From 7b1bb5a79fc5bc722c7018ed5a045c251c1ec91a Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 19 May 2026 16:47:01 -0400 Subject: [PATCH 1/2] adjust naa documentation and respective inherited docs --- R/plot_abundance_at_age.R | 7 +++--- man/plot_abundance_at_age.Rd | 43 +++++++++++++++++++++++++++++++----- man/plot_biomass_at_age.Rd | 29 ++++++++++++++++++++++++ man/plot_catch_comp.Rd | 29 ++++++++++++++++++++++++ 4 files changed, 98 insertions(+), 10 deletions(-) diff --git a/R/plot_abundance_at_age.R b/R/plot_abundance_at_age.R index 2c38be90..7b725297 100644 --- a/R/plot_abundance_at_age.R +++ b/R/plot_abundance_at_age.R @@ -1,4 +1,4 @@ -#' Plot Abundance (or Numbers) at Age (AAA or NAA) +#' Plot Abundance at Age #' #' @param dat A data frame returned from \link[stockplotr]{convert_output} #' @param facet a string or vector of strings of a column that facets the data. @@ -40,6 +40,7 @@ #' 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 #' translated to a standardized output (\link[stockplotr]{convert_output}). @@ -56,9 +57,7 @@ #' facet = "growth_pattern", #' unit_label = "fish", #' scale_amount = 1000, -#' proportional = TRUE, -#' make_rda = FALSE, -#' figures_dir = getwd() +#' proportional = TRUE #' ) #' plot_abundance_at_age( #' dat = stockplotr:::example_data, diff --git a/man/plot_abundance_at_age.Rd b/man/plot_abundance_at_age.Rd index b3b56c6e..09461ad9 100644 --- a/man/plot_abundance_at_age.Rd +++ b/man/plot_abundance_at_age.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/plot_abundance_at_age.R \name{plot_abundance_at_age} \alias{plot_abundance_at_age} -\title{Plot Abundance (or Numbers) at Age (AAA or NAA)} +\title{Plot Abundance at Age} \usage{ plot_abundance_at_age( dat, @@ -17,6 +17,7 @@ plot_abundance_at_age( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} +<<<<<<< HEAD \item{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. @@ -24,6 +25,14 @@ Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL} +======= +\item{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. + +Default: NULL (function will automatically detect and indexing in the data +and place them into group then facet)} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{unit_label}{units for abundance @@ -34,6 +43,7 @@ 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 +<<<<<<< HEAD in the legend label if proportional is set to FALSE. Default: 1,000} @@ -54,12 +64,35 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} +======= +in the legend label if proportional is set to FALSE. + +Default: 1,000.} + +\item{proportional}{Set size of points relative to abundance. When TRUE, point +size are relative to one another. When set to FALSE, point size +is relative to abundance. + +Default: TRUE} + +\item{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 "figures_dir". + +Default: FALSE} + +\item{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: getwd()} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ -A plot showing total abundance (or numbers) at age. +Plot of total abundance at age. } \description{ -Plot Abundance (or Numbers) at Age (AAA or NAA) +Plot Abundance at Age } \details{ The input is from an assessment model output file @@ -73,9 +106,7 @@ plot_abundance_at_age( facet = "growth_pattern", unit_label = "fish", scale_amount = 1000, - proportional = TRUE, - make_rda = FALSE, - figures_dir = getwd() + proportional = TRUE ) plot_abundance_at_age( dat = stockplotr:::example_data, diff --git a/man/plot_biomass_at_age.Rd b/man/plot_biomass_at_age.Rd index 854e979e..76f39b10 100644 --- a/man/plot_biomass_at_age.Rd +++ b/man/plot_biomass_at_age.Rd @@ -18,6 +18,7 @@ plot_biomass_at_age( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} +<<<<<<< HEAD \item{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. @@ -25,6 +26,14 @@ Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL} +======= +\item{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. + +Default: NULL (function will automatically detect and indexing in the data +and place them into group then facet)} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{unit_label}{units for abundance @@ -37,11 +46,19 @@ proportion is set to FALSE. Default: 1,000} +<<<<<<< HEAD \item{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`} +======= +\item{proportional}{Set size of points relative to abundance. When TRUE, point +size are relative to one another. When set to FALSE, point size +is relative to abundance. + +Default: TRUE} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{interactive}{TRUE/FALSE; indicate whether the environment in which the function is operating is interactive. This bypasses some options for @@ -51,6 +68,7 @@ Default: `TRUE`} \item{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, +<<<<<<< HEAD the .rda will be exported to the folder indicated in the argument "rda_dir". Default: `FALSE`} @@ -59,6 +77,17 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} +======= +the .rda will be exported to the folder indicated in the argument "figures_dir". + +Default: FALSE} + +\item{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: getwd()} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ A plot showing total biomass at age. diff --git a/man/plot_catch_comp.Rd b/man/plot_catch_comp.Rd index 5c22dc18..7d790498 100644 --- a/man/plot_catch_comp.Rd +++ b/man/plot_catch_comp.Rd @@ -20,8 +20,17 @@ plot_catch_comp( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} +<<<<<<< HEAD \item{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. +======= +\item{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. + +Default: NULL (function will automatically detect and indexing in the data +and place them into group then facet)} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) Default: NULL @@ -47,9 +56,17 @@ in the legend label if proportional is set to FALSE. Default: 1} +<<<<<<< HEAD \item{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 +======= +\item{proportional}{Set size of points relative to abundance. When TRUE, point +size are relative to one another. When set to FALSE, point size +is relative to abundance. + +Default: TRUE} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) Default: `TRUE`} @@ -67,6 +84,7 @@ module_name in the console. @seealso [filter_data()]} \item{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, +<<<<<<< HEAD the .rda will be exported to the folder indicated in the argument "rda_dir". Default: `FALSE`} @@ -75,6 +93,17 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} +======= +the .rda will be exported to the folder indicated in the argument "figures_dir". + +Default: FALSE} + +\item{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: getwd()} +>>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ A plot showing catch or landings composition. From 5d8c412ff2f403cd6c9c28b3b0671a24208987d3 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Tue, 26 May 2026 15:04:07 -0400 Subject: [PATCH 2/2] update doc --- DESCRIPTION | 1 + man/plot_abundance_at_age.Rd | 35 +---------------------------------- man/plot_biomass_at_age.Rd | 29 ----------------------------- man/plot_catch_comp.Rd | 29 ----------------------------- man/stockplotr-package.Rd | 1 - 5 files changed, 2 insertions(+), 93 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 02a7d01e..c96ed457 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -71,3 +71,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Config/roxygen2/version: 8.0.0 +RoxygenNote: 7.3.3 diff --git a/man/plot_abundance_at_age.Rd b/man/plot_abundance_at_age.Rd index 09461ad9..8bf76f65 100644 --- a/man/plot_abundance_at_age.Rd +++ b/man/plot_abundance_at_age.Rd @@ -17,7 +17,6 @@ plot_abundance_at_age( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} -<<<<<<< HEAD \item{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. @@ -25,14 +24,6 @@ Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL} -======= -\item{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. - -Default: NULL (function will automatically detect and indexing in the data -and place them into group then facet)} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{unit_label}{units for abundance @@ -43,7 +34,6 @@ 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 -<<<<<<< HEAD in the legend label if proportional is set to FALSE. Default: 1,000} @@ -64,32 +54,9 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} -======= -in the legend label if proportional is set to FALSE. - -Default: 1,000.} - -\item{proportional}{Set size of points relative to abundance. When TRUE, point -size are relative to one another. When set to FALSE, point size -is relative to abundance. - -Default: TRUE} - -\item{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 "figures_dir". - -Default: FALSE} - -\item{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: getwd()} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ -Plot of total abundance at age. +A plot showing total abundance (or numbers) at age. } \description{ Plot Abundance at Age diff --git a/man/plot_biomass_at_age.Rd b/man/plot_biomass_at_age.Rd index 76f39b10..854e979e 100644 --- a/man/plot_biomass_at_age.Rd +++ b/man/plot_biomass_at_age.Rd @@ -18,7 +18,6 @@ plot_biomass_at_age( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} -<<<<<<< HEAD \item{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. @@ -26,14 +25,6 @@ Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL} -======= -\item{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. - -Default: NULL (function will automatically detect and indexing in the data -and place them into group then facet)} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{unit_label}{units for abundance @@ -46,19 +37,11 @@ proportion is set to FALSE. Default: 1,000} -<<<<<<< HEAD \item{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`} -======= -\item{proportional}{Set size of points relative to abundance. When TRUE, point -size are relative to one another. When set to FALSE, point size -is relative to abundance. - -Default: TRUE} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) \item{interactive}{TRUE/FALSE; indicate whether the environment in which the function is operating is interactive. This bypasses some options for @@ -68,7 +51,6 @@ Default: `TRUE`} \item{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, -<<<<<<< HEAD the .rda will be exported to the folder indicated in the argument "rda_dir". Default: `FALSE`} @@ -77,17 +59,6 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} -======= -the .rda will be exported to the folder indicated in the argument "figures_dir". - -Default: FALSE} - -\item{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: getwd()} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ A plot showing total biomass at age. diff --git a/man/plot_catch_comp.Rd b/man/plot_catch_comp.Rd index 7d790498..5c22dc18 100644 --- a/man/plot_catch_comp.Rd +++ b/man/plot_catch_comp.Rd @@ -20,17 +20,8 @@ plot_catch_comp( \arguments{ \item{dat}{A data frame returned from \link[stockplotr]{convert_output}} -<<<<<<< HEAD \item{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. -======= -\item{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. - -Default: NULL (function will automatically detect and indexing in the data -and place them into group then facet)} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) Default: NULL @@ -56,17 +47,9 @@ in the legend label if proportional is set to FALSE. Default: 1} -<<<<<<< HEAD \item{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 -======= -\item{proportional}{Set size of points relative to abundance. When TRUE, point -size are relative to one another. When set to FALSE, point size -is relative to abundance. - -Default: TRUE} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) Default: `TRUE`} @@ -84,7 +67,6 @@ module_name in the console. @seealso [filter_data()]} \item{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, -<<<<<<< HEAD the .rda will be exported to the folder indicated in the argument "rda_dir". Default: `FALSE`} @@ -93,17 +75,6 @@ Default: `FALSE`} ("rda_files") that will be created if the argument `make_rda` = TRUE. Default: the working directory (`getwd()`)} -======= -the .rda will be exported to the folder indicated in the argument "figures_dir". - -Default: FALSE} - -\item{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: getwd()} ->>>>>>> 2e302fb (adjust naa documentation and respective inherited docs) } \value{ A plot showing catch or landings composition. diff --git a/man/stockplotr-package.Rd b/man/stockplotr-package.Rd index 0dcd782c..ce67c60e 100644 --- a/man/stockplotr-package.Rd +++ b/man/stockplotr-package.Rd @@ -22,7 +22,6 @@ Useful links: Authors: \itemize{ - \item Samantha Schiano \email{samantha.schiano@noaa.gov} (\href{https://orcid.org/0009-0003-3744-6428}{ORCID}) \item Sophie Breitbart \email{sophie.breitbart@noaa.gov} (\href{https://orcid.org/0000-0001-9641-9786}{ORCID}) [contributor] \item Steve Saul \email{steven.saul@noaa.gov} }