::str_extract(as.vector(colnames(index)), "(?<=U\\.)\\w+(?=\\.ob)")
       # Extract names from landings
       landings <- dat$t.series |>
         dplyr::select(dplyr::contains("L.") & dplyr::contains(".ob") |
@@ -1921,21 +1921,21 @@ convert_output <- function(
         # comp_data?, index_data, catch_data, weight, Ftarget, Flimit
         data_list_list <- list()
 
-        ####### Indices ####
+        ####### index ####
         # Extract index_data
         df_index <- extract[[1]]$index_data |>
           # rename all columns to lower case to match standard
           dplyr::rename_with(tolower) |>
           dplyr::rename(
             fleet = fleet_name,
-            indices_observed = observation,
+            index_observed = observation,
             block = selectivity_block,
             uncertainty = log_sd
           ) |>
           dplyr::mutate(
-            # label = "indices_observed",
+            # label = "index_observed",
             uncertainty_label = "log_sd",
-            indices_predicted = dat$quantities$index_hat
+            index_predicted = dat$quantities$index_hat
           ) |>
           dplyr::select(-c(fleet_code, q_block))
         cli::cli_alert_info("'Selectivity_block' values located in 'block' columns.")
@@ -1951,7 +1951,7 @@ convert_output <- function(
         # expand df long to have obs and pred in same column with label
         df_index_long <- df_index |>
           tidyr::pivot_longer(
-            cols = c(indices_observed, indices_predicted),
+            cols = c(index_observed, index_predicted),
             names_to = "label",
             values_to = "estimate"
           ) |>
@@ -2013,7 +2013,7 @@ convert_output <- function(
         df_comp_obs <- dat$data_list$comp_data |>
           dplyr::rename_with(tolower) |>
           dplyr::mutate(
-            label = "indices_observed"
+            label = "index_observed"
           )
 
         indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
diff --git a/R/plot_indices.R b/R/plot_index.R
similarity index 93%
rename from R/plot_indices.R
rename to R/plot_index.R
index a2a61d49..67397f6d 100644
--- a/R/plot_indices.R
+++ b/R/plot_index.R
@@ -13,7 +13,7 @@
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
 #' Default: NULL
-#' @returns A plot showing the expected and predicted indices.
+#' @returns A plot showing the expected and predicted index.
 #'
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -25,17 +25,17 @@
 #' @export
 #'
 #' @examples
-#' plot_indices(
+#' plot_index(
 #'   dat = stockplotr:::example_data,
 #'   unit_label = "fish/hr",
 #'   interactive = FALSE
 #' )
 #'
-plot_indices <- function(
+plot_index <- function(
   dat,
   unit_label = "",
   group = NULL,
-  # facet always assigned to fleet since that is how indices are calc'd -- unless replaced with NULL
+  # facet always assigned to fleet since that is how index are calc'd -- unless replaced with NULL
   facet = NULL,
   interactive = TRUE,
   module = NULL,
@@ -57,7 +57,7 @@ plot_indices <- function(
   # Filter data
   prepared_data <- filter_data(
     dat,
-    label_name = "indices",
+    label_name = "index",
     era = NULL,
     geom = "line",
     # ifelse guarantees the code doesn't miss grouping when label has > 1 value
@@ -98,8 +98,8 @@ plot_indices <- function(
     dat = prepared_data,
     x = "year",
     y = "estimate",
-    observed_label = "indices_observed",
-    predicted_label = "indices_predicted",
+    observed_label = "index_observed",
+    predicted_label = "index_predicted",
     geom = "line",
     xlab = "Year",
     ylab = "Estimated Index",
diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index 8db8bd57..737b57e8 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -80,7 +80,7 @@
 #'
 #' Default: "mt"
 #'
-#' @param indices_unit_label Units for index of abundance/CPUE
+#' @param index_unit_label Units for index of abundance/CPUE
 #'
 #' Default: ""
 #'
@@ -119,7 +119,7 @@
 #' save_all_plots(dat,
 #'   ref_line = "unfished",
 #'   ref_line_sb = "target",
-#'   indices_unit_label = "CPUE",
+#'   index_unit_label = "CPUE",
 #'   biomass_at_age_scale_amount = 1,
 #'   biomass_at_age_unit_label = "metric tons"
 #' )
@@ -150,15 +150,15 @@ save_all_plots <- function(
   # imported from plot_biomass_at_age
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  # imported from plot_indices
-  indices_unit_label = "",
+  # imported from plot_index
+  index_unit_label = "",
   # imported from table_afsc_tier- add potential unique arguments after dev
   # imported from table_bnc
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
   # imported from table_harvest_projection- add potential unique arguments after dev
-  # imported from table_indices- zero unique arguments
+  # imported from table_index- zero unique arguments
   # imported from table_landings- zero unique arguments
 ) {
   make_rda <- TRUE
@@ -419,18 +419,18 @@ save_all_plots <- function(
 
   tryCatch(
     {
-      cli::cli_h2("plot_indices")
-      plot_indices(dat,
-        unit_label = indices_unit_label,
+      cli::cli_h2("plot_index")
+      plot_index(dat,
+        unit_label = index_unit_label,
         make_rda = TRUE,
         interactive = FALSE,
         figures_dir = figures_tables_dir
       ) # |> suppressWarnings() |> invisible()
     },
     error = function(e) {
-      cli::cli_alert_danger("plot_indices failed to run.")
+      cli::cli_alert_danger("plot_index failed to run.")
       cli::cli_alert("Tip: check that your arguments are correct.")
-      cli::cli_li("indices_unit_label = {indices_unit_label}")
+      cli::cli_li("index_unit_label = {index_unit_label}")
       print(e)
     }
   )
@@ -462,8 +462,8 @@ save_all_plots <- function(
 
   # tryCatch(
   #   {
-  #     cli::cli_h2("table_indices")
-  #     table_indices(
+  #     cli::cli_h2("table_index")
+  #     table_index(
   #       dat,
   #       make_rda = TRUE,
   #       tables_dir = figures_tables_dir
@@ -472,7 +472,7 @@ save_all_plots <- function(
   #     # invisible()
   #   },
   #   error = function(e) {
-  #     cli::cli_alert_danger("table_indices failed to run.")
+  #     cli::cli_alert_danger("table_index failed to run.")
   #     cli::cli_alert("Tip: check that your arguments are correct.")
   #     print(e)
   #   }
diff --git a/R/stockplotr-package.R b/R/stockplotr-package.R
index d7ea398f..852e1bfd 100644
--- a/R/stockplotr-package.R
+++ b/R/stockplotr-package.R
@@ -21,7 +21,7 @@ globvar <- c(
   "everything", "fleet_name", "name", "value_new", "y", ".",
   # Rceattle conout terms
   "n", "observation", "selectivity_block", "log_sd", "fleet_code",
-  "q_block", "species", "indices_observed", "indices_predicted",
+  "q_block", "species", "index_observed", "index_predicted",
   "catch_h", "catch", "catch_predicted", "age0_length1", "sample_size",
   "dim_info", "label_init"
 )
diff --git a/R/table_afsc_tier.R b/R/table_afsc_tier.R
index 6ed6cd39..abb24da8 100644
--- a/R/table_afsc_tier.R
+++ b/R/table_afsc_tier.R
@@ -4,7 +4,7 @@ table_afsc_tier <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   # identify output
diff --git a/R/table_harvest_projection.R b/R/table_harvest_projection.R
index 6a3c2b20..525f91d8 100644
--- a/R/table_harvest_projection.R
+++ b/R/table_harvest_projection.R
@@ -4,7 +4,7 @@ table_harvest_projection <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   level <- c(
diff --git a/R/table_indices.R b/R/table_index.R
similarity index 89%
rename from R/table_indices.R
rename to R/table_index.R
index bcf19f70..3297c46d 100644
--- a/R/table_indices.R
+++ b/R/table_index.R
@@ -1,4 +1,4 @@
-#' Indices of abundance table
+#' Index of abundance table
 #'
 #' @inheritParams plot_recruitment
 #' @param group A string of a single column that groups the data.
@@ -23,12 +23,12 @@
 #' Default: the working directory (`getwd()`)
 #' @param label The label that will be chosen from the input file. If unspecified,
 #' the function will search the "label" column and use the first matching label
-#' in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
-#' "indices_predicted", "indices".
+#' in this ordered list: "index_weight",  "index_numbers", "index_expected",
+#' "index_predicted", "index".
 #'
 #' Default: NULL
 #'
-#' @returns A table of observed annual indices of abundance plus error,
+#' @returns A table of observed annual index of abundance plus error,
 #' stratified by fleet.
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -39,15 +39,15 @@
 #'
 #' @examples
 #' \dontrun{
-#' table_indices(dat)
+#' table_index(dat)
 #'
-#' table_indices(
+#' table_index(
 #'   dat,
 #'   make_rda = TRUE,
 #'   tables_dir = getwd()
 #' )
 #' }
-table_indices <- function(
+table_index <- function(
     dat,
     era = NULL,
     interactive = TRUE,
@@ -64,7 +64,7 @@ table_indices <- function(
   # Filter data for landings
   prepared_data <- filter_data(
     dat = dat,
-    label_name = "indices",
+    label_name = "index",
     geom = "line",
     era = era,
     module = module,
@@ -76,7 +76,7 @@ table_indices <- function(
   
   # Add check if there is any data
   if (nrow(prepared_data) == 0) {
-    cli::cli_abort("No indices data found.")
+    cli::cli_abort("No index data found.")
   }
   
   # get uncertainty label by model
@@ -115,14 +115,14 @@ table_indices <- function(
   id_col_vals <- table_data_info[[3]]
   
   # id_group_vals <- sapply(id_cols, function(x) unique(prepared_data[[x]]), simplify = FALSE)
-  # TODO: add check if there is a indices column for every error column -- if not remove the error (can keep indices)
+  # TODO: add check if there is a index column for every error column -- if not remove the error (can keep index)
   
-  # merge error and indices columns and rename
+  # merge error and index columns and rename
   df_list <- merge_error(
     table_data,
     uncert_lab,
     fleets,
-    label = "indices",
+    label = "index",
     unit_label = "" # should this be CPUE?
   )
   
@@ -136,7 +136,7 @@ table_indices <- function(
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
     
-    # Caption contains no key quantities for indices table
+    # Caption contains no key quantities for index table
     # So, export captions/alt text csv if absent
     if (!file.exists(fs::path(getwd(), "captions_alt_text.csv"))) {
       caps_alttext <- utils::read.csv(
diff --git a/R/utils.R b/R/utils.R
index 0ec7bb18..9c1e3265 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -89,7 +89,7 @@ SS3_extract_df <- function(dat, label) {
   # Identify all values to be treated as NA
   na_values <- c("", "-", "#")
 
-  # Find the row indices using a vectorized approach
+  # Find the row index using a vectorized approach
   start_row <- which(apply(dat, 1, function(row) any(row == label)))[2]
 
   # If the label is not found or is not the second instance, return NA
diff --git a/R/utils_rda.R b/R/utils_rda.R
index a2125ecc..8ab617ca 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -404,11 +404,11 @@ create_rda <- function(
 # mod.fit.catch.max <- # maximum catch
 
 
-## mod_fit_abun (model fit to abundance indices plot)- don't code quantities yet
-# start year of model fit to abundance indices plot
+## mod_fit_abun (model fit to abundance index plot)- don't code quantities yet
+# start year of model fit to abundance index plot
 # mod.fit.abun.start.year <-
 
-# end year of model fit to abundance indices plot
+# end year of model fit to abundance index plot
 # mod.fit.abun.end.year <-
 
 ## mod_fit_discards- will be by fleet
diff --git a/inst/resources/bam_var_names.csv b/inst/resources/bam_var_names.csv
index e919aa30..84a4c385 100644
--- a/inst/resources/bam_var_names.csv
+++ b/inst/resources/bam_var_names.csv
@@ -209,12 +209,12 @@ t.series,total.L.klb,landings_weight
 t.series,total.L.knum,landings_numbers
 t.series,total.D.klb,discards_weight
 t.series,total.D.knum,discards_numbers
-t.series,U.ob,indices_observed
-t.series,U.pr,indices_predicted
-t.series,cv.U,indices_cv
-t.series,u.ob,indices_observed
-t.series,u.pr,indices_predicted
-t.series,cv.u,indices_cv
+t.series,U.ob,index_observed
+t.series,U.pr,index_predicted
+t.series,cv.U,index_cv
+t.series,u.ob,index_observed
+t.series,u.pr,index_predicted
+t.series,cv.u,index_cv
 t.series,q.rate.mult,catchability_rate
 t.series,q.DD.mult,q_DD_mult
 t.series,q.DD.B.4plus,q_DD_B_4plus
diff --git a/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv
index 517017da..3ccf825b 100644
--- a/inst/resources/captions_alt_text_template.csv
+++ b/inst/resources/captions_alt_text_template.csv
@@ -12,7 +12,7 @@ maturity.schedule,figure,The relationship between the proportion mature and fish
 fecundity.at.length,figure,Fecundity (in number of eggs) as a function of fish length. ,"Point and line graph showing observations of measured fecundity and measured length from the same fish and an exponential fit through those points displayed as a line. The x axis shows length in fecundity.length.units, which spans from fecundity.length.min to fecundity.length.max. The y axis shows fecundity in fecundity.units, which spans from fecundity.min to fecundity.max."
 catch,figure,"Historical catch for each year in which there is composition data, for each fleet or survey.","Cumulative area plot showing the catch for each year and fleet or survey. The x axis shows the year, which spans from catch.year.min to catch.year.max. The y axis shows the proportion of the total catch by each fleet or survey and spans from tot.catch.min to tot.catch.max."
 CAL,figure,"Histograms showing the proportion of the catch in each length group, each year for which there is composition data, for fleet or survey fleet.or.survey.name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each length group. The x axis of each histogram contains length intervals, which span from cal.length.min to cal.length.max. The y axis of each histogram contains the proportion of the catch and spans from 0--1."
-indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
+index,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
 abundance_at_age,figure,Model estimate of population numbers at age over time. The relative size of each bubble for a given year and age indicates the relative abundance in that category compared with others. ,"Bubble plot showing relative age proportions over time. The x axis shows the year, which spans from pop.naa.start.year to pop.naa.end.year. The y axis shows age in years, which spans from pop.naa.age.min to pop.naa.age.max. The size of the bubbles range from pop.naa.fish.min to pop.naa.fish.max."
 mod.fit.catch,figure,Observed catch from the data input file (points) and model estimated catch (line) over time for fleet.or.survey.name. ,"Point and line graph showing observed catch from the data input file as points and model estimated catch as a line over time for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.catch.start.year to mod.fit.catch.end.year. The y axis shows catch in mod.fit.catch.units, which spans from mod.fit.catch.min to mod.fit.catch.max."
 mod.fit.abun,figure,Assessment model fits to input catch per unit of effort index values over time calculated from fleet.or.survey.name.,"Point and line graph showing the assessment model fit, displayed as a line, to input catch per unit effort index values, displayed as points over time, for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.abun.start.year to mod.fit.abun.end.year. The y axis shows catch per unit effort in cpue.units, which spans from cpue.min to cpue.max."
@@ -37,7 +37,7 @@ life.history.params,table,Life history parameters used in the stock assessment m
 landings,table,Landed catch by fleet and year in landings.units.,
 discards,table,Discarded catch by fleet and year in discards.tbl.units.,
 age.length.key,table,Age-length key: the proportion of fish for each age that belong to a particular length group. ,
-indices,table,Calculated indices of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
+index,table,Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
 model.runs,table,"The base configuration and alternative sensitivity analysis configurations of the stock assessment model, in which parameters and/or data input streams are changed from one configuration to another.",
 derived.quantities,table,Derived quantities calculated by the base configuration of the stock assessment model.,
 est.params,table,Parameters used in the base stock assessment model and whether the parameter was estimated by the model or fixed (i.e. not allowed to be estimated or changed by the model). CVs for estimated models are provided.,
diff --git a/inst/resources/fims_var_names.csv b/inst/resources/fims_var_names.csv
index 3a678437..abfe593c 100644
--- a/inst/resources/fims_var_names.csv
+++ b/inst/resources/fims_var_names.csv
@@ -2,10 +2,10 @@ module_name,label,alt_label
 Fleet,age_to_length_conversion,
 Fleet,agecomp_expected,age_composition_expected
 Fleet,agecomp_proportion,age_composition_proportion
-Fleet,index_expected,indices_expected
-Fleet,index_naa,indices
-Fleet,index_nal,indices
-Fleet,index_numbers,indices_numbers
+Fleet,index_expected,index_expected
+Fleet,index_naa,index
+Fleet,index_nal,index
+Fleet,index_numbers,index_numbers
 Fleet,index_waa,indicies_weight
 Fleet,index_weight,indicies_weight
 Fleet,landings_expected,
@@ -34,9 +34,9 @@ selectivity,slope,
 ,AgeCompositionExpected,age_composition_expected
 ,AgeCompositionProportion,age_composition_proportion
 ,FMort,fishing_mortality
-,IndexExpected,indices_expected
-,IndexNumberAtAge,indices_numbers
-,IndexNumberAtLength,indices_numbers
+,IndexExpected,index_expected
+,IndexNumberAtAge,index_numbers
+,IndexNumberAtLength,index_numbers
 ,LandingsExpected,landings_expected
 ,LandingsNumberAtAge,landings_numbers
 ,LandingsNumberAtLength,landings_numbers
diff --git a/inst/resources/ss3_var_names.csv b/inst/resources/ss3_var_names.csv
index 13053e5a..5d97027a 100644
--- a/inst/resources/ss3_var_names.csv
+++ b/inst/resources/ss3_var_names.csv
@@ -57,9 +57,9 @@ OVERALL_COMPS,female,
 OVERALL_COMPS,male,
 BIOMASS_AT_AGE,biomass,
 CATCH,obs,landings_observed_weight
-INDEX_2,obs,indices_observed
+INDEX_2,obs,index_observed
 CATCH,exp,landings_predicted_weight
-INDEX_2,exp,indices_predicted
+INDEX_2,exp,index_predicted
 CATCH,mult,
 CATCH,exp*mult,
 CATCH,f,
diff --git a/man/plot_indices.Rd b/man/plot_index.Rd
similarity index 94%
rename from man/plot_indices.Rd
rename to man/plot_index.Rd
index cec8ad08..d7f15a22 100644
--- a/man/plot_indices.Rd
+++ b/man/plot_index.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_indices.R
-\name{plot_indices}
-\alias{plot_indices}
+% Please edit documentation in R/plot_index.R
+\name{plot_index}
+\alias{plot_index}
 \title{Plot Index of Abundance}
 \usage{
-plot_indices(
+plot_index(
   dat,
   unit_label = "",
   group = NULL,
@@ -73,7 +73,7 @@ The folder is created within the path if it does not exist.}
 \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}}
 }
 \value{
-A plot showing the expected and predicted indices.
+A plot showing the expected and predicted index.
 }
 \description{
 Plot Index of Abundance
@@ -85,7 +85,7 @@ There are options to return a `ggplot2` object or export an .rda object
 containing associated caption and alternative text for the figure.
 }
 \examples{
-plot_indices(
+plot_index(
   dat = stockplotr:::example_data,
   unit_label = "fish/hr",
   interactive = FALSE
diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd
index 45bc0e8a..b4f73106 100644
--- a/man/save_all_plots.Rd
+++ b/man/save_all_plots.Rd
@@ -22,7 +22,7 @@ save_all_plots(
   abundance_at_age_unit_label = "fish",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  indices_unit_label = "",
+  index_unit_label = "",
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
@@ -121,7 +121,7 @@ Default: 1}
 
 Default: "mt"}
 
-\item{indices_unit_label}{Units for index of abundance/CPUE
+\item{index_unit_label}{Units for index of abundance/CPUE
 
 Default: ""}
 
@@ -153,7 +153,7 @@ translated to a standardized output (\link[stockplotr]{convert_output}).
 save_all_plots(dat,
   ref_line = "unfished",
   ref_line_sb = "target",
-  indices_unit_label = "CPUE",
+  index_unit_label = "CPUE",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "metric tons"
 )
diff --git a/man/table_indices.Rd b/man/table_index.Rd
similarity index 87%
rename from man/table_indices.Rd
rename to man/table_index.Rd
index 9eaedaec..f7c1ef99 100644
--- a/man/table_indices.Rd
+++ b/man/table_index.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/table_indices.R
-\name{table_indices}
-\alias{table_indices}
-\title{Indices of abundance table}
+% Please edit documentation in R/table_index.R
+\name{table_index}
+\alias{table_index}
+\title{Index of abundance table}
 \usage{
-table_indices(
+table_index(
   dat,
   era = NULL,
   interactive = TRUE,
@@ -58,8 +58,8 @@ module_name in the console. @seealso [filter_data()]}
 
 \item{label}{The label that will be chosen from the input file. If unspecified,
 the function will search the "label" column and use the first matching label
-in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
-"indices_predicted", "indices".
+in this ordered list: "index_weight",  "index_numbers", "index_expected",
+"index_predicted", "index".
 
 Default: NULL}
 
@@ -80,11 +80,11 @@ rda files ("tables") that will be created if the argument `make_rda` = TRUE.
 Default: the working directory (`getwd()`)}
 }
 \value{
-A table of observed annual indices of abundance plus error,
+A table of observed annual index of abundance plus error,
 stratified by fleet.
 }
 \description{
-Indices of abundance table
+Index of abundance table
 }
 \details{
 The input is from an assessment model output file
@@ -94,9 +94,9 @@ containing a gt-based table, caption, and LaTeX-based table.
 }
 \examples{
 \dontrun{
-table_indices(dat)
+table_index(dat)
 
-table_indices(
+table_index(
   dat,
   make_rda = TRUE,
   tables_dir = getwd()
diff --git a/tests/testthat/test-html_all_figs_tables.R b/tests/testthat/test-html_all_figs_tables.R
index cbc7bb7a..bf4c423f 100644
--- a/tests/testthat/test-html_all_figs_tables.R
+++ b/tests/testthat/test-html_all_figs_tables.R
@@ -12,7 +12,7 @@ load(file.path(
 #     recruitment_scale_amount = 1,
 #     ref_line = c("unfished" = 1000),
 #     ref_line_sb = "msy",
-#     indices_unit_label = "CPUE",
+#     index_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
@@ -49,7 +49,7 @@ load(file.path(
 #       recruitment_scale_amount = 1,
 #       ref_line = c("unfished"=1000),
 #       ref_line_sb = "msy",
-#       indices_unit_label = "CPUE",
+#       index_unit_label = "CPUE",
 #       figures_tables_dir = getwd()
 #     ) |>
 #       suppressWarnings()
@@ -79,7 +79,7 @@ load(file.path(
 #     ref_line = "unfished",
 #     ref_point = 1000,
 #     ref_line_sb = "msy",
-#     indices_unit_label = "CPUE",
+#     index_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
diff --git a/tests/testthat/test-plot_indices.R b/tests/testthat/test-plot_indices.R
index e4053e74..cccf9df2 100644
--- a/tests/testthat/test-plot_indices.R
+++ b/tests/testthat/test-plot_indices.R
@@ -4,31 +4,31 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("plot_indices generates plots without errors", {
+test_that("plot_index generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_indices(out_new)
+    plot_index(out_new)
   )
 
 
   # expect ggplot object is returned
   expect_s3_class(
-    plot_indices(out_new),
+    plot_index(out_new),
     "gg"
   )
 })
 
 test_that("rda file made when indicated", {
   # export rda
-  plot_indices(out_new,
+  plot_index(out_new,
     make_rda = TRUE,
     unit_label = "metric tons",
     figures_dir = getwd()
   )
 
-  # expect that both figures dir and the indices_figure.rda file exist
+  # expect that both figures dir and the index_figure.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "indices_figure.rda")))
+  expect_true(file.exists(fs::path(getwd(), "figures", "index_figure.rda")))
 
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index 1b268f39..05f3d345 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -11,7 +11,6 @@ test_that("save_all_plots works when all figures/tables are plotted", {
     recruitment_scale_amount = 1,
     ref_line = c("unfished" = 1000),
     ref_line_sb = c("msy"),
-    # indices_unit_label = "CPUE",
     figures_tables_dir = getwd(),
     interactive = FALSE
   )
@@ -23,7 +22,7 @@ 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(
     "biomass_figure.rda",
-    "indices_figure.rda",
+    "index_figure.rda",
     "fishing_mortality_figure.rda",
     "landings_figure.rda",
     "natural_mortality_figure.rda",
@@ -43,7 +42,7 @@ 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",
-    #  "indices.abundance_table.rda",
+    #  "index_table.rda",
     "landings_table.rda"
   )
   expect_equal(
diff --git a/tests/testthat/test-table_indices.R b/tests/testthat/test-table_indices.R
index 17a2fe4a..13f2cc78 100644
--- a/tests/testthat/test-table_indices.R
+++ b/tests/testthat/test-table_indices.R
@@ -4,10 +4,10 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("table_indices generates plots without errors", {
+test_that("table_index generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    table_indices(
+    table_index(
       out_new,
       interactive = FALSE
     )
@@ -15,7 +15,7 @@ test_that("table_indices generates plots without errors", {
   
   # expect error-free plot with many arguments
   expect_no_error(
-    table_indices(
+    table_index(
       dat = out_new,
       make_rda = FALSE,
       tables_dir = getwd()
@@ -26,7 +26,7 @@ test_that("table_indices generates plots without errors", {
   # expect gt object is returned
   # adjust this test to work for multiple output tables
   # expect_s3_class(
-  #   table_indices(
+  #   table_index(
   #     dat = out_new,
   #     unit_label = "mt",
   #     era = NULL,
@@ -41,15 +41,15 @@ test_that("table_indices generates plots without errors", {
 
 test_that("rda file made when indicated", {
   # export rda
-  table_indices(
+  table_index(
     dat = out_new,
     make_rda = TRUE,
     tables_dir = getwd()
   )
   
-  # expect that both tables dir and the indices_table.rda file exist
+  # expect that both tables dir and the index_table.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "indices_table.rda")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "index_table.rda")))
   
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/vignettes/convert_output_details.Rmd b/vignettes/convert_output_details.Rmd
index dd3b10f2..5f51ef25 100644
--- a/vignettes/convert_output_details.Rmd
+++ b/vignettes/convert_output_details.Rmd
@@ -135,7 +135,7 @@ Another hurdle to tackle is naming conventions. We have attempted to create a st
 
 6. Labels follow a hierarchy of the sorts where the leading word is the topic followed by descriptive adjectives. For example, catch_discard, catch_retained, biomass_msy, etc.
 
-7. All labels are singular and *not* plural. For example, catch instead of catches, landing instead of landings, or index instead of indices.
+7. All labels are singular and *not* plural. For example, catch instead of catches, landing instead of landings, or index instead of index.
 
 7. In cases where a label could not be standardized, the same label was kept in the converted output. We hope that these remaining names can be standardized in the future through collaboration with the respective analysts using them.
 
diff --git a/vignettes/faqs.Rmd b/vignettes/faqs.Rmd
index 6f860fbd..51155a14 100644
--- a/vignettes/faqs.Rmd
+++ b/vignettes/faqs.Rmd
@@ -21,7 +21,7 @@ For more context, please read the function documentation and refer to the docume
 # Captions and alternative text (alt text)
 ## How are captions and alt text constructed?
 
-When a plotting function (e.g., `plot_biomass()`, `table_indices()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
+When a plotting function (e.g., `plot_biomass()`, `table_index()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
 
 As stated in the [Accessibility vignette's "Your to-do list" section](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#your-to-do-list), **you should always:**
 

From bede312ee4d24635ccf38d0fde04eea2a943b703 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 5 Jun 2026 09:06:53 -0400
Subject: [PATCH 06/10] update gitignore and Rbuildignore

---
 .Rbuildignore | 2 ++
 .gitignore    | 1 +
 2 files changed, 3 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index c33ea379..e5aba7db 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.positai$
+^\.claude$
diff --git a/.gitignore b/.gitignore
index 1d947447..32db5cb3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ docs
 stockplotr.Rproj
 *.Rproj
 !vignettes/figures/
+.positai

From e8788aedfccc5d98dedea719b1cf030335063b33 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 5 Jun 2026 09:09:42 -0400
Subject: [PATCH 07/10] bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 46a2a9d9..d4e15fbf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: stockplotr
 Title: Tables and Figures for Stock Assessments
-Version: 0.12.0
+Version: 0.12.0.9000
 Authors@R: c(
     person("Samantha", "Schiano", , "samantha.schiano@noaa.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0003-3744-6428")),

From b74e1aba761f362f3efe6ec4014e7ce7aa3da64c Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 5 Jun 2026 10:11:31 -0400
Subject: [PATCH 08/10] Revert "convert "indices" to "index""

This reverts commit 3b8d9cc70d3c918ecfd125fe96b9c0f2cc0c4bfc.
---
 NAMESPACE                                     |  4 +--
 R/convert_output.R                            | 18 ++++++-------
 R/{plot_index.R => plot_indices.R}            | 14 +++++-----
 R/save_all_plots.R                            | 26 +++++++++----------
 R/stockplotr-package.R                        |  2 +-
 R/table_afsc_tier.R                           |  2 +-
 R/table_harvest_projection.R                  |  2 +-
 R/{table_index.R => table_indices.R}          | 26 +++++++++----------
 R/utils.R                                     |  2 +-
 R/utils_rda.R                                 |  6 ++---
 inst/resources/bam_var_names.csv              | 12 ++++-----
 inst/resources/captions_alt_text_template.csv |  4 +--
 inst/resources/fims_var_names.csv             | 14 +++++-----
 inst/resources/ss3_var_names.csv              |  4 +--
 man/{plot_index.Rd => plot_indices.Rd}        | 12 ++++-----
 man/save_all_plots.Rd                         |  6 ++---
 man/{table_index.Rd => table_indices.Rd}      | 22 ++++++++--------
 tests/testthat/test-html_all_figs_tables.R    |  6 ++---
 tests/testthat/test-plot_indices.R            | 12 ++++-----
 tests/testthat/test-save_all_plots.R          |  5 ++--
 tests/testthat/test-table_indices.R           | 14 +++++-----
 vignettes/convert_output_details.Rmd          |  2 +-
 vignettes/faqs.Rmd                            |  2 +-
 23 files changed, 109 insertions(+), 108 deletions(-)
 rename R/{plot_index.R => plot_indices.R} (93%)
 rename R/{table_index.R => table_indices.R} (89%)
 rename man/{plot_index.Rd => plot_indices.Rd} (94%)
 rename man/{table_index.Rd => table_indices.Rd} (87%)

diff --git a/NAMESPACE b/NAMESPACE
index e5c39491..a2cbce9b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,7 +14,7 @@ export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
 export(plot_fishing_mortality)
-export(plot_index)
+export(plot_indices)
 export(plot_landings)
 export(plot_natural_mortality)
 export(plot_obsvpred)
@@ -27,6 +27,6 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
-export(table_index)
+export(table_indices)
 export(table_landings)
 export(theme_noaa)
diff --git a/R/convert_output.R b/R/convert_output.R
index 5e37dd59..78ebad67 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -1262,10 +1262,10 @@ convert_output <- function(
 
     # Find fleet names
     if (is.null(fleet_names)) {
-      # Extract names from index
-      index <- dat$t.series |>
+      # Extract names from indices
+      indices <- dat$t.series |>
         dplyr::select(dplyr::contains("U.") & dplyr::contains(".ob"))
-      fleets_ind <- stringr::str_extract(as.vector(colnames(index)), "(?<=U\\.)\\w+(?=\\.ob)")
+      fleets_ind <- stringr::str_extract(as.vector(colnames(indices)), "(?<=U\\.)\\w+(?=\\.ob)")
       # Extract names from landings
       landings <- dat$t.series |>
         dplyr::select(dplyr::contains("L.") & dplyr::contains(".ob") |
@@ -1921,21 +1921,21 @@ convert_output <- function(
         # comp_data?, index_data, catch_data, weight, Ftarget, Flimit
         data_list_list <- list()
 
-        ####### index ####
+        ####### Indices ####
         # Extract index_data
         df_index <- extract[[1]]$index_data |>
           # rename all columns to lower case to match standard
           dplyr::rename_with(tolower) |>
           dplyr::rename(
             fleet = fleet_name,
-            index_observed = observation,
+            indices_observed = observation,
             block = selectivity_block,
             uncertainty = log_sd
           ) |>
           dplyr::mutate(
-            # label = "index_observed",
+            # label = "indices_observed",
             uncertainty_label = "log_sd",
-            index_predicted = dat$quantities$index_hat
+            indices_predicted = dat$quantities$index_hat
           ) |>
           dplyr::select(-c(fleet_code, q_block))
         cli::cli_alert_info("'Selectivity_block' values located in 'block' columns.")
@@ -1951,7 +1951,7 @@ convert_output <- function(
         # expand df long to have obs and pred in same column with label
         df_index_long <- df_index |>
           tidyr::pivot_longer(
-            cols = c(index_observed, index_predicted),
+            cols = c(indices_observed, indices_predicted),
             names_to = "label",
             values_to = "estimate"
           ) |>
@@ -2013,7 +2013,7 @@ convert_output <- function(
         df_comp_obs <- dat$data_list$comp_data |>
           dplyr::rename_with(tolower) |>
           dplyr::mutate(
-            label = "index_observed"
+            label = "indices_observed"
           )
 
         indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
diff --git a/R/plot_index.R b/R/plot_indices.R
similarity index 93%
rename from R/plot_index.R
rename to R/plot_indices.R
index 67397f6d..a2a61d49 100644
--- a/R/plot_index.R
+++ b/R/plot_indices.R
@@ -13,7 +13,7 @@
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
 #' Default: NULL
-#' @returns A plot showing the expected and predicted index.
+#' @returns A plot showing the expected and predicted indices.
 #'
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -25,17 +25,17 @@
 #' @export
 #'
 #' @examples
-#' plot_index(
+#' plot_indices(
 #'   dat = stockplotr:::example_data,
 #'   unit_label = "fish/hr",
 #'   interactive = FALSE
 #' )
 #'
-plot_index <- function(
+plot_indices <- function(
   dat,
   unit_label = "",
   group = NULL,
-  # facet always assigned to fleet since that is how index are calc'd -- unless replaced with NULL
+  # facet always assigned to fleet since that is how indices are calc'd -- unless replaced with NULL
   facet = NULL,
   interactive = TRUE,
   module = NULL,
@@ -57,7 +57,7 @@ plot_index <- function(
   # Filter data
   prepared_data <- filter_data(
     dat,
-    label_name = "index",
+    label_name = "indices",
     era = NULL,
     geom = "line",
     # ifelse guarantees the code doesn't miss grouping when label has > 1 value
@@ -98,8 +98,8 @@ plot_index <- function(
     dat = prepared_data,
     x = "year",
     y = "estimate",
-    observed_label = "index_observed",
-    predicted_label = "index_predicted",
+    observed_label = "indices_observed",
+    predicted_label = "indices_predicted",
     geom = "line",
     xlab = "Year",
     ylab = "Estimated Index",
diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index 737b57e8..8db8bd57 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -80,7 +80,7 @@
 #'
 #' Default: "mt"
 #'
-#' @param index_unit_label Units for index of abundance/CPUE
+#' @param indices_unit_label Units for index of abundance/CPUE
 #'
 #' Default: ""
 #'
@@ -119,7 +119,7 @@
 #' save_all_plots(dat,
 #'   ref_line = "unfished",
 #'   ref_line_sb = "target",
-#'   index_unit_label = "CPUE",
+#'   indices_unit_label = "CPUE",
 #'   biomass_at_age_scale_amount = 1,
 #'   biomass_at_age_unit_label = "metric tons"
 #' )
@@ -150,15 +150,15 @@ save_all_plots <- function(
   # imported from plot_biomass_at_age
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  # imported from plot_index
-  index_unit_label = "",
+  # imported from plot_indices
+  indices_unit_label = "",
   # imported from table_afsc_tier- add potential unique arguments after dev
   # imported from table_bnc
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
   # imported from table_harvest_projection- add potential unique arguments after dev
-  # imported from table_index- zero unique arguments
+  # imported from table_indices- zero unique arguments
   # imported from table_landings- zero unique arguments
 ) {
   make_rda <- TRUE
@@ -419,18 +419,18 @@ save_all_plots <- function(
 
   tryCatch(
     {
-      cli::cli_h2("plot_index")
-      plot_index(dat,
-        unit_label = index_unit_label,
+      cli::cli_h2("plot_indices")
+      plot_indices(dat,
+        unit_label = indices_unit_label,
         make_rda = TRUE,
         interactive = FALSE,
         figures_dir = figures_tables_dir
       ) # |> suppressWarnings() |> invisible()
     },
     error = function(e) {
-      cli::cli_alert_danger("plot_index failed to run.")
+      cli::cli_alert_danger("plot_indices failed to run.")
       cli::cli_alert("Tip: check that your arguments are correct.")
-      cli::cli_li("index_unit_label = {index_unit_label}")
+      cli::cli_li("indices_unit_label = {indices_unit_label}")
       print(e)
     }
   )
@@ -462,8 +462,8 @@ save_all_plots <- function(
 
   # tryCatch(
   #   {
-  #     cli::cli_h2("table_index")
-  #     table_index(
+  #     cli::cli_h2("table_indices")
+  #     table_indices(
   #       dat,
   #       make_rda = TRUE,
   #       tables_dir = figures_tables_dir
@@ -472,7 +472,7 @@ save_all_plots <- function(
   #     # invisible()
   #   },
   #   error = function(e) {
-  #     cli::cli_alert_danger("table_index failed to run.")
+  #     cli::cli_alert_danger("table_indices failed to run.")
   #     cli::cli_alert("Tip: check that your arguments are correct.")
   #     print(e)
   #   }
diff --git a/R/stockplotr-package.R b/R/stockplotr-package.R
index 852e1bfd..d7ea398f 100644
--- a/R/stockplotr-package.R
+++ b/R/stockplotr-package.R
@@ -21,7 +21,7 @@ globvar <- c(
   "everything", "fleet_name", "name", "value_new", "y", ".",
   # Rceattle conout terms
   "n", "observation", "selectivity_block", "log_sd", "fleet_code",
-  "q_block", "species", "index_observed", "index_predicted",
+  "q_block", "species", "indices_observed", "indices_predicted",
   "catch_h", "catch", "catch_predicted", "age0_length1", "sample_size",
   "dim_info", "label_init"
 )
diff --git a/R/table_afsc_tier.R b/R/table_afsc_tier.R
index abb24da8..6ed6cd39 100644
--- a/R/table_afsc_tier.R
+++ b/R/table_afsc_tier.R
@@ -4,7 +4,7 @@ table_afsc_tier <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_index.R for reference)
+  # (see table_indices.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   # identify output
diff --git a/R/table_harvest_projection.R b/R/table_harvest_projection.R
index 525f91d8..6a3c2b20 100644
--- a/R/table_harvest_projection.R
+++ b/R/table_harvest_projection.R
@@ -4,7 +4,7 @@ table_harvest_projection <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_index.R for reference)
+  # (see table_indices.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   level <- c(
diff --git a/R/table_index.R b/R/table_indices.R
similarity index 89%
rename from R/table_index.R
rename to R/table_indices.R
index 3297c46d..bcf19f70 100644
--- a/R/table_index.R
+++ b/R/table_indices.R
@@ -1,4 +1,4 @@
-#' Index of abundance table
+#' Indices of abundance table
 #'
 #' @inheritParams plot_recruitment
 #' @param group A string of a single column that groups the data.
@@ -23,12 +23,12 @@
 #' Default: the working directory (`getwd()`)
 #' @param label The label that will be chosen from the input file. If unspecified,
 #' the function will search the "label" column and use the first matching label
-#' in this ordered list: "index_weight",  "index_numbers", "index_expected",
-#' "index_predicted", "index".
+#' in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
+#' "indices_predicted", "indices".
 #'
 #' Default: NULL
 #'
-#' @returns A table of observed annual index of abundance plus error,
+#' @returns A table of observed annual indices of abundance plus error,
 #' stratified by fleet.
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -39,15 +39,15 @@
 #'
 #' @examples
 #' \dontrun{
-#' table_index(dat)
+#' table_indices(dat)
 #'
-#' table_index(
+#' table_indices(
 #'   dat,
 #'   make_rda = TRUE,
 #'   tables_dir = getwd()
 #' )
 #' }
-table_index <- function(
+table_indices <- function(
     dat,
     era = NULL,
     interactive = TRUE,
@@ -64,7 +64,7 @@ table_index <- function(
   # Filter data for landings
   prepared_data <- filter_data(
     dat = dat,
-    label_name = "index",
+    label_name = "indices",
     geom = "line",
     era = era,
     module = module,
@@ -76,7 +76,7 @@ table_index <- function(
   
   # Add check if there is any data
   if (nrow(prepared_data) == 0) {
-    cli::cli_abort("No index data found.")
+    cli::cli_abort("No indices data found.")
   }
   
   # get uncertainty label by model
@@ -115,14 +115,14 @@ table_index <- function(
   id_col_vals <- table_data_info[[3]]
   
   # id_group_vals <- sapply(id_cols, function(x) unique(prepared_data[[x]]), simplify = FALSE)
-  # TODO: add check if there is a index column for every error column -- if not remove the error (can keep index)
+  # TODO: add check if there is a indices column for every error column -- if not remove the error (can keep indices)
   
-  # merge error and index columns and rename
+  # merge error and indices columns and rename
   df_list <- merge_error(
     table_data,
     uncert_lab,
     fleets,
-    label = "index",
+    label = "indices",
     unit_label = "" # should this be CPUE?
   )
   
@@ -136,7 +136,7 @@ table_index <- function(
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
     
-    # Caption contains no key quantities for index table
+    # Caption contains no key quantities for indices table
     # So, export captions/alt text csv if absent
     if (!file.exists(fs::path(getwd(), "captions_alt_text.csv"))) {
       caps_alttext <- utils::read.csv(
diff --git a/R/utils.R b/R/utils.R
index 9c1e3265..0ec7bb18 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -89,7 +89,7 @@ SS3_extract_df <- function(dat, label) {
   # Identify all values to be treated as NA
   na_values <- c("", "-", "#")
 
-  # Find the row index using a vectorized approach
+  # Find the row indices using a vectorized approach
   start_row <- which(apply(dat, 1, function(row) any(row == label)))[2]
 
   # If the label is not found or is not the second instance, return NA
diff --git a/R/utils_rda.R b/R/utils_rda.R
index 8ab617ca..a2125ecc 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -404,11 +404,11 @@ create_rda <- function(
 # mod.fit.catch.max <- # maximum catch
 
 
-## mod_fit_abun (model fit to abundance index plot)- don't code quantities yet
-# start year of model fit to abundance index plot
+## mod_fit_abun (model fit to abundance indices plot)- don't code quantities yet
+# start year of model fit to abundance indices plot
 # mod.fit.abun.start.year <-
 
-# end year of model fit to abundance index plot
+# end year of model fit to abundance indices plot
 # mod.fit.abun.end.year <-
 
 ## mod_fit_discards- will be by fleet
diff --git a/inst/resources/bam_var_names.csv b/inst/resources/bam_var_names.csv
index 84a4c385..e919aa30 100644
--- a/inst/resources/bam_var_names.csv
+++ b/inst/resources/bam_var_names.csv
@@ -209,12 +209,12 @@ t.series,total.L.klb,landings_weight
 t.series,total.L.knum,landings_numbers
 t.series,total.D.klb,discards_weight
 t.series,total.D.knum,discards_numbers
-t.series,U.ob,index_observed
-t.series,U.pr,index_predicted
-t.series,cv.U,index_cv
-t.series,u.ob,index_observed
-t.series,u.pr,index_predicted
-t.series,cv.u,index_cv
+t.series,U.ob,indices_observed
+t.series,U.pr,indices_predicted
+t.series,cv.U,indices_cv
+t.series,u.ob,indices_observed
+t.series,u.pr,indices_predicted
+t.series,cv.u,indices_cv
 t.series,q.rate.mult,catchability_rate
 t.series,q.DD.mult,q_DD_mult
 t.series,q.DD.B.4plus,q_DD_B_4plus
diff --git a/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv
index 3ccf825b..517017da 100644
--- a/inst/resources/captions_alt_text_template.csv
+++ b/inst/resources/captions_alt_text_template.csv
@@ -12,7 +12,7 @@ maturity.schedule,figure,The relationship between the proportion mature and fish
 fecundity.at.length,figure,Fecundity (in number of eggs) as a function of fish length. ,"Point and line graph showing observations of measured fecundity and measured length from the same fish and an exponential fit through those points displayed as a line. The x axis shows length in fecundity.length.units, which spans from fecundity.length.min to fecundity.length.max. The y axis shows fecundity in fecundity.units, which spans from fecundity.min to fecundity.max."
 catch,figure,"Historical catch for each year in which there is composition data, for each fleet or survey.","Cumulative area plot showing the catch for each year and fleet or survey. The x axis shows the year, which spans from catch.year.min to catch.year.max. The y axis shows the proportion of the total catch by each fleet or survey and spans from tot.catch.min to tot.catch.max."
 CAL,figure,"Histograms showing the proportion of the catch in each length group, each year for which there is composition data, for fleet or survey fleet.or.survey.name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each length group. The x axis of each histogram contains length intervals, which span from cal.length.min to cal.length.max. The y axis of each histogram contains the proportion of the catch and spans from 0--1."
-index,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
+indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
 abundance_at_age,figure,Model estimate of population numbers at age over time. The relative size of each bubble for a given year and age indicates the relative abundance in that category compared with others. ,"Bubble plot showing relative age proportions over time. The x axis shows the year, which spans from pop.naa.start.year to pop.naa.end.year. The y axis shows age in years, which spans from pop.naa.age.min to pop.naa.age.max. The size of the bubbles range from pop.naa.fish.min to pop.naa.fish.max."
 mod.fit.catch,figure,Observed catch from the data input file (points) and model estimated catch (line) over time for fleet.or.survey.name. ,"Point and line graph showing observed catch from the data input file as points and model estimated catch as a line over time for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.catch.start.year to mod.fit.catch.end.year. The y axis shows catch in mod.fit.catch.units, which spans from mod.fit.catch.min to mod.fit.catch.max."
 mod.fit.abun,figure,Assessment model fits to input catch per unit of effort index values over time calculated from fleet.or.survey.name.,"Point and line graph showing the assessment model fit, displayed as a line, to input catch per unit effort index values, displayed as points over time, for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.abun.start.year to mod.fit.abun.end.year. The y axis shows catch per unit effort in cpue.units, which spans from cpue.min to cpue.max."
@@ -37,7 +37,7 @@ life.history.params,table,Life history parameters used in the stock assessment m
 landings,table,Landed catch by fleet and year in landings.units.,
 discards,table,Discarded catch by fleet and year in discards.tbl.units.,
 age.length.key,table,Age-length key: the proportion of fish for each age that belong to a particular length group. ,
-index,table,Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
+indices,table,Calculated indices of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
 model.runs,table,"The base configuration and alternative sensitivity analysis configurations of the stock assessment model, in which parameters and/or data input streams are changed from one configuration to another.",
 derived.quantities,table,Derived quantities calculated by the base configuration of the stock assessment model.,
 est.params,table,Parameters used in the base stock assessment model and whether the parameter was estimated by the model or fixed (i.e. not allowed to be estimated or changed by the model). CVs for estimated models are provided.,
diff --git a/inst/resources/fims_var_names.csv b/inst/resources/fims_var_names.csv
index abfe593c..3a678437 100644
--- a/inst/resources/fims_var_names.csv
+++ b/inst/resources/fims_var_names.csv
@@ -2,10 +2,10 @@ module_name,label,alt_label
 Fleet,age_to_length_conversion,
 Fleet,agecomp_expected,age_composition_expected
 Fleet,agecomp_proportion,age_composition_proportion
-Fleet,index_expected,index_expected
-Fleet,index_naa,index
-Fleet,index_nal,index
-Fleet,index_numbers,index_numbers
+Fleet,index_expected,indices_expected
+Fleet,index_naa,indices
+Fleet,index_nal,indices
+Fleet,index_numbers,indices_numbers
 Fleet,index_waa,indicies_weight
 Fleet,index_weight,indicies_weight
 Fleet,landings_expected,
@@ -34,9 +34,9 @@ selectivity,slope,
 ,AgeCompositionExpected,age_composition_expected
 ,AgeCompositionProportion,age_composition_proportion
 ,FMort,fishing_mortality
-,IndexExpected,index_expected
-,IndexNumberAtAge,index_numbers
-,IndexNumberAtLength,index_numbers
+,IndexExpected,indices_expected
+,IndexNumberAtAge,indices_numbers
+,IndexNumberAtLength,indices_numbers
 ,LandingsExpected,landings_expected
 ,LandingsNumberAtAge,landings_numbers
 ,LandingsNumberAtLength,landings_numbers
diff --git a/inst/resources/ss3_var_names.csv b/inst/resources/ss3_var_names.csv
index 5d97027a..13053e5a 100644
--- a/inst/resources/ss3_var_names.csv
+++ b/inst/resources/ss3_var_names.csv
@@ -57,9 +57,9 @@ OVERALL_COMPS,female,
 OVERALL_COMPS,male,
 BIOMASS_AT_AGE,biomass,
 CATCH,obs,landings_observed_weight
-INDEX_2,obs,index_observed
+INDEX_2,obs,indices_observed
 CATCH,exp,landings_predicted_weight
-INDEX_2,exp,index_predicted
+INDEX_2,exp,indices_predicted
 CATCH,mult,
 CATCH,exp*mult,
 CATCH,f,
diff --git a/man/plot_index.Rd b/man/plot_indices.Rd
similarity index 94%
rename from man/plot_index.Rd
rename to man/plot_indices.Rd
index d7f15a22..cec8ad08 100644
--- a/man/plot_index.Rd
+++ b/man/plot_indices.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_index.R
-\name{plot_index}
-\alias{plot_index}
+% Please edit documentation in R/plot_indices.R
+\name{plot_indices}
+\alias{plot_indices}
 \title{Plot Index of Abundance}
 \usage{
-plot_index(
+plot_indices(
   dat,
   unit_label = "",
   group = NULL,
@@ -73,7 +73,7 @@ The folder is created within the path if it does not exist.}
 \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}}
 }
 \value{
-A plot showing the expected and predicted index.
+A plot showing the expected and predicted indices.
 }
 \description{
 Plot Index of Abundance
@@ -85,7 +85,7 @@ There are options to return a `ggplot2` object or export an .rda object
 containing associated caption and alternative text for the figure.
 }
 \examples{
-plot_index(
+plot_indices(
   dat = stockplotr:::example_data,
   unit_label = "fish/hr",
   interactive = FALSE
diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd
index b4f73106..45bc0e8a 100644
--- a/man/save_all_plots.Rd
+++ b/man/save_all_plots.Rd
@@ -22,7 +22,7 @@ save_all_plots(
   abundance_at_age_unit_label = "fish",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  index_unit_label = "",
+  indices_unit_label = "",
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
@@ -121,7 +121,7 @@ Default: 1}
 
 Default: "mt"}
 
-\item{index_unit_label}{Units for index of abundance/CPUE
+\item{indices_unit_label}{Units for index of abundance/CPUE
 
 Default: ""}
 
@@ -153,7 +153,7 @@ translated to a standardized output (\link[stockplotr]{convert_output}).
 save_all_plots(dat,
   ref_line = "unfished",
   ref_line_sb = "target",
-  index_unit_label = "CPUE",
+  indices_unit_label = "CPUE",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "metric tons"
 )
diff --git a/man/table_index.Rd b/man/table_indices.Rd
similarity index 87%
rename from man/table_index.Rd
rename to man/table_indices.Rd
index f7c1ef99..9eaedaec 100644
--- a/man/table_index.Rd
+++ b/man/table_indices.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/table_index.R
-\name{table_index}
-\alias{table_index}
-\title{Index of abundance table}
+% Please edit documentation in R/table_indices.R
+\name{table_indices}
+\alias{table_indices}
+\title{Indices of abundance table}
 \usage{
-table_index(
+table_indices(
   dat,
   era = NULL,
   interactive = TRUE,
@@ -58,8 +58,8 @@ module_name in the console. @seealso [filter_data()]}
 
 \item{label}{The label that will be chosen from the input file. If unspecified,
 the function will search the "label" column and use the first matching label
-in this ordered list: "index_weight",  "index_numbers", "index_expected",
-"index_predicted", "index".
+in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
+"indices_predicted", "indices".
 
 Default: NULL}
 
@@ -80,11 +80,11 @@ rda files ("tables") that will be created if the argument `make_rda` = TRUE.
 Default: the working directory (`getwd()`)}
 }
 \value{
-A table of observed annual index of abundance plus error,
+A table of observed annual indices of abundance plus error,
 stratified by fleet.
 }
 \description{
-Index of abundance table
+Indices of abundance table
 }
 \details{
 The input is from an assessment model output file
@@ -94,9 +94,9 @@ containing a gt-based table, caption, and LaTeX-based table.
 }
 \examples{
 \dontrun{
-table_index(dat)
+table_indices(dat)
 
-table_index(
+table_indices(
   dat,
   make_rda = TRUE,
   tables_dir = getwd()
diff --git a/tests/testthat/test-html_all_figs_tables.R b/tests/testthat/test-html_all_figs_tables.R
index bf4c423f..cbc7bb7a 100644
--- a/tests/testthat/test-html_all_figs_tables.R
+++ b/tests/testthat/test-html_all_figs_tables.R
@@ -12,7 +12,7 @@ load(file.path(
 #     recruitment_scale_amount = 1,
 #     ref_line = c("unfished" = 1000),
 #     ref_line_sb = "msy",
-#     index_unit_label = "CPUE",
+#     indices_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
@@ -49,7 +49,7 @@ load(file.path(
 #       recruitment_scale_amount = 1,
 #       ref_line = c("unfished"=1000),
 #       ref_line_sb = "msy",
-#       index_unit_label = "CPUE",
+#       indices_unit_label = "CPUE",
 #       figures_tables_dir = getwd()
 #     ) |>
 #       suppressWarnings()
@@ -79,7 +79,7 @@ load(file.path(
 #     ref_line = "unfished",
 #     ref_point = 1000,
 #     ref_line_sb = "msy",
-#     index_unit_label = "CPUE",
+#     indices_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
diff --git a/tests/testthat/test-plot_indices.R b/tests/testthat/test-plot_indices.R
index cccf9df2..e4053e74 100644
--- a/tests/testthat/test-plot_indices.R
+++ b/tests/testthat/test-plot_indices.R
@@ -4,31 +4,31 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("plot_index generates plots without errors", {
+test_that("plot_indices generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_index(out_new)
+    plot_indices(out_new)
   )
 
 
   # expect ggplot object is returned
   expect_s3_class(
-    plot_index(out_new),
+    plot_indices(out_new),
     "gg"
   )
 })
 
 test_that("rda file made when indicated", {
   # export rda
-  plot_index(out_new,
+  plot_indices(out_new,
     make_rda = TRUE,
     unit_label = "metric tons",
     figures_dir = getwd()
   )
 
-  # expect that both figures dir and the index_figure.rda file exist
+  # expect that both figures dir and the indices_figure.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "index_figure.rda")))
+  expect_true(file.exists(fs::path(getwd(), "figures", "indices_figure.rda")))
 
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index 05f3d345..1b268f39 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -11,6 +11,7 @@ test_that("save_all_plots works when all figures/tables are plotted", {
     recruitment_scale_amount = 1,
     ref_line = c("unfished" = 1000),
     ref_line_sb = c("msy"),
+    # indices_unit_label = "CPUE",
     figures_tables_dir = getwd(),
     interactive = FALSE
   )
@@ -22,7 +23,7 @@ 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(
     "biomass_figure.rda",
-    "index_figure.rda",
+    "indices_figure.rda",
     "fishing_mortality_figure.rda",
     "landings_figure.rda",
     "natural_mortality_figure.rda",
@@ -42,7 +43,7 @@ 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",
-    #  "index_table.rda",
+    #  "indices.abundance_table.rda",
     "landings_table.rda"
   )
   expect_equal(
diff --git a/tests/testthat/test-table_indices.R b/tests/testthat/test-table_indices.R
index 13f2cc78..17a2fe4a 100644
--- a/tests/testthat/test-table_indices.R
+++ b/tests/testthat/test-table_indices.R
@@ -4,10 +4,10 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("table_index generates plots without errors", {
+test_that("table_indices generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    table_index(
+    table_indices(
       out_new,
       interactive = FALSE
     )
@@ -15,7 +15,7 @@ test_that("table_index generates plots without errors", {
   
   # expect error-free plot with many arguments
   expect_no_error(
-    table_index(
+    table_indices(
       dat = out_new,
       make_rda = FALSE,
       tables_dir = getwd()
@@ -26,7 +26,7 @@ test_that("table_index generates plots without errors", {
   # expect gt object is returned
   # adjust this test to work for multiple output tables
   # expect_s3_class(
-  #   table_index(
+  #   table_indices(
   #     dat = out_new,
   #     unit_label = "mt",
   #     era = NULL,
@@ -41,15 +41,15 @@ test_that("table_index generates plots without errors", {
 
 test_that("rda file made when indicated", {
   # export rda
-  table_index(
+  table_indices(
     dat = out_new,
     make_rda = TRUE,
     tables_dir = getwd()
   )
   
-  # expect that both tables dir and the index_table.rda file exist
+  # expect that both tables dir and the indices_table.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "index_table.rda")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "indices_table.rda")))
   
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/vignettes/convert_output_details.Rmd b/vignettes/convert_output_details.Rmd
index 5f51ef25..dd3b10f2 100644
--- a/vignettes/convert_output_details.Rmd
+++ b/vignettes/convert_output_details.Rmd
@@ -135,7 +135,7 @@ Another hurdle to tackle is naming conventions. We have attempted to create a st
 
 6. Labels follow a hierarchy of the sorts where the leading word is the topic followed by descriptive adjectives. For example, catch_discard, catch_retained, biomass_msy, etc.
 
-7. All labels are singular and *not* plural. For example, catch instead of catches, landing instead of landings, or index instead of index.
+7. All labels are singular and *not* plural. For example, catch instead of catches, landing instead of landings, or index instead of indices.
 
 7. In cases where a label could not be standardized, the same label was kept in the converted output. We hope that these remaining names can be standardized in the future through collaboration with the respective analysts using them.
 
diff --git a/vignettes/faqs.Rmd b/vignettes/faqs.Rmd
index 51155a14..6f860fbd 100644
--- a/vignettes/faqs.Rmd
+++ b/vignettes/faqs.Rmd
@@ -21,7 +21,7 @@ For more context, please read the function documentation and refer to the docume
 # Captions and alternative text (alt text)
 ## How are captions and alt text constructed?
 
-When a plotting function (e.g., `plot_biomass()`, `table_index()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
+When a plotting function (e.g., `plot_biomass()`, `table_indices()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
 
 As stated in the [Accessibility vignette's "Your to-do list" section](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#your-to-do-list), **you should always:**
 

From 38cd437283dc7fb62b1d26bb7aa5c1d55643c2bd Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 5 Jun 2026 10:19:39 -0400
Subject: [PATCH 09/10] change selected names to index from indices,
 maintaining native names for models

---
 R/convert_output.R                |  4 ++--
 inst/resources/bam_var_names.csv  | 12 ++++++------
 inst/resources/fims_var_names.csv | 18 +++++++++---------
 inst/resources/ss3_var_names.csv  |  4 ++--
 4 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/R/convert_output.R b/R/convert_output.R
index 78ebad67..9251e658 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -1933,7 +1933,7 @@ convert_output <- function(
             uncertainty = log_sd
           ) |>
           dplyr::mutate(
-            # label = "indices_observed",
+            # label = "index_observed",
             uncertainty_label = "log_sd",
             indices_predicted = dat$quantities$index_hat
           ) |>
@@ -2013,7 +2013,7 @@ convert_output <- function(
         df_comp_obs <- dat$data_list$comp_data |>
           dplyr::rename_with(tolower) |>
           dplyr::mutate(
-            label = "indices_observed"
+            label = "index_observed"
           )
 
         indexing_vars_cols <- colnames(df_comp_obs)[!grepl("comp", colnames(df_comp_obs))]
diff --git a/inst/resources/bam_var_names.csv b/inst/resources/bam_var_names.csv
index e919aa30..84a4c385 100644
--- a/inst/resources/bam_var_names.csv
+++ b/inst/resources/bam_var_names.csv
@@ -209,12 +209,12 @@ t.series,total.L.klb,landings_weight
 t.series,total.L.knum,landings_numbers
 t.series,total.D.klb,discards_weight
 t.series,total.D.knum,discards_numbers
-t.series,U.ob,indices_observed
-t.series,U.pr,indices_predicted
-t.series,cv.U,indices_cv
-t.series,u.ob,indices_observed
-t.series,u.pr,indices_predicted
-t.series,cv.u,indices_cv
+t.series,U.ob,index_observed
+t.series,U.pr,index_predicted
+t.series,cv.U,index_cv
+t.series,u.ob,index_observed
+t.series,u.pr,index_predicted
+t.series,cv.u,index_cv
 t.series,q.rate.mult,catchability_rate
 t.series,q.DD.mult,q_DD_mult
 t.series,q.DD.B.4plus,q_DD_B_4plus
diff --git a/inst/resources/fims_var_names.csv b/inst/resources/fims_var_names.csv
index 3a678437..3d295826 100644
--- a/inst/resources/fims_var_names.csv
+++ b/inst/resources/fims_var_names.csv
@@ -2,12 +2,12 @@ module_name,label,alt_label
 Fleet,age_to_length_conversion,
 Fleet,agecomp_expected,age_composition_expected
 Fleet,agecomp_proportion,age_composition_proportion
-Fleet,index_expected,indices_expected
-Fleet,index_naa,indices
-Fleet,index_nal,indices
-Fleet,index_numbers,indices_numbers
-Fleet,index_waa,indicies_weight
-Fleet,index_weight,indicies_weight
+Fleet,index_expected,
+Fleet,index_naa,index
+Fleet,index_nal,index
+Fleet,index_numbers,
+Fleet,index_waa,index_weight
+Fleet,index_weight,
 Fleet,landings_expected,
 Fleet,landings_naa,landings
 Fleet,landings_nal,landings
@@ -34,9 +34,9 @@ selectivity,slope,
 ,AgeCompositionExpected,age_composition_expected
 ,AgeCompositionProportion,age_composition_proportion
 ,FMort,fishing_mortality
-,IndexExpected,indices_expected
-,IndexNumberAtAge,indices_numbers
-,IndexNumberAtLength,indices_numbers
+,IndexExpected,index_expected
+,IndexNumberAtAge,index_numbers
+,IndexNumberAtLength,index_numbers
 ,LandingsExpected,landings_expected
 ,LandingsNumberAtAge,landings_numbers
 ,LandingsNumberAtLength,landings_numbers
diff --git a/inst/resources/ss3_var_names.csv b/inst/resources/ss3_var_names.csv
index 13053e5a..5d97027a 100644
--- a/inst/resources/ss3_var_names.csv
+++ b/inst/resources/ss3_var_names.csv
@@ -57,9 +57,9 @@ OVERALL_COMPS,female,
 OVERALL_COMPS,male,
 BIOMASS_AT_AGE,biomass,
 CATCH,obs,landings_observed_weight
-INDEX_2,obs,indices_observed
+INDEX_2,obs,index_observed
 CATCH,exp,landings_predicted_weight
-INDEX_2,exp,indices_predicted
+INDEX_2,exp,index_predicted
 CATCH,mult,
 CATCH,exp*mult,
 CATCH,f,

From 0fe60af0988b9f6d3538bef241972e4e78a9df5f Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 5 Jun 2026 10:41:00 -0400
Subject: [PATCH 10/10] rename "indices" to "index" throughout package (except
 for converter)

---
 NAMESPACE                                     |  4 +--
 R/{plot_indices.R => plot_index.R}            | 12 ++++-----
 R/save_all_plots.R                            | 26 +++++++++----------
 R/table_afsc_tier.R                           |  2 +-
 R/table_harvest_projection.R                  |  2 +-
 R/{table_indices.R => table_index.R}          | 26 +++++++++----------
 R/utils_rda.R                                 |  6 ++---
 inst/resources/captions_alt_text_template.csv |  4 +--
 man/{plot_indices.Rd => plot_index.Rd}        | 12 ++++-----
 man/save_all_plots.Rd                         |  6 ++---
 man/{table_indices.Rd => table_index.Rd}      | 22 ++++++++--------
 tests/testthat/test-html_all_figs_tables.R    |  6 ++---
 tests/testthat/test-plot_indices.R            | 12 ++++-----
 tests/testthat/test-save_all_plots.R          |  6 ++---
 tests/testthat/test-table_indices.R           | 14 +++++-----
 vignettes/faqs.Rmd                            |  2 +-
 16 files changed, 81 insertions(+), 81 deletions(-)
 rename R/{plot_indices.R => plot_index.R} (95%)
 rename R/{table_indices.R => table_index.R} (89%)
 rename man/{plot_indices.Rd => plot_index.Rd} (94%)
 rename man/{table_indices.Rd => table_index.Rd} (87%)

diff --git a/NAMESPACE b/NAMESPACE
index a2cbce9b..e5c39491 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,7 +14,7 @@ export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
 export(plot_fishing_mortality)
-export(plot_indices)
+export(plot_index)
 export(plot_landings)
 export(plot_natural_mortality)
 export(plot_obsvpred)
@@ -27,6 +27,6 @@ export(process_data)
 export(process_table)
 export(reference_line)
 export(save_all_plots)
-export(table_indices)
+export(table_index)
 export(table_landings)
 export(theme_noaa)
diff --git a/R/plot_indices.R b/R/plot_index.R
similarity index 95%
rename from R/plot_indices.R
rename to R/plot_index.R
index a2a61d49..3adb37cc 100644
--- a/R/plot_indices.R
+++ b/R/plot_index.R
@@ -13,7 +13,7 @@
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
 #' Default: NULL
-#' @returns A plot showing the expected and predicted indices.
+#' @returns A plot showing the expected and predicted index.
 #'
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -25,13 +25,13 @@
 #' @export
 #'
 #' @examples
-#' plot_indices(
+#' plot_index(
 #'   dat = stockplotr:::example_data,
 #'   unit_label = "fish/hr",
 #'   interactive = FALSE
 #' )
 #'
-plot_indices <- function(
+plot_index <- function(
   dat,
   unit_label = "",
   group = NULL,
@@ -57,7 +57,7 @@ plot_indices <- function(
   # Filter data
   prepared_data <- filter_data(
     dat,
-    label_name = "indices",
+    label_name = "index",
     era = NULL,
     geom = "line",
     # ifelse guarantees the code doesn't miss grouping when label has > 1 value
@@ -98,8 +98,8 @@ plot_indices <- function(
     dat = prepared_data,
     x = "year",
     y = "estimate",
-    observed_label = "indices_observed",
-    predicted_label = "indices_predicted",
+    observed_label = "index_observed",
+    predicted_label = "index_predicted",
     geom = "line",
     xlab = "Year",
     ylab = "Estimated Index",
diff --git a/R/save_all_plots.R b/R/save_all_plots.R
index 8db8bd57..737b57e8 100644
--- a/R/save_all_plots.R
+++ b/R/save_all_plots.R
@@ -80,7 +80,7 @@
 #'
 #' Default: "mt"
 #'
-#' @param indices_unit_label Units for index of abundance/CPUE
+#' @param index_unit_label Units for index of abundance/CPUE
 #'
 #' Default: ""
 #'
@@ -119,7 +119,7 @@
 #' save_all_plots(dat,
 #'   ref_line = "unfished",
 #'   ref_line_sb = "target",
-#'   indices_unit_label = "CPUE",
+#'   index_unit_label = "CPUE",
 #'   biomass_at_age_scale_amount = 1,
 #'   biomass_at_age_unit_label = "metric tons"
 #' )
@@ -150,15 +150,15 @@ save_all_plots <- function(
   # imported from plot_biomass_at_age
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  # imported from plot_indices
-  indices_unit_label = "",
+  # imported from plot_index
+  index_unit_label = "",
   # imported from table_afsc_tier- add potential unique arguments after dev
   # imported from table_bnc
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
   # imported from table_harvest_projection- add potential unique arguments after dev
-  # imported from table_indices- zero unique arguments
+  # imported from table_index- zero unique arguments
   # imported from table_landings- zero unique arguments
 ) {
   make_rda <- TRUE
@@ -419,18 +419,18 @@ save_all_plots <- function(
 
   tryCatch(
     {
-      cli::cli_h2("plot_indices")
-      plot_indices(dat,
-        unit_label = indices_unit_label,
+      cli::cli_h2("plot_index")
+      plot_index(dat,
+        unit_label = index_unit_label,
         make_rda = TRUE,
         interactive = FALSE,
         figures_dir = figures_tables_dir
       ) # |> suppressWarnings() |> invisible()
     },
     error = function(e) {
-      cli::cli_alert_danger("plot_indices failed to run.")
+      cli::cli_alert_danger("plot_index failed to run.")
       cli::cli_alert("Tip: check that your arguments are correct.")
-      cli::cli_li("indices_unit_label = {indices_unit_label}")
+      cli::cli_li("index_unit_label = {index_unit_label}")
       print(e)
     }
   )
@@ -462,8 +462,8 @@ save_all_plots <- function(
 
   # tryCatch(
   #   {
-  #     cli::cli_h2("table_indices")
-  #     table_indices(
+  #     cli::cli_h2("table_index")
+  #     table_index(
   #       dat,
   #       make_rda = TRUE,
   #       tables_dir = figures_tables_dir
@@ -472,7 +472,7 @@ save_all_plots <- function(
   #     # invisible()
   #   },
   #   error = function(e) {
-  #     cli::cli_alert_danger("table_indices failed to run.")
+  #     cli::cli_alert_danger("table_index failed to run.")
   #     cli::cli_alert("Tip: check that your arguments are correct.")
   #     print(e)
   #   }
diff --git a/R/table_afsc_tier.R b/R/table_afsc_tier.R
index 6ed6cd39..abb24da8 100644
--- a/R/table_afsc_tier.R
+++ b/R/table_afsc_tier.R
@@ -4,7 +4,7 @@ table_afsc_tier <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   # identify output
diff --git a/R/table_harvest_projection.R b/R/table_harvest_projection.R
index 6a3c2b20..525f91d8 100644
--- a/R/table_harvest_projection.R
+++ b/R/table_harvest_projection.R
@@ -4,7 +4,7 @@ table_harvest_projection <- function() {
   # -adds make_rda and tables_dir as arguments
   # -defines topic_label, fig_or_table; and
   # -makes an rda if make_rda = TRUE
-  # (see table_indices.R for reference)
+  # (see table_index.R for reference)
   # for the rda-related fxns to work, the final table has to be called tab
 
   level <- c(
diff --git a/R/table_indices.R b/R/table_index.R
similarity index 89%
rename from R/table_indices.R
rename to R/table_index.R
index bcf19f70..3297c46d 100644
--- a/R/table_indices.R
+++ b/R/table_index.R
@@ -1,4 +1,4 @@
-#' Indices of abundance table
+#' Index of abundance table
 #'
 #' @inheritParams plot_recruitment
 #' @param group A string of a single column that groups the data.
@@ -23,12 +23,12 @@
 #' Default: the working directory (`getwd()`)
 #' @param label The label that will be chosen from the input file. If unspecified,
 #' the function will search the "label" column and use the first matching label
-#' in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
-#' "indices_predicted", "indices".
+#' in this ordered list: "index_weight",  "index_numbers", "index_expected",
+#' "index_predicted", "index".
 #'
 #' Default: NULL
 #'
-#' @returns A table of observed annual indices of abundance plus error,
+#' @returns A table of observed annual index of abundance plus error,
 #' stratified by fleet.
 #' @details The input is from an assessment model output file
 #' translated to a standardized output (\link[stockplotr]{convert_output}).
@@ -39,15 +39,15 @@
 #'
 #' @examples
 #' \dontrun{
-#' table_indices(dat)
+#' table_index(dat)
 #'
-#' table_indices(
+#' table_index(
 #'   dat,
 #'   make_rda = TRUE,
 #'   tables_dir = getwd()
 #' )
 #' }
-table_indices <- function(
+table_index <- function(
     dat,
     era = NULL,
     interactive = TRUE,
@@ -64,7 +64,7 @@ table_indices <- function(
   # Filter data for landings
   prepared_data <- filter_data(
     dat = dat,
-    label_name = "indices",
+    label_name = "index",
     geom = "line",
     era = era,
     module = module,
@@ -76,7 +76,7 @@ table_indices <- function(
   
   # Add check if there is any data
   if (nrow(prepared_data) == 0) {
-    cli::cli_abort("No indices data found.")
+    cli::cli_abort("No index data found.")
   }
   
   # get uncertainty label by model
@@ -115,14 +115,14 @@ table_indices <- function(
   id_col_vals <- table_data_info[[3]]
   
   # id_group_vals <- sapply(id_cols, function(x) unique(prepared_data[[x]]), simplify = FALSE)
-  # TODO: add check if there is a indices column for every error column -- if not remove the error (can keep indices)
+  # TODO: add check if there is a index column for every error column -- if not remove the error (can keep index)
   
-  # merge error and indices columns and rename
+  # merge error and index columns and rename
   df_list <- merge_error(
     table_data,
     uncert_lab,
     fleets,
-    label = "indices",
+    label = "index",
     unit_label = "" # should this be CPUE?
   )
   
@@ -136,7 +136,7 @@ table_indices <- function(
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
     
-    # Caption contains no key quantities for indices table
+    # Caption contains no key quantities for index table
     # So, export captions/alt text csv if absent
     if (!file.exists(fs::path(getwd(), "captions_alt_text.csv"))) {
       caps_alttext <- utils::read.csv(
diff --git a/R/utils_rda.R b/R/utils_rda.R
index a2125ecc..8ab617ca 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -404,11 +404,11 @@ create_rda <- function(
 # mod.fit.catch.max <- # maximum catch
 
 
-## mod_fit_abun (model fit to abundance indices plot)- don't code quantities yet
-# start year of model fit to abundance indices plot
+## mod_fit_abun (model fit to abundance index plot)- don't code quantities yet
+# start year of model fit to abundance index plot
 # mod.fit.abun.start.year <-
 
-# end year of model fit to abundance indices plot
+# end year of model fit to abundance index plot
 # mod.fit.abun.end.year <-
 
 ## mod_fit_discards- will be by fleet
diff --git a/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv
index 517017da..3ccf825b 100644
--- a/inst/resources/captions_alt_text_template.csv
+++ b/inst/resources/captions_alt_text_template.csv
@@ -12,7 +12,7 @@ maturity.schedule,figure,The relationship between the proportion mature and fish
 fecundity.at.length,figure,Fecundity (in number of eggs) as a function of fish length. ,"Point and line graph showing observations of measured fecundity and measured length from the same fish and an exponential fit through those points displayed as a line. The x axis shows length in fecundity.length.units, which spans from fecundity.length.min to fecundity.length.max. The y axis shows fecundity in fecundity.units, which spans from fecundity.min to fecundity.max."
 catch,figure,"Historical catch for each year in which there is composition data, for each fleet or survey.","Cumulative area plot showing the catch for each year and fleet or survey. The x axis shows the year, which spans from catch.year.min to catch.year.max. The y axis shows the proportion of the total catch by each fleet or survey and spans from tot.catch.min to tot.catch.max."
 CAL,figure,"Histograms showing the proportion of the catch in each length group, each year for which there is composition data, for fleet or survey fleet.or.survey.name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each length group. The x axis of each histogram contains length intervals, which span from cal.length.min to cal.length.max. The y axis of each histogram contains the proportion of the catch and spans from 0--1."
-indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
+index,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95\\% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time, stratified by survey/fleet. The x axis shows the year, which spans from cpue.start.year to cpue.end.year. The y axis shows CPUE in cpue.units, which spans from cpue.min to cpue.max."
 abundance_at_age,figure,Model estimate of population numbers at age over time. The relative size of each bubble for a given year and age indicates the relative abundance in that category compared with others. ,"Bubble plot showing relative age proportions over time. The x axis shows the year, which spans from pop.naa.start.year to pop.naa.end.year. The y axis shows age in years, which spans from pop.naa.age.min to pop.naa.age.max. The size of the bubbles range from pop.naa.fish.min to pop.naa.fish.max."
 mod.fit.catch,figure,Observed catch from the data input file (points) and model estimated catch (line) over time for fleet.or.survey.name. ,"Point and line graph showing observed catch from the data input file as points and model estimated catch as a line over time for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.catch.start.year to mod.fit.catch.end.year. The y axis shows catch in mod.fit.catch.units, which spans from mod.fit.catch.min to mod.fit.catch.max."
 mod.fit.abun,figure,Assessment model fits to input catch per unit of effort index values over time calculated from fleet.or.survey.name.,"Point and line graph showing the assessment model fit, displayed as a line, to input catch per unit effort index values, displayed as points over time, for fleet.or.survey.name. The x axis shows years, which spans from mod.fit.abun.start.year to mod.fit.abun.end.year. The y axis shows catch per unit effort in cpue.units, which spans from cpue.min to cpue.max."
@@ -37,7 +37,7 @@ life.history.params,table,Life history parameters used in the stock assessment m
 landings,table,Landed catch by fleet and year in landings.units.,
 discards,table,Discarded catch by fleet and year in discards.tbl.units.,
 age.length.key,table,Age-length key: the proportion of fish for each age that belong to a particular length group. ,
-indices,table,Calculated indices of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
+index,table,Calculated index of abundance and corresponding CVs for the fleets and surveys identified in the column headers. ,
 model.runs,table,"The base configuration and alternative sensitivity analysis configurations of the stock assessment model, in which parameters and/or data input streams are changed from one configuration to another.",
 derived.quantities,table,Derived quantities calculated by the base configuration of the stock assessment model.,
 est.params,table,Parameters used in the base stock assessment model and whether the parameter was estimated by the model or fixed (i.e. not allowed to be estimated or changed by the model). CVs for estimated models are provided.,
diff --git a/man/plot_indices.Rd b/man/plot_index.Rd
similarity index 94%
rename from man/plot_indices.Rd
rename to man/plot_index.Rd
index cec8ad08..d7f15a22 100644
--- a/man/plot_indices.Rd
+++ b/man/plot_index.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_indices.R
-\name{plot_indices}
-\alias{plot_indices}
+% Please edit documentation in R/plot_index.R
+\name{plot_index}
+\alias{plot_index}
 \title{Plot Index of Abundance}
 \usage{
-plot_indices(
+plot_index(
   dat,
   unit_label = "",
   group = NULL,
@@ -73,7 +73,7 @@ The folder is created within the path if it does not exist.}
 \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}}
 }
 \value{
-A plot showing the expected and predicted indices.
+A plot showing the expected and predicted index.
 }
 \description{
 Plot Index of Abundance
@@ -85,7 +85,7 @@ There are options to return a `ggplot2` object or export an .rda object
 containing associated caption and alternative text for the figure.
 }
 \examples{
-plot_indices(
+plot_index(
   dat = stockplotr:::example_data,
   unit_label = "fish/hr",
   interactive = FALSE
diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd
index 45bc0e8a..b4f73106 100644
--- a/man/save_all_plots.Rd
+++ b/man/save_all_plots.Rd
@@ -22,7 +22,7 @@ save_all_plots(
   abundance_at_age_unit_label = "fish",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "mt",
-  indices_unit_label = "",
+  index_unit_label = "",
   biomass_unit_label = "mt",
   catch_unit_label = "mt",
   catch_scale_amount = 1
@@ -121,7 +121,7 @@ Default: 1}
 
 Default: "mt"}
 
-\item{indices_unit_label}{Units for index of abundance/CPUE
+\item{index_unit_label}{Units for index of abundance/CPUE
 
 Default: ""}
 
@@ -153,7 +153,7 @@ translated to a standardized output (\link[stockplotr]{convert_output}).
 save_all_plots(dat,
   ref_line = "unfished",
   ref_line_sb = "target",
-  indices_unit_label = "CPUE",
+  index_unit_label = "CPUE",
   biomass_at_age_scale_amount = 1,
   biomass_at_age_unit_label = "metric tons"
 )
diff --git a/man/table_indices.Rd b/man/table_index.Rd
similarity index 87%
rename from man/table_indices.Rd
rename to man/table_index.Rd
index 9eaedaec..f7c1ef99 100644
--- a/man/table_indices.Rd
+++ b/man/table_index.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/table_indices.R
-\name{table_indices}
-\alias{table_indices}
-\title{Indices of abundance table}
+% Please edit documentation in R/table_index.R
+\name{table_index}
+\alias{table_index}
+\title{Index of abundance table}
 \usage{
-table_indices(
+table_index(
   dat,
   era = NULL,
   interactive = TRUE,
@@ -58,8 +58,8 @@ module_name in the console. @seealso [filter_data()]}
 
 \item{label}{The label that will be chosen from the input file. If unspecified,
 the function will search the "label" column and use the first matching label
-in this ordered list: "indices_weight",  "indices_numbers", "indices_expected",
-"indices_predicted", "indices".
+in this ordered list: "index_weight",  "index_numbers", "index_expected",
+"index_predicted", "index".
 
 Default: NULL}
 
@@ -80,11 +80,11 @@ rda files ("tables") that will be created if the argument `make_rda` = TRUE.
 Default: the working directory (`getwd()`)}
 }
 \value{
-A table of observed annual indices of abundance plus error,
+A table of observed annual index of abundance plus error,
 stratified by fleet.
 }
 \description{
-Indices of abundance table
+Index of abundance table
 }
 \details{
 The input is from an assessment model output file
@@ -94,9 +94,9 @@ containing a gt-based table, caption, and LaTeX-based table.
 }
 \examples{
 \dontrun{
-table_indices(dat)
+table_index(dat)
 
-table_indices(
+table_index(
   dat,
   make_rda = TRUE,
   tables_dir = getwd()
diff --git a/tests/testthat/test-html_all_figs_tables.R b/tests/testthat/test-html_all_figs_tables.R
index cbc7bb7a..bf4c423f 100644
--- a/tests/testthat/test-html_all_figs_tables.R
+++ b/tests/testthat/test-html_all_figs_tables.R
@@ -12,7 +12,7 @@ load(file.path(
 #     recruitment_scale_amount = 1,
 #     ref_line = c("unfished" = 1000),
 #     ref_line_sb = "msy",
-#     indices_unit_label = "CPUE",
+#     index_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
@@ -49,7 +49,7 @@ load(file.path(
 #       recruitment_scale_amount = 1,
 #       ref_line = c("unfished"=1000),
 #       ref_line_sb = "msy",
-#       indices_unit_label = "CPUE",
+#       index_unit_label = "CPUE",
 #       figures_tables_dir = getwd()
 #     ) |>
 #       suppressWarnings()
@@ -79,7 +79,7 @@ load(file.path(
 #     ref_line = "unfished",
 #     ref_point = 1000,
 #     ref_line_sb = "msy",
-#     indices_unit_label = "CPUE",
+#     index_unit_label = "CPUE",
 #     figures_tables_dir = getwd()
 #   ) |>
 #     suppressWarnings()
diff --git a/tests/testthat/test-plot_indices.R b/tests/testthat/test-plot_indices.R
index e4053e74..cccf9df2 100644
--- a/tests/testthat/test-plot_indices.R
+++ b/tests/testthat/test-plot_indices.R
@@ -4,31 +4,31 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("plot_indices generates plots without errors", {
+test_that("plot_index generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    plot_indices(out_new)
+    plot_index(out_new)
   )
 
 
   # expect ggplot object is returned
   expect_s3_class(
-    plot_indices(out_new),
+    plot_index(out_new),
     "gg"
   )
 })
 
 test_that("rda file made when indicated", {
   # export rda
-  plot_indices(out_new,
+  plot_index(out_new,
     make_rda = TRUE,
     unit_label = "metric tons",
     figures_dir = getwd()
   )
 
-  # expect that both figures dir and the indices_figure.rda file exist
+  # expect that both figures dir and the index_figure.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "figures")))
-  expect_true(file.exists(fs::path(getwd(), "figures", "indices_figure.rda")))
+  expect_true(file.exists(fs::path(getwd(), "figures", "index_figure.rda")))
 
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/tests/testthat/test-save_all_plots.R b/tests/testthat/test-save_all_plots.R
index 1b268f39..f5ebfca2 100644
--- a/tests/testthat/test-save_all_plots.R
+++ b/tests/testthat/test-save_all_plots.R
@@ -11,7 +11,7 @@ test_that("save_all_plots works when all figures/tables are plotted", {
     recruitment_scale_amount = 1,
     ref_line = c("unfished" = 1000),
     ref_line_sb = c("msy"),
-    # indices_unit_label = "CPUE",
+    # index_unit_label = "CPUE",
     figures_tables_dir = getwd(),
     interactive = FALSE
   )
@@ -23,7 +23,7 @@ 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(
     "biomass_figure.rda",
-    "indices_figure.rda",
+    "index_figure.rda",
     "fishing_mortality_figure.rda",
     "landings_figure.rda",
     "natural_mortality_figure.rda",
@@ -43,7 +43,7 @@ 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",
-    #  "indices.abundance_table.rda",
+    #  "index.abundance_table.rda",
     "landings_table.rda"
   )
   expect_equal(
diff --git a/tests/testthat/test-table_indices.R b/tests/testthat/test-table_indices.R
index 17a2fe4a..13f2cc78 100644
--- a/tests/testthat/test-table_indices.R
+++ b/tests/testthat/test-table_indices.R
@@ -4,10 +4,10 @@ load(file.path(
   "std_output.rda"
 ))
 
-test_that("table_indices generates plots without errors", {
+test_that("table_index generates plots without errors", {
   # expect error-free plot with minimal arguments
   expect_no_error(
-    table_indices(
+    table_index(
       out_new,
       interactive = FALSE
     )
@@ -15,7 +15,7 @@ test_that("table_indices generates plots without errors", {
   
   # expect error-free plot with many arguments
   expect_no_error(
-    table_indices(
+    table_index(
       dat = out_new,
       make_rda = FALSE,
       tables_dir = getwd()
@@ -26,7 +26,7 @@ test_that("table_indices generates plots without errors", {
   # expect gt object is returned
   # adjust this test to work for multiple output tables
   # expect_s3_class(
-  #   table_indices(
+  #   table_index(
   #     dat = out_new,
   #     unit_label = "mt",
   #     era = NULL,
@@ -41,15 +41,15 @@ test_that("table_indices generates plots without errors", {
 
 test_that("rda file made when indicated", {
   # export rda
-  table_indices(
+  table_index(
     dat = out_new,
     make_rda = TRUE,
     tables_dir = getwd()
   )
   
-  # expect that both tables dir and the indices_table.rda file exist
+  # expect that both tables dir and the index_table.rda file exist
   expect_true(dir.exists(fs::path(getwd(), "tables")))
-  expect_true(file.exists(fs::path(getwd(), "tables", "indices_table.rda")))
+  expect_true(file.exists(fs::path(getwd(), "tables", "index_table.rda")))
   
   # erase temporary testing files
   file.remove(fs::path(getwd(), "captions_alt_text.csv"))
diff --git a/vignettes/faqs.Rmd b/vignettes/faqs.Rmd
index 6f860fbd..51155a14 100644
--- a/vignettes/faqs.Rmd
+++ b/vignettes/faqs.Rmd
@@ -21,7 +21,7 @@ For more context, please read the function documentation and refer to the docume
 # Captions and alternative text (alt text)
 ## How are captions and alt text constructed?
 
-When a plotting function (e.g., `plot_biomass()`, `table_indices()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
+When a plotting function (e.g., `plot_biomass()`, `table_index()`, `save_all_plots()`) is run, placeholders within the plot's associated alt text and captions are replaced with key quantities (see the [{asar} package's Accessibility vignette](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html) and the {stockplotr} ["How captions and alternative text are generated" vignette](https://nmfs-ost.github.io/stockplotr/articles/how-caps-alttext-are-made.html) for more details).
 
 As stated in the [Accessibility vignette's "Your to-do list" section](https://nmfs-ost.github.io/asar/articles/accessibility_guide.html#your-to-do-list), **you should always:**