From 25ea20e6c454575ebd45d46f91418a4879d11f17 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Fri, 16 Oct 2026 15:05:45 -0400 Subject: [PATCH 1/4] add deprecation of report.sso message using lifecycle --- DESCRIPTION | 4 +++- NAMESPACE | 2 ++ R/convert_output.R | 16 +++++++++++++++- 3 files changed, 20 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9f6906c5..f4fb9c1a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -42,6 +42,7 @@ Imports: ggplot2 (>= 4.0.0), glue, gt, + lifecycle, purrr, rlang, scales, @@ -61,9 +62,10 @@ Suggests: testthat (>= 3.0.0) VignetteBuilder: knitr -Config/roxygen2/version: 8.1.0 +Config/roxygen2/version: 8.1.1 Config/testthat/edition: 3 Config/testthat/parallel: false Encoding: UTF-8 Language: en-US LazyData: true +Roxygen: list(markdown = TRUE) diff --git a/NAMESPACE b/NAMESPACE index a89a4c9c..0de5d9df 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +export(calculate_reference_point) export(convert_output) export(create_latex_table) export(create_rda) @@ -35,3 +36,4 @@ export(table_projections) export(table_total_catch) export(theme_noaa) export(theme_table) +importFrom(lifecycle,deprecated) diff --git a/R/convert_output.R b/R/convert_output.R index 9671f705..597e552c 100644 --- a/R/convert_output.R +++ b/R/convert_output.R @@ -3,7 +3,7 @@ #' Format stock assessment output file to a standardized tibble. #' #' @param file Path. Assessment model output file path. Currently accepts SS3 -#' Report.sso file, BAM .rda file, Rceattle model object, and FIMS model object. +#' `r4ss::ss_output()` or Report.sso file (being deprecated), BAM .rda file, Rceattle model object, and FIMS model object. #' @param model String. Assessment model used in evaluation #' #' Default: NULL @@ -48,6 +48,20 @@ convert_output <- function( fleet_names = NULL, save_dir = NULL ) { + + if (grepl("Report.sso", file)) { + lifecycle::deprecate_warn( + when = "2.8.0", + what = I("convert_output(file = 'Report.sso')"), + details = c( + i = "Please use the returned object from `r4ss::ss_output()`", + i = "File will be compatible until Oct. 1, 2027" + ) + ) + + custom_params <- setNames(param_values, param_names) + } + # check if entered save_dir exists so doesn't waste user time finding this out at the end if (!is.null(save_dir)) { if (!grepl(".rda", save_dir)) { From d1e09479aab9eb344f0a5143e23bc39d4c039c30 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Fri, 16 Oct 2026 15:28:23 -0400 Subject: [PATCH 2/4] update documentation for functions based on roxygen2::roxygen2_md() and add lifecycle icons --- R/stockplotr-package.R | 1 + R/utils_plot.R | 9 +++- man/calc_kqs.Rd | 2 +- man/calculate_reference_point.Rd | 29 +++++++++++ man/convert_output.Rd | 14 +++--- man/create_rda.Rd | 4 +- man/example_data.Rd | 66 +++++++++++++------------- man/export_kqs.Rd | 2 +- man/export_rda.Rd | 2 +- man/extract_caps_alttext.Rd | 4 +- man/extract_sis_data.Rd | 8 ++-- man/figures/lifecycle-deprecated.svg | 21 ++++++++ man/figures/lifecycle-experimental.svg | 21 ++++++++ man/figures/lifecycle-stable.svg | 29 +++++++++++ man/figures/lifecycle-superseded.svg | 21 ++++++++ man/fill_in_kqs.Rd | 4 +- man/filter_data.Rd | 10 ++-- man/insert_kqs.Rd | 2 +- man/plot_aa.Rd | 2 +- man/plot_abundance_at_age.Rd | 18 +++---- man/plot_biomass.Rd | 34 ++++++------- man/plot_biomass_at_age.Rd | 18 +++---- man/plot_catch_comp.Rd | 18 +++---- man/plot_discard.Rd | 24 +++++----- man/plot_error.Rd | 4 +- man/plot_fishing_mortality.Rd | 28 ++++++----- man/plot_index.Rd | 20 ++++---- man/plot_landings.Rd | 22 ++++----- man/plot_natural_mortality.Rd | 20 ++++---- man/plot_obsvpred.Rd | 2 +- man/plot_recruitment.Rd | 20 ++++---- man/plot_recruitment_deviations.Rd | 22 ++++----- man/plot_selectivity.Rd | 20 ++++---- man/plot_spawning_biomass.Rd | 34 ++++++------- man/plot_stock_recruitment.Rd | 18 +++---- man/plot_timeseries.Rd | 2 +- man/process_data.Rd | 2 +- man/save_all_plots.Rd | 34 ++++++------- man/table_biomass_abundance_catch.Rd | 22 ++++----- man/table_index.Rd | 22 ++++----- man/table_landings.Rd | 22 ++++----- man/table_projections.Rd | 18 +++---- man/table_total_catch.Rd | 22 ++++----- man/theme_noaa.Rd | 2 +- 44 files changed, 425 insertions(+), 294 deletions(-) create mode 100644 man/calculate_reference_point.Rd create mode 100644 man/figures/lifecycle-deprecated.svg create mode 100644 man/figures/lifecycle-experimental.svg create mode 100644 man/figures/lifecycle-stable.svg create mode 100644 man/figures/lifecycle-superseded.svg diff --git a/R/stockplotr-package.R b/R/stockplotr-package.R index 177d517b..85464e7c 100644 --- a/R/stockplotr-package.R +++ b/R/stockplotr-package.R @@ -2,6 +2,7 @@ "_PACKAGE" ## usethis namespace: start +#' @importFrom lifecycle deprecated ## usethis namespace: end NULL diff --git a/R/utils_plot.R b/R/utils_plot.R index 1f45f7c3..9d3696ec 100644 --- a/R/utils_plot.R +++ b/R/utils_plot.R @@ -875,8 +875,13 @@ get_id <- function(dat) { #------------------------------------------------------------------------------ -# Calculate reference value point - +#' Calculate reference value point +#' +#' @inheritParams plot_spawning_biomass dat lbs +#' @param reference_name a string of the name of the reference point (e.g. "spawning biomass msy") +#' +#' @returns the value of the reference point name found in the dat file. +#' @export calculate_reference_point <- function( dat, reference_name, diff --git a/man/calc_kqs.Rd b/man/calc_kqs.Rd index 0691185a..8b3a2a7b 100644 --- a/man/calc_kqs.Rd +++ b/man/calc_kqs.Rd @@ -25,7 +25,7 @@ calc_kqs( \item{relative}{Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value.} -\item{module}{Character vector. Module name found in `dat$module_name`.} +\item{module}{Character vector. Module name found in \code{dat$module_name}.} \item{...}{Additional arguments to be passed to the function.} } diff --git a/man/calculate_reference_point.Rd b/man/calculate_reference_point.Rd new file mode 100644 index 00000000..86e38307 --- /dev/null +++ b/man/calculate_reference_point.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils_plot.R +\name{calculate_reference_point} +\alias{calculate_reference_point} +\title{Calculate reference value point} +\usage{ +calculate_reference_point(dat, reference_name, lbs = FALSE) +} +\arguments{ +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) +returned from \link[stockplotr]{convert_output}. + +If inputting a list of tibbles, the first tibble's reference point defined +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} + +\item{reference_name}{a string of the name of the reference point (e.g. "spawning biomass msy")} + +\item{lbs}{Logical. TRUE/FALSE; indicate whether to convert the y-axis values from +kilograms to pounds. The default units match the default in the +unit_label argument - 'mt'. + +Default: \code{FALSE}} +} +\value{ +the value of the reference point name found in the dat file. +} +\description{ +Calculate reference value point +} diff --git a/man/convert_output.Rd b/man/convert_output.Rd index 30168090..782b50e7 100644 --- a/man/convert_output.Rd +++ b/man/convert_output.Rd @@ -8,7 +8,7 @@ convert_output(file, model = NULL, fleet_names = NULL, save_dir = NULL) } \arguments{ \item{file}{Path. Assessment model output file path. Currently accepts SS3 -Report.sso file, BAM .rda file, Rceattle model object, and FIMS model object.} +\code{r4ss::ss_output()} or Report.sso file (being deprecated), BAM .rda file, Rceattle model object, and FIMS model object.} \item{model}{String. Assessment model used in evaluation @@ -17,11 +17,11 @@ Default: NULL Options: "ss3", "bam", "fims", "rceattle"} \item{fleet_names}{Character vector. Names of fleets in the assessment model as - shortened in the output file or names of fleets to replace the native fleet - names in the output. For example, if fleet names in the model are 1, 2, 3 - then fleet_names = c("fleet1" = 1, "fleet2" = 2, "fleet3" = 3). +shortened in the output file or names of fleets to replace the native fleet +names in the output. For example, if fleet names in the model are 1, 2, 3 +then fleet_names = c("fleet1" = 1, "fleet2" = 2, "fleet3" = 3). - Default: NULL} +Default: NULL} \item{save_dir}{Path. Full file path to save the converted output file. If saved file name is not indicated, the file will be saved as "std_output.rda" @@ -31,8 +31,8 @@ Default: NULL} } \value{ A reformatted and standardized tibble of assessment model results - for application in building stock assessment reports and to easily - adapt results among regional assessments. +for application in building stock assessment reports and to easily +adapt results among regional assessments. } \description{ Format stock assessment output file to a standardized tibble. diff --git a/man/create_rda.Rd b/man/create_rda.Rd index d94521c6..987c1e61 100644 --- a/man/create_rda.Rd +++ b/man/create_rda.Rd @@ -27,7 +27,7 @@ alternative text for the object} \item{dir}{Path. Directory to where the rda will be saved -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} \item{ref_line}{String. Reference line value @@ -67,5 +67,5 @@ create_rda( } } \seealso{ -[export_rda()], [extract_caps_alttext()] +\code{\link[=export_rda]{export_rda()}}, \code{\link[=extract_caps_alttext]{extract_caps_alttext()}} } diff --git a/man/example_data.Rd b/man/example_data.Rd index d3ed947c..a2eb7a9d 100644 --- a/man/example_data.Rd +++ b/man/example_data.Rd @@ -7,39 +7,39 @@ \format{ A tibble with 591109 rows and 33 variables: \describe{ - \item{label}{Standard name for estimate or value name} - \item{estimate}{Actual value of the label} - \item{year}{Annual indexing value} - \item{fleet}{Names of fleets or surveys indexed by the data} - \item{sex}{Native reference to male, female, unknown, or none} - \item{area}{Specified areas by the model} - \item{growth_pattern}{Indexing column of data} - \item{uncertainty}{Value of uncertainty associated with the label column} - \item{uncertainty_label}{Uncertainty label or name associated with the label columns} - \item{module_name}{Name of keyword (SS3) or list indexing in the original model output for tracking purposes} - \item{time}{Time sometimes referenced in decimals to the year and month} - \item{era}{"time" for current time series in model; "fore" representing the projected or forecasted years of the model} - \item{month}{Month factor} - \item{season}{Season usually associated with year} - \item{subseason}{Subseason when used} - \item{birthseas}{Birthseason found in SS3} - \item{initial}{Initial input value in the model when available associated with the label column} - \item{likelihood}{Likelihood value for the data point} - \item{platoon}{Platoon also an SS3 indexing value} - \item{age}{Age of fish} - \item{bio_pattern}{Indexing column of data} - \item{settlement}{Indexing column of data} - \item{morph}{Indexing column of data} - \item{type}{Indexing column of data} - \item{factor}{Indexing column of data} - \item{part}{Indexing column of data} - \item{kind}{Indexing column of data} - \item{nsim}{Indexing column of data} - \item{bin}{Indexing column of data} - \item{age_a}{Alternative age column} - \item{length_bins}{Length bins for composition or other length based data} - \item{count}{Indexing column of data} - \item{block}{Indexing column of data} +\item{label}{Standard name for estimate or value name} +\item{estimate}{Actual value of the label} +\item{year}{Annual indexing value} +\item{fleet}{Names of fleets or surveys indexed by the data} +\item{sex}{Native reference to male, female, unknown, or none} +\item{area}{Specified areas by the model} +\item{growth_pattern}{Indexing column of data} +\item{uncertainty}{Value of uncertainty associated with the label column} +\item{uncertainty_label}{Uncertainty label or name associated with the label columns} +\item{module_name}{Name of keyword (SS3) or list indexing in the original model output for tracking purposes} +\item{time}{Time sometimes referenced in decimals to the year and month} +\item{era}{"time" for current time series in model; "fore" representing the projected or forecasted years of the model} +\item{month}{Month factor} +\item{season}{Season usually associated with year} +\item{subseason}{Subseason when used} +\item{birthseas}{Birthseason found in SS3} +\item{initial}{Initial input value in the model when available associated with the label column} +\item{likelihood}{Likelihood value for the data point} +\item{platoon}{Platoon also an SS3 indexing value} +\item{age}{Age of fish} +\item{bio_pattern}{Indexing column of data} +\item{settlement}{Indexing column of data} +\item{morph}{Indexing column of data} +\item{type}{Indexing column of data} +\item{factor}{Indexing column of data} +\item{part}{Indexing column of data} +\item{kind}{Indexing column of data} +\item{nsim}{Indexing column of data} +\item{bin}{Indexing column of data} +\item{age_a}{Alternative age column} +\item{length_bins}{Length bins for composition or other length based data} +\item{count}{Indexing column of data} +\item{block}{Indexing column of data} } } \usage{ diff --git a/man/export_kqs.Rd b/man/export_kqs.Rd index 4bcd9e56..f6c1edcb 100644 --- a/man/export_kqs.Rd +++ b/man/export_kqs.Rd @@ -27,5 +27,5 @@ export_kqs( } } \seealso{ -[fill_in_kqs()], [insert_kqs()] +\code{\link[=fill_in_kqs]{fill_in_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}} } diff --git a/man/export_rda.Rd b/man/export_rda.Rd index 61643d69..a5eb873e 100644 --- a/man/export_rda.Rd +++ b/man/export_rda.Rd @@ -76,5 +76,5 @@ export_rda( } } \seealso{ -[create_rda()], [extract_caps_alttext()] +\code{\link[=create_rda]{create_rda()}}, \code{\link[=extract_caps_alttext]{extract_caps_alttext()}} } diff --git a/man/extract_caps_alttext.Rd b/man/extract_caps_alttext.Rd index afe42269..738ede21 100644 --- a/man/extract_caps_alttext.Rd +++ b/man/extract_caps_alttext.Rd @@ -19,7 +19,7 @@ Default: NULL} \item{dir}{Path. The directory containing the "captions_alt_text.csv" file. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A figure's caption and alternative text, in a list, or a table's caption. @@ -44,5 +44,5 @@ extract_caps_alttext( } } \seealso{ -[export_rda()], [create_rda()] +\code{\link[=export_rda]{export_rda()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/extract_sis_data.Rd b/man/extract_sis_data.Rd index 7f7042dc..e040f9fb 100644 --- a/man/extract_sis_data.Rd +++ b/man/extract_sis_data.Rd @@ -17,20 +17,20 @@ existing sis_assmt_template.csv file. Default: The working directory.} -\item{key_quantities_dir}{Path. Location of the existing key_quantities.csv +\item{key_quantities_dir}{Path. Location of the existing key_quantities.csv file. Default: The working directory.} -\item{figures_tables_dir}{Path. Location of the existing 'figures' and +\item{figures_tables_dir}{Path. Location of the existing 'figures' and 'tables' directories. Default: The working directory.} } \description{ Semi-automate the extraction of key quantities from model results and time -series data from exported figure/table `.rda` files for eventual transmittance -to SIS via `asar::export_to_sis()`. +series data from exported figure/table \code{.rda} files for eventual transmittance +to SIS via \code{asar::export_to_sis()}. } \details{ See the "Automating data extraction for SIS" vignette for a diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 00000000..b61c57c3 --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg new file mode 100644 index 00000000..5d88fc2c --- /dev/null +++ b/man/figures/lifecycle-experimental.svg @@ -0,0 +1,21 @@ + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 00000000..9bf21e76 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1,29 @@ + + lifecycle: stable + + + + + + + + + + + + + + + + lifecycle + + + + stable + + + diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg new file mode 100644 index 00000000..db8d757f --- /dev/null +++ b/man/figures/lifecycle-superseded.svg @@ -0,0 +1,21 @@ + + lifecycle: superseded + + + + + + + + + + + + + + + lifecycle + + superseded + + diff --git a/man/fill_in_kqs.Rd b/man/fill_in_kqs.Rd index a6d81aa5..5444c09f 100644 --- a/man/fill_in_kqs.Rd +++ b/man/fill_in_kqs.Rd @@ -22,7 +22,7 @@ newly-added values of key quantities indicated via ellipsis. Substitute key quantities' values into template } \details{ -The returned dataframe is input for [fill_in_kqs()]. +The returned dataframe is input for \code{\link[=fill_in_kqs]{fill_in_kqs()}}. } \examples{ \dontrun{ @@ -34,5 +34,5 @@ fill_in_kqs( } } \seealso{ -[export_kqs()], [insert_kqs()] +\code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}} } diff --git a/man/filter_data.Rd b/man/filter_data.Rd index 6836fea3..129fea0d 100644 --- a/man/filter_data.Rd +++ b/man/filter_data.Rd @@ -17,22 +17,22 @@ filter_data( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{label_name}{String. Name of the label used to filter the data.} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{era}{String. Era of data. @@ -63,7 +63,7 @@ Default: 1} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} } \value{ a data frame that is preformatted for plotting with ggplot2. diff --git a/man/insert_kqs.Rd b/man/insert_kqs.Rd index 421b878d..9d7446ef 100644 --- a/man/insert_kqs.Rd +++ b/man/insert_kqs.Rd @@ -27,5 +27,5 @@ insert_kqs( } } \seealso{ -[fill_in_kqs()], [export_kqs()] +\code{\link[=fill_in_kqs]{fill_in_kqs()}}, \code{\link[=export_kqs]{export_kqs()}} } diff --git a/man/plot_aa.Rd b/man/plot_aa.Rd index 75b249d7..20953927 100644 --- a/man/plot_aa.Rd +++ b/man/plot_aa.Rd @@ -58,7 +58,7 @@ Options: Including, but not limited to: "sex", "area", "fleet"} size are relative to one another while when set to FALSE, point size is relative to z -Default: `TRUE`} +Default: \code{TRUE}} \item{...}{Inherited arguments from internal functions from \link[ggplot2]{geom_point}} diff --git a/man/plot_abundance_at_age.Rd b/man/plot_abundance_at_age.Rd index 11d6e85b..2c87df83 100644 --- a/man/plot_abundance_at_age.Rd +++ b/man/plot_abundance_at_age.Rd @@ -44,30 +44,30 @@ Default: 1,000} size are relative to one another while when set to FALSE, point size is relative to z -Default: `TRUE`} +Default: \code{TRUE}} -\item{module}{(Optional) A string indicating the module_name found in `dat$module_name`. +\item{module}{(Optional) A string indicating the module_name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{interactive}{A logical value indicating if the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to produce an .rda file containing a list with the figure/table, caption, and alternative text (if figure). If TRUE, the .rda will be exported to the folder indicated in the argument "rda_dir". -Default: `FALSE`} +Default: \code{FALSE}} \item{figures_dir}{Path. Folder containing the generated .rda files -("rda_files") that will be created if the argument `make_rda` = TRUE. +("rda_files") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A plot showing total abundance (or numbers) at age. @@ -78,7 +78,7 @@ Plot Abundance at Age \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -96,5 +96,5 @@ plot_abundance_at_age( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_aa()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_aa]{plot_aa()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_biomass.Rd b/man/plot_biomass.Rd index 65f9bb76..33bc9913 100644 --- a/man/plot_biomass.Rd +++ b/man/plot_biomass.Rd @@ -22,11 +22,11 @@ plot_biomass( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{geom}{String. Geom used for the plot. @@ -46,12 +46,12 @@ Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", Default: NULL} \item{ref_line}{String. Type of reference point to - compare biomass to. The default `"msy"` looks for - `"biomass_msy"` in the `"label"` column of `dat`. The actual - searching in `dat` is case-agnostic and will work with either upper- or - lower-case letters. However, you must use one of the options specified in the - default list to ensure that the label on the figure looks correct - regardless of how it is specified in `dat`. +compare biomass to. The default \code{"msy"} looks for +\code{"biomass_msy"} in the \code{"label"} column of \code{dat}. The actual +searching in \code{dat} is case-agnostic and will work with either upper- or +lower-case letters. However, you must use one of the options specified in the +default list to ensure that the label on the figure looks correct +regardless of how it is specified in \code{dat}. Default: "msy" @@ -67,13 +67,13 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} Default: "mt"} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{scale_amount}{Number. A number to scale the y-axis values. @@ -82,23 +82,23 @@ Default: 1} \item{relative}{Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value. -Default: `FALSE`} +Default: \code{FALSE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}} } @@ -111,7 +111,7 @@ Plot Total Biomass \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -131,5 +131,5 @@ plot_biomass( ) } \seealso{ -[convert_output()], [plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=calculate_reference_point]{calculate_reference_point()}}, \code{\link[=reference_line]{reference_line()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_biomass_at_age.Rd b/man/plot_biomass_at_age.Rd index 4464d444..e58c2227 100644 --- a/man/plot_biomass_at_age.Rd +++ b/man/plot_biomass_at_age.Rd @@ -42,32 +42,32 @@ Default: 1,000} size are relative to one another while when set to FALSE, point size is relative to z -Default: `TRUE`} +Default: \code{TRUE}} -\item{module}{(Optional) A string indicating the module_name found in `dat$module_name`. +\item{module}{(Optional) A string indicating the module_name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment in which the function is operating is interactive. This bypasses some options for filtering when preparing data for the plot. -Default: `TRUE`} +Default: \code{TRUE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to produce an .rda file containing a list with the figure/table, caption, and alternative text (if figure). If TRUE, the .rda will be exported to the folder indicated in the argument "rda_dir". -Default: `FALSE`} +Default: \code{FALSE}} \item{figures_dir}{Path. Folder containing the generated .rda files -("rda_files") that will be created if the argument `make_rda` = TRUE. +("rda_files") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A plot showing total biomass at age. @@ -78,7 +78,7 @@ Plot Total Biomass at Age (BAA) \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -97,5 +97,5 @@ plot_biomass_at_age( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_aa()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_aa]{plot_aa()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_catch_comp.Rd b/man/plot_catch_comp.Rd index ff309d9a..9bcfe44b 100644 --- a/man/plot_catch_comp.Rd +++ b/man/plot_catch_comp.Rd @@ -51,30 +51,30 @@ Default: 1} size are relative to one another while when set to FALSE, point size is relative to z -Default: `TRUE`} +Default: \code{TRUE}} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to produce an .rda file containing a list with the figure/table, caption, and alternative text (if figure). If TRUE, the .rda will be exported to the folder indicated in the argument "rda_dir". -Default: `FALSE`} +Default: \code{FALSE}} \item{figures_dir}{Path. Folder containing the generated .rda files -("rda_files") that will be created if the argument `make_rda` = TRUE. +("rda_files") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A plot showing catch or landings composition. @@ -88,7 +88,7 @@ in the output file. The current plot function does not combine all sources of catch. The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -113,5 +113,5 @@ plot_catch_comp( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_aa()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_aa]{plot_aa()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_discard.Rd b/man/plot_discard.Rd index a9e49355..4add2f87 100644 --- a/man/plot_discard.Rd +++ b/man/plot_discard.Rd @@ -19,11 +19,11 @@ plot_discard( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{group}{String. Single column that groups the data. @@ -50,7 +50,7 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} kilograms to pounds. The default units match the default in the unit_label argument - 'mt'. -Default: `FALSE`} +Default: \code{FALSE}} \item{scale_amount}{Number. A number to scale the y-axis values. @@ -58,25 +58,25 @@ Default: 1} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} } @@ -89,12 +89,12 @@ Plot discards as a line graph. \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \note{ All plotting functions automatically recognize indexing variables and will -use them in groupings and/or facetting. @seealso [process_data()]. +use them in groupings and/or facetting. @seealso \code{\link[=process_data]{process_data()}}. } \examples{ plot_discard( @@ -103,5 +103,5 @@ plot_discard( ) } \seealso{ -[convert_output()], [plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=calculate_reference_point]{calculate_reference_point()}}, \code{\link[=reference_line]{reference_line()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_error.Rd b/man/plot_error.Rd index 7dcaff1e..ee4aaf1d 100644 --- a/man/plot_error.Rd +++ b/man/plot_error.Rd @@ -52,13 +52,13 @@ Default: NULL} Default: "Year"} \item{ylab}{String. Y-axis label. If NULL, it will be set to the name - of `y`. +of \code{y}. Default: NULL} \item{hline}{Logical. TRUE/FALSE; indicate whether to place a horizontal line at 1 -Default: `TRUE`} +Default: \code{TRUE}} \item{...}{Inherited arguments from internal functions from ggplot2::geom_xx} } diff --git a/man/plot_fishing_mortality.Rd b/man/plot_fishing_mortality.Rd index 0d38a9ca..c0c449b1 100644 --- a/man/plot_fishing_mortality.Rd +++ b/man/plot_fishing_mortality.Rd @@ -19,11 +19,11 @@ plot_fishing_mortality( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{geom}{String. Geom used for the plot. @@ -46,9 +46,11 @@ Default: NULL} custom). When multiple models are being compared, a reference line for each model will appear, if desired. The following options can be used to customize the reference line: -1. all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc -2. custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat -3. input vector of labels - ref_line = c("msy", "target") +\enumerate{ +\item all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc +\item custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat +\item input vector of labels - ref_line = c("msy", "target") +} Default: "msy" @@ -61,29 +63,29 @@ Default: "time" Options: "early", "time", "fore" (forecast), or NULL (all data)} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}} } @@ -96,7 +98,7 @@ Plot fishing mortality timeseries \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -116,5 +118,5 @@ plot_fishing_mortality( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [reference_line()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=reference_line]{reference_line()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_index.Rd b/man/plot_index.Rd index 4b4473ef..19572601 100644 --- a/man/plot_index.Rd +++ b/man/plot_index.Rd @@ -18,11 +18,11 @@ plot_index( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{String. Index of abundance/CPUE units @@ -43,15 +43,15 @@ Options: May include, but is not limited to: "fleet", "year", "area", NULL} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{focus}{Character vector. Column name or names used to filter data. (i.e. select names of fleets to zoom into the plot) @@ -59,14 +59,14 @@ module_name in the console. @seealso [filter_data()]} Default: NULL} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} @@ -81,7 +81,7 @@ Plot Index of Abundance \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -93,5 +93,5 @@ plot_index( } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_obsvpred()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_obsvpred]{plot_obsvpred()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_landings.Rd b/man/plot_landings.Rd index 31fb4f0f..b005bfa2 100644 --- a/man/plot_landings.Rd +++ b/man/plot_landings.Rd @@ -21,11 +21,11 @@ plot_landings( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{String. Spawning biomass unit. @@ -52,7 +52,7 @@ Default: NULL} kilograms to pounds. The default units match the default in the unit_label argument - 'mt'. -Default: `FALSE`} +Default: \code{FALSE}} \item{era}{String. Era of data. @@ -64,27 +64,27 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} Default: 1} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} @@ -99,7 +99,7 @@ Plot observed landings \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -119,5 +119,5 @@ plot_landings( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_natural_mortality.Rd b/man/plot_natural_mortality.Rd index abafecba..0e6bddf5 100644 --- a/man/plot_natural_mortality.Rd +++ b/man/plot_natural_mortality.Rd @@ -17,11 +17,11 @@ plot_natural_mortality( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{group}{String. Single column that groups the data. @@ -42,25 +42,25 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} @@ -75,7 +75,7 @@ Plot natural mortality (M) at age \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -86,5 +86,5 @@ plot_natural_mortality( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_obsvpred.Rd b/man/plot_obsvpred.Rd index a7278dcd..91122682 100644 --- a/man/plot_obsvpred.Rd +++ b/man/plot_obsvpred.Rd @@ -48,7 +48,7 @@ Options: "point" and "area"} Default: "Year"} \item{ylab}{String. Y-axis label. If NULL, it will be set to the name - of `y`. +of \code{y}. Default: NULL} diff --git a/man/plot_recruitment.Rd b/man/plot_recruitment.Rd index 976126de..7c05f910 100644 --- a/man/plot_recruitment.Rd +++ b/man/plot_recruitment.Rd @@ -18,11 +18,11 @@ plot_recruitment( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{String. Units for recruitment @@ -51,25 +51,25 @@ Default: NULL} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} } @@ -82,7 +82,7 @@ Plot Recruitment \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -102,5 +102,5 @@ plot_recruitment( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_recruitment_deviations.Rd b/man/plot_recruitment_deviations.Rd index ae6f320c..80369856 100644 --- a/man/plot_recruitment_deviations.Rd +++ b/man/plot_recruitment_deviations.Rd @@ -15,19 +15,19 @@ plot_recruitment_deviations( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{era}{String. Era of data. @@ -37,17 +37,17 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} @@ -62,7 +62,7 @@ Plot recruitment deviations \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \note{ @@ -83,6 +83,6 @@ plot_recruitment_deviations( ) } \seealso{ -[convert_output()], [plot_error()], [filter_data()], -[process_data()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=plot_error]{plot_error()}}, \code{\link[=filter_data]{filter_data()}}, +\code{\link[=process_data]{process_data()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_selectivity.Rd b/man/plot_selectivity.Rd index 4f662d40..122d47ee 100644 --- a/man/plot_selectivity.Rd +++ b/man/plot_selectivity.Rd @@ -17,11 +17,11 @@ plot_selectivity( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{units for length-based selectivity. @@ -40,25 +40,25 @@ Default: NULL} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} @@ -73,7 +73,7 @@ Plot selectivity \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -90,5 +90,5 @@ plot_selectivity( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_spawning_biomass.Rd b/man/plot_spawning_biomass.Rd index fb2467a7..43e1e35f 100644 --- a/man/plot_spawning_biomass.Rd +++ b/man/plot_spawning_biomass.Rd @@ -23,11 +23,11 @@ plot_spawning_biomass( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{geom}{String. Geom used for the plot. @@ -50,9 +50,11 @@ Default: NULL} custom). When multiple models are being compared, a reference line for each model will appear, if desired. The following options can be used to customize the reference line: -1. all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc -2. custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat -3. input vector of labels - ref_line = c("msy", "target") +\enumerate{ +\item all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc +\item custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat +\item input vector of labels - ref_line = c("msy", "target") +} Default: "msy" @@ -73,15 +75,15 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} kilograms to pounds. The default units match the default in the unit_label argument - 'mt'. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{scale_amount}{Number. A number to scale the y-axis values. @@ -90,23 +92,23 @@ Default: 1} \item{relative}{Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value. -Default: `FALSE`} +Default: \code{FALSE}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{...}{Arguments called from \link[ggplot2]{geom_line} or \link[ggplot2]{geom_point}} } @@ -120,12 +122,12 @@ also be made relative to this reference line rather than in absolute units. \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \note{ All plotting functions automatically recognize indexing variables and will -use them in groupings and/or facetting. @seealso [process_data()]. +use them in groupings and/or facetting. @seealso \code{\link[=process_data]{process_data()}}. } \examples{ plot_spawning_biomass( @@ -152,5 +154,5 @@ plot_spawning_biomass( } } \seealso{ -[convert_output()], [plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=calculate_reference_point]{calculate_reference_point()}}, \code{\link[=reference_line]{reference_line()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_stock_recruitment.Rd b/man/plot_stock_recruitment.Rd index 748fba4a..ebd87c62 100644 --- a/man/plot_stock_recruitment.Rd +++ b/man/plot_stock_recruitment.Rd @@ -17,11 +17,11 @@ plot_stock_recruitment( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{spawning_biomass_label}{String. Units for spawning biomass @@ -44,27 +44,27 @@ Default: "time" Options: "early", "time", "fore" (forecast), or NULL (all data)} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{scale_amount}{Number. A number to scale the y-axis values. Default: 1} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{figures_dir}{Path. Path to the "figures" folder. -Default: `getwd()` +Default: \code{getwd()} The folder is created within the path if it does not exist.} } @@ -77,7 +77,7 @@ Plot Stock Recruit Relationship \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a `ggplot2` object or export an .rda object +There are options to return a \code{ggplot2} object or export an .rda object containing associated caption and alternative text for the figure. } \examples{ @@ -90,5 +90,5 @@ plot_stock_recruitment( ) } \seealso{ -[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_data]{process_data()}}, \code{\link[=plot_timeseries]{plot_timeseries()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/plot_timeseries.Rd b/man/plot_timeseries.Rd index 461eb4a8..bd6a7c01 100644 --- a/man/plot_timeseries.Rd +++ b/man/plot_timeseries.Rd @@ -40,7 +40,7 @@ Options: "point" and "area"} Default: "Year"} \item{ylab}{String. Y-axis label. If NULL, it will be set to the name - of `y`. +of \code{y}. Default: NULL} diff --git a/man/process_data.Rd b/man/process_data.Rd index 616fda5d..efe357eb 100644 --- a/man/process_data.Rd +++ b/man/process_data.Rd @@ -27,7 +27,7 @@ Default: NULL} kilograms to pounds. The default units match the default in the unit_label argument - 'metric tons'. -Default: `FALSE`} +Default: \code{FALSE}} } \value{ List of 3 objects: diff --git a/man/save_all_plots.Rd b/man/save_all_plots.Rd index 617d8ea6..9e5d34a7 100644 --- a/man/save_all_plots.Rd +++ b/man/save_all_plots.Rd @@ -32,11 +32,11 @@ save_all_plots( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{recruitment_unit_label}{String. Recruitment units @@ -52,28 +52,28 @@ Default: 1} \item{relative}{Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value. -Default: `FALSE`} +Default: \code{FALSE}} \item{proportional}{Logical. TRUE/FALSE; scale size of bubble plots -Default: `TRUE`} +Default: \code{TRUE}} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{figures_tables_dir}{Path. The location of the folder containing figures and tables ("figures" and "tables"). -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} \item{ref_line}{String. Type of reference point to -compare biomass to. The default is `"msy"`, which looks for -`"biomass_msy"` in the `"label"` column of `dat`. The actual -searching in `dat` is case agnostic and will work with either upper- or +compare biomass to. The default is \code{"msy"}, which looks for +\code{"biomass_msy"} in the \code{"label"} column of \code{dat}. The actual +searching in \code{dat} is case agnostic and will work with either upper- or lower-case letters but you must use one of the options specified in the default list to ensure that the label on the figure looks correct -regardless of how it is specified in `dat`. Other possibilities may include +regardless of how it is specified in \code{dat}. Other possibilities may include "target", "MSY", and "unfished". When the reference cannot be found, indicate the reference line in the form c("label" = value). @@ -86,7 +86,7 @@ Options: Including, but not limited to: "target", "MSY", "unfished"} Default: "mt"} \item{biomass_scale_amount}{Number. A number describing how much to scale down the -biomass quantities shown on the y axis. See `recruitment_scale_amount`. +biomass quantities shown on the y axis. See \code{recruitment_scale_amount}. Default: 1} @@ -99,11 +99,11 @@ Default: "mt"} Default: "mt"} \item{spawning_biomass_scale_amount}{Number. A number describing how much to scale down the -spawning biomass quantities shown on the y axis. See `recruitment_scale_amount`. +spawning biomass quantities shown on the y axis. See \code{recruitment_scale_amount}. Default: 1} -\item{ref_line_sb}{String. Same as `ref_line`, but this argument is +\item{ref_line_sb}{String. Same as \code{ref_line}, but this argument is applied to plot_spawning_biomass. Default: "msy" @@ -111,7 +111,7 @@ Default: "msy" Options: Including, but not limited to: "target", "MSY", "unfished"} \item{abundance_at_age_scale_amount}{Number. A number describing how much to scale down the -abundance quantities shown via bubble size. See `recruitment_scale_amount`. +abundance quantities shown via bubble size. See \code{recruitment_scale_amount}. Default: 1} @@ -120,7 +120,7 @@ Default: 1} Default: "fish"} \item{biomass_at_age_scale_amount}{Number. A number describing how much to scale down the -biomass quantities shown via bubble size. See `recruitment_scale_amount`. +biomass quantities shown via bubble size. See \code{recruitment_scale_amount}. Default: 1} @@ -141,7 +141,7 @@ Default: c("biomass" = "mt", "abundance" = "fish", "catch" = "mt")} Default: "mt"} \item{catch_scale_amount}{Number. A number describing how much to scale down the -catch quantities shown via bubble size. See `recruitment_scale_amount`. +catch quantities shown via bubble size. See \code{recruitment_scale_amount}. Default: 1} @@ -178,5 +178,5 @@ save_all_plots(dat, } } \seealso{ -[convert_output()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/table_biomass_abundance_catch.Rd b/man/table_biomass_abundance_catch.Rd index b986886a..98dc12d1 100644 --- a/man/table_biomass_abundance_catch.Rd +++ b/man/table_biomass_abundance_catch.Rd @@ -18,11 +18,11 @@ table_biomass_abundance_catch( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{Character vector. Abbreviated unit label for each quantity @@ -36,7 +36,7 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{group}{A string of a single column that groups the data. @@ -52,13 +52,13 @@ Default: "sum" Options: "sum" or "mean"} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{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 @@ -68,14 +68,14 @@ in this ordered list: "landings_weight", "landings_numbers", "landings_expected Default: NULL} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{tables_dir}{The location of the folder containing the table -rda files ("tables") that will be created if the argument `make_rda` = TRUE. -Default: the working directory (`getwd()`)} +rda files ("tables") that will be created if the argument \code{make_rda} = TRUE. +Default: the working directory (\code{getwd()})} } \value{ A table of biomass, abundance, catch, and spawning biomass. @@ -85,7 +85,7 @@ Biomass, abundance, and catch time series table } \details{ There are -options to return a [gt::gt()] object or export an rda object containing +options to return a \code{\link[gt:gt]{gt::gt()}} object or export an rda object containing a gt-based table, caption, and LaTeX-based table. } \examples{ @@ -98,5 +98,5 @@ table_biomass_abundance_catch(stockplotr::example_data, ) } \seealso{ -[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_table]{process_table()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/table_index.Rd b/man/table_index.Rd index 1a3e9a63..96a8327a 100644 --- a/man/table_index.Rd +++ b/man/table_index.Rd @@ -18,11 +18,11 @@ table_index( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{era}{String. Era of data. @@ -32,7 +32,7 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{group}{String. Single column that groups the data. @@ -48,13 +48,13 @@ Default: "sum" Options: "sum" or "mean"} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{label}{String. 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 @@ -69,15 +69,15 @@ table will be rounded to. Default: 2} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{tables_dir}{Path. The location of the folder containing the generated table -rda files ("tables") that will be created if the argument `make_rda` = TRUE. +rda files ("tables") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A table of observed annual index of abundance plus error, @@ -89,7 +89,7 @@ Index 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 +There are options to return a \code{\link[gt:gt]{gt::gt()}} object or export an rda object containing a gt-based table, caption, and LaTeX-based table. } \examples{ @@ -104,5 +104,5 @@ table_index( } } \seealso{ -[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_table]{process_table()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/table_landings.Rd b/man/table_landings.Rd index a354a69b..ee28d9b0 100644 --- a/man/table_landings.Rd +++ b/man/table_landings.Rd @@ -20,11 +20,11 @@ table_landings( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{String. Abbreviated landings units @@ -38,7 +38,7 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} \item{group}{String. Single column that groups the data. @@ -54,13 +54,13 @@ Default: "sum" Options: "sum" or "mean"} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{label}{String. 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 @@ -79,15 +79,15 @@ Default: 2} Default: 1} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{tables_dir}{Path. The location of the folder containing the generated table -rda files ("tables") that will be created if the argument `make_rda` = TRUE. +rda files ("tables") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A table ready of landed catch by fleet and year. @@ -98,7 +98,7 @@ Landed catch by fleet and year 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 +There are options to return a \code{\link[gt:gt]{gt::gt()}} object or export an rda object containing a gt-based table, caption, and LaTeX-based table. } \examples{ @@ -111,5 +111,5 @@ table_landings( ) } \seealso{ -[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_table]{process_table()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/table_projections.Rd b/man/table_projections.Rd index 6ec1930f..43a312cc 100644 --- a/man/table_projections.Rd +++ b/man/table_projections.Rd @@ -14,11 +14,11 @@ table_projections( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{Character vector. Abbreviated unit label for each quantity @@ -27,26 +27,26 @@ Default: c("catch" = "mt", "spawning_biomass" = "mt", \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{tables_dir}{Path. The location of the folder containing the generated table -rda files ("tables") that will be created if the argument `make_rda` = TRUE. +rda files ("tables") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A formatted gt table object. diff --git a/man/table_total_catch.Rd b/man/table_total_catch.Rd index 88edb47a..855b5835 100644 --- a/man/table_total_catch.Rd +++ b/man/table_total_catch.Rd @@ -17,11 +17,11 @@ table_total_catch( ) } \arguments{ -\item{dat}{Data frame or list. A tibble or named list of tibbles (input as `list()`) +\item{dat}{Data frame or list. A tibble or named list of tibbles (input as \code{list()}) returned from \link[stockplotr]{convert_output}. If inputting a list of tibbles, the first tibble's reference point defined -in `ref_line` is used to plot a reference line or calculate relative spawning biomass.} +in \code{ref_line} is used to plot a reference line or calculate relative spawning biomass.} \item{unit_label}{String. Abbreviated catch units @@ -35,15 +35,15 @@ Options: "early", "time", "fore" (forecast), or NULL (all data)} \item{interactive}{Logical. TRUE/FALSE; indicate whether the environment is interactive. -Default: `FALSE`} +Default: \code{FALSE}} -\item{module}{Character vector. (Optional) Module name found in `dat$module_name`. +\item{module}{Character vector. (Optional) Module name found in \code{dat$module_name}. If selecting >1 module, place them in a vector like c("module1", "module2"). Default: NULL If the interactive and >1 module_name is found, user will select the -module_name in the console. @seealso [filter_data()]} +module_name in the console. @seealso \code{\link[=filter_data]{filter_data()}}} \item{scale_amount}{Number. A number to scale the y-axis values. @@ -55,15 +55,15 @@ table will be rounded to. Default: 2} \item{make_rda}{Logical. TRUE/FALSE; indicate whether to save the object and -make an automated caption and alternative text in the form of an `rda` object. If TRUE, +make an automated caption and alternative text in the form of an \code{rda} object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". -Default: `FALSE`.} +Default: \code{FALSE}.} \item{tables_dir}{Path. The location of the folder containing the generated table -rda files ("tables") that will be created if the argument `make_rda` = TRUE. +rda files ("tables") that will be created if the argument \code{make_rda} = TRUE. -Default: the working directory (`getwd()`)} +Default: the working directory (\code{getwd()})} } \value{ A table ready of landed catch by fleet and year. @@ -74,7 +74,7 @@ Catch (table) by fleet, gear type, sector \details{ The input is from an assessment model output file translated to a standardized output (\link[stockplotr]{convert_output}). -There are options to return a [gt::gt()] object or export an rda object +There are options to return a \code{\link[gt:gt]{gt::gt()}} object or export an rda object containing a gt-based table, caption, and LaTeX-based table. } \examples{ @@ -91,5 +91,5 @@ table_total_catch( ) } \seealso{ -[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()] +\code{\link[=convert_output]{convert_output()}}, \code{\link[=filter_data]{filter_data()}}, \code{\link[=process_table]{process_table()}}, \code{\link[=export_kqs]{export_kqs()}}, \code{\link[=insert_kqs]{insert_kqs()}}, \code{\link[=create_rda]{create_rda()}} } diff --git a/man/theme_noaa.Rd b/man/theme_noaa.Rd index 3f928018..a5a7234c 100644 --- a/man/theme_noaa.Rd +++ b/man/theme_noaa.Rd @@ -11,7 +11,7 @@ theme_noaa(discrete = TRUE, ...) Default: TRUE} -\item{...}{Arguments passed to `ggplot2::theme()`.} +\item{...}{Arguments passed to \code{ggplot2::theme()}.} } \value{ A list applying a theme to a ggplot2 object. From 01d7a033ea82f9530d7de820ce1fa43dcd9ea428 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Fri, 16 Oct 2026 15:53:59 -0400 Subject: [PATCH 3/4] fix missing closing bracket --- R/convert_output.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/convert_output.R b/R/convert_output.R index 597e552c..f4ea92c5 100644 --- a/R/convert_output.R +++ b/R/convert_output.R @@ -58,8 +58,6 @@ convert_output <- function( i = "File will be compatible until Oct. 1, 2027" ) ) - - custom_params <- setNames(param_values, param_names) } # check if entered save_dir exists so doesn't waste user time finding this out at the end From 8f5d5014ebdfa886f4f5d94431e84d647aa0f45d Mon Sep 17 00:00:00 2001 From: "Sam (Schiano) Bredeck" <125507018+Schiano-NOAA@users.noreply.github.com> Date: Fri, 16 Oct 2026 16:07:15 -0400 Subject: [PATCH 4/4] Update R/utils_plot.R Co-authored-by: Sophie Breitbart --- R/utils_plot.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils_plot.R b/R/utils_plot.R index 9d3696ec..691b52fd 100644 --- a/R/utils_plot.R +++ b/R/utils_plot.R @@ -878,7 +878,7 @@ get_id <- function(dat) { #' Calculate reference value point #' #' @inheritParams plot_spawning_biomass dat lbs -#' @param reference_name a string of the name of the reference point (e.g. "spawning biomass msy") +#' @param reference_name String. Name of the reference point (e.g. "spawning biomass msy") #' #' @returns the value of the reference point name found in the dat file. #' @export