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[feat] Update biomass/abundance/catch table #373

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[feat] Update biomass/abundance/catch table #373

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36a9a22
Add key quantities to bnc caption; remove unnecessary 'year' arg from…
sbreitbart-NOAA May 26, 2026
920f66a
Continue "revamping" bnc table to match structure and formatting of l…
sbreitbart-NOAA May 27, 2026
fb42918
Add bnc table to save_all_plots() and its test; update bnc tests
sbreitbart-NOAA Jun 11, 2026
07abe98
Troubleshoot failing bnc table pipeline
sbreitbart-NOAA Sep 11, 2026
59e5281
Update function as per coworking; change name from bnc to spelled-out…
sbreitbart-NOAA Sep 23, 2026
46152cd
Update rda-exporting portion of bnc table function
sbreitbart-NOAA Sep 24, 2026
d77a8cc
Update alt text/captions/kqs templates with bnc table values
sbreitbart-NOAA Sep 24, 2026
d2acc8c
Remove unused unit_label as arg from create_rda(); update documentation
sbreitbart-NOAA Sep 24, 2026
11c78e3
Streamline bac table's unit label arguments
sbreitbart-NOAA Sep 24, 2026
4f79947
Update tests and documentation
sbreitbart-NOAA Sep 24, 2026
1bfca09
Remove warning from test
sbreitbart-NOAA Sep 24, 2026
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ export(process_data)
export(process_table)
export(reference_line)
export(save_all_plots)
export(table_biomass_abundance_catch)
export(table_index)
export(table_landings)
export(table_projections)
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3 changes: 1 addition & 2 deletions R/plot_abundance_at_age.R
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Expand Up @@ -182,8 +182,7 @@ plot_abundance_at_age <- function(
# get name of function and remove "plot_" from it
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat,
unit_label = "mt"
dat
)
}
plot
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3 changes: 1 addition & 2 deletions R/plot_biomass.R
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Original file line number Diff line number Diff line change
Expand Up @@ -322,8 +322,7 @@ plot_biomass <- function(
dat = rp_dat,
dir = figures_dir,
ref_line = ifelse(!is.null(names(ref_line)), names(ref_line), ref_line),
scale_amount = scale_amount,
unit_label = unit_label
scale_amount = scale_amount
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_biomass_at_age.R
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Original file line number Diff line number Diff line change
Expand Up @@ -146,8 +146,7 @@ plot_biomass_at_age <- function(
# get name of function and remove "plot_" from it
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat,
unit_label = "mt"
dat
)
}
plot
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3 changes: 1 addition & 2 deletions R/plot_catch_comp.R
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Original file line number Diff line number Diff line change
Expand Up @@ -170,8 +170,7 @@ plot_catch_comp <- function(
# get name of function and remove "plot_" from it
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat,
unit_label = "mt"
dat
)
}
plot
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3 changes: 1 addition & 2 deletions R/plot_discard.R
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Original file line number Diff line number Diff line change
Expand Up @@ -147,8 +147,7 @@ plot_discard <- function(
fig_or_table = "figure",
dat = discards,
dir = figures_dir,
scale_amount = scale_amount,
unit_label = unit_label
scale_amount = scale_amount
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_fishing_mortality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -195,8 +195,7 @@ plot_fishing_mortality <- function(
dat = dat,
dir = figures_dir,
ref_line = ifelse(!is.null(names(ref_line)), names(ref_line), ref_line),
scale_amount = 1,
unit_label = "" # no unit for F
scale_amount = 1
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_index.R
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Original file line number Diff line number Diff line change
Expand Up @@ -162,8 +162,7 @@ plot_index <- function(
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat = dat,
dir = figures_dir,
unit_label = unit_label
dir = figures_dir
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_landings.R
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Original file line number Diff line number Diff line change
Expand Up @@ -143,8 +143,7 @@ plot_landings <- function(
fig_or_table = "figure",
dat = dat,
dir = figures_dir,
scale_amount = scale_amount,
unit_label = unit_label
scale_amount = scale_amount
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_recruitment.R
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Original file line number Diff line number Diff line change
Expand Up @@ -182,8 +182,7 @@ plot_recruitment <- function(
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat = dat,
dir = figures_dir # ,
# unit_label = unit_label
dir = figures_dir
)
}
final
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3 changes: 1 addition & 2 deletions R/plot_recruitment_deviations.R
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Expand Up @@ -112,8 +112,7 @@ plot_recruitment_deviations <- function(
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat = selected_dat,
dir = figures_dir,
unit_label = ""
dir = figures_dir
)
}
final
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3 changes: 1 addition & 2 deletions R/plot_selectivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -179,8 +179,7 @@ plot_selectivity <- function(
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat = dat,
dir = figures_dir # ,
# unit_label = unit_label
dir = figures_dir
)
}
final
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3 changes: 1 addition & 2 deletions R/plot_spawning_biomass.R
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Original file line number Diff line number Diff line change
Expand Up @@ -296,8 +296,7 @@ plot_spawning_biomass <- function(
dat = rp_dat,
dir = figures_dir,
ref_line = ifelse(!is.null(names(ref_line)), names(ref_line), ref_line),
scale_amount = scale_amount,
unit_label = unit_label
scale_amount = scale_amount
)
}
# Output final plot
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3 changes: 1 addition & 2 deletions R/plot_stock_recruitment.R
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Original file line number Diff line number Diff line change
Expand Up @@ -217,8 +217,7 @@ plot_stock_recruitment <- function(
topic_label = gsub("plot_", "", utils::tail(as.character(sys.call()[[1]]), n = 1)),
fig_or_table = "figure",
dat = dat,
dir = figures_dir # ,
# unit_label = unit_label
dir = figures_dir
)
}
final +
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4 changes: 4 additions & 0 deletions R/process_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,9 @@ process_table <- function(
id_group <- group
} else {
id_group <- index_variables[-grep("year|age|length_bin", index_variables)]
if (length(id_group) == 0) {
id_group <- NULL
}
}
cols <- index_variables[grep("year|age|length_bin", index_variables)]

Expand All @@ -397,6 +400,7 @@ process_table <- function(
} else if (!is.null(id_group)) {
if (length(id_group) > 1) {
cli::cli_alert_warning("Data contains >1 indexing variable. Selecting {id_group[1]}.")
id_group <- id_group[1]
}
if (length(id_group) > 0 && any(is.na(dat[[id_group]]))) {
dat <- dat |>
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55 changes: 24 additions & 31 deletions R/save_all_plots.R
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@Schiano-NOAA Schiano-NOAA Sep 25, 2026

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I feel like there has to be an automated way to update this function whenever we add a new figure_* or table_*

Original file line number Diff line number Diff line change
Expand Up @@ -84,10 +84,6 @@
#'
#' Default: ""
#'
#' @param biomass_unit_label String. Abbreviated biomass units
#'
#' Default: "mt"
#'
#' @param catch_unit_label String. Abbreviated catch units
#'
#' Default: "mt"
Expand Down Expand Up @@ -146,6 +142,7 @@ save_all_plots <- function(
figures_tables_dir = getwd(),
# imported from plot_biomass
ref_line = "msy",
biomass_unit_label = "mt",
biomass_scale_amount = 1,
# imported from plot_landings
landings_unit_label = "mt",
Expand All @@ -163,12 +160,11 @@ save_all_plots <- function(
biomass_at_age_unit_label = "mt",
# imported from plot_index
index_unit_label = "",
# imported from table_afsc_tier- add potential unique arguments after dev
# imported from table_bnc
biomass_unit_label = "mt",
# imported from table_biomass_abundance_catch
bac_unit_label = c("biomass" = "mt", "abundance" = "fish", "catch" = "mt"),

@Schiano-NOAA Schiano-NOAA Sep 25, 2026

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I don't think this argument is in the roxygen documentation. Could you also change it to bnc?

# imported from plot_catch_comp
catch_unit_label = "mt",
catch_scale_amount = 1,
# imported from table_harvest_projection- add potential unique arguments after dev
# imported from table_index- zero unique arguments
# imported from table_landings- zero unique arguments
# imported from table_projections
Expand Down Expand Up @@ -469,29 +465,26 @@ save_all_plots <- function(
)

# tables
# tryCatch(
# {
# cli::cli_h2("table_bnc")
# table_bnc(
# dat,
# biomass_unit_label,
# catch_unit_label,
# spawning_biomass_label,
# make_rda = TRUE,
# tables_dir = figures_tables_dir
# ) # |>
# # suppressWarnings() |>
# # invisible()
# },
# error = function(e) {
# cli::cli_alert_danger("table_bnc failed to run.")
# cli::cli_alert("Tip: check that your arguments are correct.")
# cli::cli_li("biomass_unit_label = {biomass_unit_label}")
# cli::cli_li("catch_unit_label = {catch_unit_label}")
# cli::cli_li("spawning_biomass_label = {spawning_biomass_label}")
# print(e)
# }
# )
tryCatch(
{
cli::cli_h2("table_biomass_abundance_catch")
table_biomass_abundance_catch(
dat,
unit_label = bac_unit_label,
interactive = interactive,
make_rda = TRUE,
tables_dir = figures_tables_dir
) # |>
# suppressWarnings() |>
# invisible()
},
error = function(e) {
cli::cli_alert_danger("table_biomass_abundance_catch failed to run.")
cli::cli_alert("Tip: check that your arguments are correct.")
cli::cli_li("unit_label = {bac_unit_label}")
print(e)
}
)

tryCatch(
{
Expand Down
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