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Convert "spawning recruitment" to "stock recruitment" #174

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Merged
sbreitbart-NOAA merged 1 commit into from
Jan 8, 2026
Merged

Convert "spawning recruitment" to "stock recruitment" #174

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2 changes: 1 addition & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ export(plot_landings)
export(plot_natural_mortality)
export(plot_recruitment)
export(plot_recruitment_deviations)
export(plot_spawn_recruitment)
export(plot_spawning_biomass)
export(plot_stock_recruitment)
export(plot_timeseries)
export(process_data)
export(reference_line)
Expand Down
8 changes: 4 additions & 4 deletions R/plot_spawn_recruitment.R → R/plot_stock_recruitment.R
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#' Plot Spawn-Recruit Relationship
#' Plot Stock Recruit Relationship
#'
#' @inheritParams plot_spawning_biomass
#' @param interactive Indicate whether the environment the
Expand All @@ -8,21 +8,21 @@
#' @param spawning_biomass_label Units for spawning biomass
#' @param recruitment_label units for recruitment
#'
#' @return Plot the spawn recruitment relationship from an assessment model output file
#' @return Plot the stock recruitment relationship from an assessment model output file
#' translated to a standardized output (\link[asar]{convert_output}). There are options to return a
#' [ggplot2::ggplot()] object or export an rda object containing associated
#' caption and alternative text for the figure.
#' @export
#'
#' @examples
#' plot_spawn_recruitment(
#' plot_stock_recruitment(
#' dat = stockplotr:::example_data,
#' interactive = FALSE,
#' spawning_biomass_label = "metric tons",
#' recruitment_label = "metric tons",
#' module = "SPAWN_RECRUIT"
#' )
plot_spawn_recruitment <- function(
plot_stock_recruitment <- function(
dat,
spawning_biomass_label = "mt",
recruitment_label = "mt",
Expand Down
4 changes: 2 additions & 2 deletions R/save_all_plots.R
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Expand Up @@ -70,7 +70,7 @@ save_all_plots <- function(
# imported from plot_landings
landings_unit_label = "mt",
# imported from plot_recruitment_deviations- zero unique arguments
# imported from plot_spawn_recruitment
# imported from plot_stock_recruitment
spawning_biomass_label = "mt",
spawning_biomass_scale_amount = 1,
# imported from plot_spawning_biomass
Expand Down Expand Up @@ -189,7 +189,7 @@ save_all_plots <- function(
}
)

# plot_spawn_recruitment(dat,
# plot_stock_recruitment(dat,
# spawning_biomass_label,
# recruitment_label = recruitment_unit_label,
# make_rda,
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4 changes: 2 additions & 2 deletions R/utils_rda.R
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Expand Up @@ -549,7 +549,7 @@ add_more_key_quants <- function(
}

if (!is.null(sr_ssb_units)) {
### this is for plot_spawn_recruitment, since there are two units
### this is for plot_stock_recruitment, since there are two units
#### replace sr.ssb.units with sr_ssb_units
topic_cap_alt <- topic_cap_alt |>
dplyr::mutate(alt_text = stringr::str_replace_all(
Expand All @@ -562,7 +562,7 @@ add_more_key_quants <- function(
}

if (!is.null(sr_recruitment_units)) {
### this is for plot_spawn_recruitment, since there are two units
### this is for plot_stock_recruitment, since there are two units
#### replace sr.units with sr_recruitment_units
topic_cap_alt <- topic_cap_alt |>
dplyr::mutate(alt_text = stringr::str_replace_all(
Expand Down
16 changes: 8 additions & 8 deletions man/plot_spawn_recruitment.Rd → man/plot_stock_recruitment.Rd
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10 changes: 5 additions & 5 deletions tests/testthat/test-plot_spawn_recruitment.R → tests/testthat/test-plot_stock_recruitment.R
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Expand Up @@ -4,17 +4,17 @@ load(file.path(
"std_output.rda"
))

test_that("plot_spawn_recruitment generates plots without errors", {
test_that("plot_stock_recruitment generates plots without errors", {
# expect error-free plot with minimal arguments
expect_no_error(
stockplotr::plot_spawn_recruitment(
stockplotr::plot_stock_recruitment(
dat = out_new
)
)

# expect error-free plot with many arguments
expect_no_error(
stockplotr::plot_spawn_recruitment(
stockplotr::plot_stock_recruitment(
out_new,
spawning_biomass_label = "mt",
recruitment_label = "mt",
Expand All @@ -26,7 +26,7 @@ test_that("plot_spawn_recruitment generates plots without errors", {

# expect ggplot object is returned
expect_s3_class(
stockplotr::plot_spawn_recruitment(
stockplotr::plot_stock_recruitment(
out_new,
spawning_biomass_label = "mt",
recruitment_label = "mt",
Expand All @@ -39,7 +39,7 @@ test_that("plot_spawn_recruitment generates plots without errors", {

test_that("rda file made when indicated", {
# export rda
plot_spawn_recruitment(
plot_stock_recruitment(
out_new,
spawning_biomass_label = "mt",
recruitment_label = "mt",
Expand Down
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