[doc] Add default and optional values for arguments in documentation

DESCRIPTION

@@ -70,4 +70,4 @@ Config/testthat/parallel: false
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.0.0

R/add_theme.R

@@ -3,6 +3,8 @@
 #' @param x table or figures object from ggplot, base r plot, gt table, flextable, or kable extra
 #' @param discrete TRUE/FALSE indicate if data input is discrete. Specifically applied to plots.
 #'
+#' Default: TRUE
+#'
 #' @returns Add the standard formatting for stock assessment reports for any
 #' figure or table.
 #' @details Currently, the function is able to format objects from:

R/convert_output.R

@@ -3,12 +3,19 @@
 #' Format stock assessment output files to a standardized format.
 #'
 #' @param file Assessment model output file path
-#' @param model Assessment model used in evaluation ("ss3", "bam",
-#'  "fims", "rceattle).
+#' @param model Assessment model used in evaluation
+#' 
+#' Default: NULL
+#' 
+#' Options: "ss3", "bam", "fims", "rceattle"
 #' @param fleet_names Names of fleets in the assessment model as
 #'  shortened in the output file. If fleet names are not properly read, then
 #'  indicate the fleets names as an acronym in a vector
+#'  
+#'  Default: NULL
 #' @param save_dir File path to save the converted output file.
+#' 
+#' Default: NULL
 #'
 #' @author Samantha Schiano
 #'

R/html_all_figs_tables.R

@@ -5,6 +5,8 @@
 #' @param figures_tables_dir The location of the folder containing
 #' figures and tables ("figures" and "tables").
 #'
+#' Default: The current working directory (`getwd()`)
+#'
 #' @returns A folder ("all_tables_figures") in your working directory containing
 #' html and qmd files that show all tables and figures.
 #' 

R/plot_abundance_at_age.R

@@ -1,26 +1,44 @@
 #' Plot Abundance (or Numbers) at Age (AAA or NAA)
 #'
 #' @param dat A data frame returned from \link[stockplotr]{convert_output}
-#' @param facet a string or vector of strings of column(s) that
-#' groups the data (e.g. "fleet", "sex", "area", etc.). Set facet = "none" to
-#' summarize the data in a single plot.
+#' @param facet a string or vector of strings of a column that facets the data.
+#' Set facet = "none" to summarize the data in a single plot.
+#' 
+#' Default: NULL
+#' 
+#' Options: Including, but not limited to: "year", "area", "fleet", "sex", "none",
+#' NULL
+#' 
 #' @param unit_label units for abundance
+#' 
+#' Default: "fish"
+#' 
 #' @param scale_amount A number describing how much to scale down the abundance at
 #' age. Please choose a value ranging from 1-1,000,000,000 (one billion) in orders
 #' of magnitude (e.g., 1, 10, 100, 1000, etc.). For example, scale_amount = 100
 #' would scale down a value from 500,000 --> 5,000 and would report abundance in
 #' hundreds of fish (if "fish" was the unit_label). This scale will be reflected
-#' in the legend label if proportional is set to FALSE. The default is 1,000.
+#' in the legend label if proportional is set to FALSE.
+#' 
+#' Default: 1,000
+#' 
 #' @param proportional Set size of points relative to z when TRUE, point
 #' size are relative to one another while when set to FALSE, point size
 #' is relative to z
+#' 
+#' Default: `TRUE`
+#' 
 #' @param make_rda 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 is FALSE.
+#' 
+#' Default: `FALSE`
+#' 
 #' @param figures_dir The location of the folder containing the generated .rda files
 #' ("rda_files") that will be created if the argument `make_rda` = TRUE.
-#' Default is the working directory.
+#' 
+#' Default: the working directory (`getwd()`)
+#' 
 #' @returns A plot showing total abundance (or numbers) at age.
 #' 
 #' @details The input is from an assessment model output file

R/plot_biomass.R

@@ -2,14 +2,19 @@
 #'
 #' @inheritParams plot_spawning_biomass
 #' @param unit_label units for biomass
+#' 
+#' Default: "mt"
 #' @param ref_line A string specifying the type of reference you want to
-#'   compare biomass to. The default is `"msy"`, which looks for
+#'   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 but you must use one of the options specified in the
+#'   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`. Other possibilities may include
-#'   "target", "MSY", and "unfished".
+#'   regardless of how it is specified in `dat`.
+#'   
+#' Default: "msy"
+#' 
+#' Options: Including, but not limited to: "target", "MSY", "unfished"
 #' @returns A plot showing total biomass.
 #' 
 #' @details The input is from an assessment model output file
@@ -43,7 +48,7 @@ plot_biomass <- function(
   facet = NULL,
   ref_line = "msy",
   era = NULL,
-  unit_label = "metric tons",
+  unit_label = "mt",
   module = NULL,
   scale_amount = 1,
   relative = FALSE,

R/plot_biomass_at_age.R

@@ -5,9 +5,14 @@
 #' age. For example, scale_amount = 100 would scale down a value
 #' from 500,000 --> 5,000. This scale will be reflected in the legend label if
 #' proportion is set to FALSE.
+#'
+#' Default: 1,000
+#'
 #' @param interactive TRUE/FALSE; indicate whether the environment in which the
 #' function is operating  is interactive. This bypasses some options for
-#' filtering when preparing data for the plot. Default is FALSE.
+#' filtering when preparing data for the plot.
+#'
+#' Default: `TRUE`
 #' 
 #' @returns A plot showing total biomass at age.
 #' 
@@ -40,7 +45,7 @@ plot_biomass_at_age <- function(
   unit_label = "mt",
   scale_amount = 1000,
   proportional = TRUE,
-  interactive = FALSE,
+  interactive = TRUE,
   make_rda = FALSE,
   figures_dir = getwd()
 ) {

R/plot_catch_comp.R

@@ -2,22 +2,36 @@
 #'
 #' @inheritParams plot_abundance_at_age
 #' @param unit_label indicate the name of the units of catch as to label the axis
+#' 
+#' Default: "mt"
+#' 
 #' @param scale_amount A number describing how much to scale down the catch at
 #' age. Please choose a value ranging from 1-1,000,000,000 (one billion) in orders
 #' of magnitude (e.g., 1, 10, 100, 1000, etc.). For example, scale_amount = 100
 #' would scale down a value from 500,000 --> 5,000 and would report catch in
 #' hundreds of the 'unit_label'. This scale will be reflected
-#' in the legend label if proportional is set to FALSE. The default is 1.
-#' @param era a string naming the era of data such as historical ("early"), current ("time"), or
-#' projected ("fore") data if filtering should occur. Default is set to "time" which is
-#' the current time. To plot all data, set era to NULL.
-#' @param interactive TRUE/FALSE; indicate whether the environment in which the
-#' function is operating  is interactive. This bypasses some options for
-#' filtering when preparing data for the plot. Default is FALSE.
-#' @param module (Optional) A string indicating the linked module_name associated
-#' with the label for the plot if known. Default is NULL. By default, the function
-#' will select the most relevant module if more than 1 exists.
+#' in the legend label if proportional is set to FALSE.
+#' 
+#' Default: 1
+#' 
+#' @param era A string naming the era of data.
+#'
+#' Default: "time"
 #'
+#' Options: "early", "time", "fore" (forecast), or NULL (all data)
+#' 
+#' @param interactive A logical value indicating if the environment is interactive.
+#'
+#' Default: `FALSE`
+#' 
+#' @param 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()]
+#' 
 #' @returns A plot showing catch or landings composition.
 #' 
 #' @details This plot is made only when catch or landings are explicitly named

R/plot_indices.R

@@ -1,12 +1,18 @@
 #' Plot Index of Abundance
 #'
 #' @inheritParams plot_spawning_biomass
-#' @param facet a string or vector of strings of a column that facets the data
-#' (e.g. "year", "area", etc.) "fleet" is always added on to any faceting selections
+#' @param facet a string or vector of strings of a column that facets the data. "fleet" is always added on to any faceting selections
+#'
+#' Default: NULL
+#'
+#' Options: May include, but is not limited to: "fleet", "year", "area", NULL
 #' @param unit_label units for index of abundance/CPUE
+#'
+#' Default: ""
 #' @param focus a string or vector of strings indicating how data should be
 #' filtered. (i.e. select names of fleets to zoom into the plot)
 #'
+#' Default: NULL
 #' @returns A plot showing the expected and predicted indices.
 #' 
 #' @details The input is from an assessment model output file

R/plot_landings.R

@@ -30,7 +30,7 @@
 #' )
 plot_landings <- function(
   dat,
-  unit_label = "metric tons",
+  unit_label = "mt",
   geom = "line",
   group = NULL,
   facet = NULL,

R/plot_recruitment.R

@@ -3,6 +3,8 @@
 #' @inheritParams plot_spawning_biomass
 #' @param unit_label units for recruitment
 #'
+#' Default: "mt"
+#'
 #' @returns A plot showing recruitment over time.
 #' 
 #' @details The input is from an assessment model output file

R/plot_spawning_biomass.R

@@ -13,12 +13,13 @@
 #' Default: "line".
 #'
 #' Options: "line", "point", or "area"
-#' @param group A string of a single column that groups the data (e.g. "fleet",
-#' "sex", "area", etc.).
+#' @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 facet A string or vector of strings of a column name.
 #'
 #' Default: NULL
@@ -35,13 +36,14 @@
 #' If the reference point is not found in the data, set ref_line = c("name" = value).
 #' @param unit_label A string specifying spawning biomass unit.
 #'
-#' Default: "metric tons"
+#' Default: "mt"
 #' @param lbs A logical value indicating whether to convert the y-axis values from
 #' kilograms to pounds. The default units match the default in the
-#' unit_label argument - 'metric tons'. 
+#' unit_label argument - 'mt'. 
 #'
 #' Default: `FALSE`
 #' @param 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
 #'
@@ -107,7 +109,7 @@ plot_spawning_biomass <- function(
   group = NULL,
   facet = NULL,
   ref_line = "msy",
-  unit_label = "metric tons",
+  unit_label = "mt",
   era = NULL,
   lbs = FALSE,
   module = NULL,

R/plot_stock_recruitment.R

@@ -5,9 +5,17 @@
 #' plot is being made in is interactive. By default, this
 #' is set to false. If true, dependent on your data, a
 #' option menu will pop-up.
+#'
+#' Default: TRUE
+#'
 #' @param spawning_biomass_label Units for spawning biomass
+#'
+#' Default: "mt"
+#' 
 #' @param recruitment_label units for recruitment
 #'
+#' Default: "mt"
+#'
 #' @returns A plot showing the stock recruitment relationship.
 #' 
 #' @details The input is from an assessment model output file

R/process_data.R

@@ -6,17 +6,29 @@
 #'
 #' @param dat Pre-filtered data from \link[stockplotr]{filter_data} following a
 #' long format data.
-#' @param group A string identifying the indexing variable of the data. If you
-#' want to just summarize the data across all factors, set group = "none".
+#' @param group A string identifying the indexing variable of the data.
+#' To remove any groups and summarize data across all factors, set
+#' group = "none". Setting group = NULL will keep any grouping
+#' variables identified in the data by the function.
+#'
+#' Default: NULL
+#'
+#' Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL
 #' @param facet A string or vector of strings identifying the faceting
 #' variable(s) of the data.
+#'
+#' Default: NULL
 #' @param lbs A logical value indicating whether to convert the y-axis values from
 #' kilograms to pounds. The default units match the default in the
 #' unit_label argument - 'metric tons'. 
 #'
 #' Default: `FALSE`
 #' @param method A string describing the method of summarizing data when group
-#' is set to "none". Options are "sum" or "mean". Default is "sum".
+#' is set to "none".
+#'
+#' Default: "sum"
+#'
+#' Options: "sum" or "mean"
 #'
 #' @returns List of 3 objects:
 #' \item{data}{A data frame of the processed data ready for plotting.}
@@ -360,6 +372,8 @@ process_data <- function(
 #'
 #' @inheritParams process_data
 #' @param label A string or vector of strings identifying the label values to filter the data.
+#' 
+#' Default: NULL
 #'
 #' @returns A dataframe of processed data ready for formatting into a table.
 #' @details Input is an object created with \link[stockplotr]{filter_data}.
@@ -369,7 +383,7 @@ process_data <- function(
 #' @examples {
 #'   filtered <- filter_data(
 #'     dat = stockplotr:::example_data,
-#'     label_name = "landings",
+#'     label = "landings",
 #'     geom = "line",
 #'     era = "time"
 #'   )