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Redesign key quantity extraction/insertion pipeline #205

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c907fa3
Create first draft of key quantities template csv; start drafting pip…
sbreitbart-NOAA Mar 5, 2026
97965cb
Finished draft of key quantities pipeline for landings plot
sbreitbart-NOAA Mar 12, 2026
f749fce
Reorder KQs in plot_landings() by logical grouping; update plot_recru…
sbreitbart-NOAA Mar 17, 2026
7359734
update plot_fishing_mortality() to work with new KQ extraction/insert…
sbreitbart-NOAA Mar 17, 2026
5f2412b
update plot_stock_recruitment() to work with new KQ extraction/insert…
sbreitbart-NOAA Mar 17, 2026
a231fbe
update plot_abundance_at_age() to work with new KQ extraction/inserti…
sbreitbart-NOAA Mar 18, 2026
2a828cc
update plot_biomass_at_age() to work with new KQ extraction/insertion…
sbreitbart-NOAA Mar 18, 2026
03bf02b
update plot_indices() to work with new KQ extraction/insertion design
sbreitbart-NOAA Mar 18, 2026
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1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ Imports:
naniar,
prodlim,
quarto,
rlang,
scales,
stats,
stringr,
Expand Down
27 changes: 26 additions & 1 deletion R/plot_abundance_at_age.R
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ plot_abundance_at_age <- function(
) {
# Create label for abundance units in legend
abundance_label <- label_magnitude(
label = "Abudance",
label = "Abundance",
unit_label = unit_label,
scale_amount = scale_amount
)
Expand Down Expand Up @@ -111,6 +111,31 @@ plot_abundance_at_age <- function(
)
# export figure to rda if argument = T
if (make_rda == TRUE) {

# Obtain relevant key quantities for captions/alt text
pop.naa.start.year <- min(data$year)
pop.naa.end.year <- max(data$year)
pop.naa.age.min <- min(data$age)
pop.naa.age.max <- max(data$age)
pop.naa.fish.min <- min(data$estimate)
pop.naa.fish.max <- max(data$estimate)

# calculate & export key quantities
export_kqs(pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max)

# Add key quantities to captions/alt text
insert_kqs(pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max)

create_rda(
object = plot,
# get name of function and remove "plot_" from it
Expand Down
25 changes: 25 additions & 0 deletions R/plot_biomass_at_age.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,31 @@ plot_biomass_at_age <- function(
)
# export figure to rda if argument = T
if (make_rda == TRUE) {

# Obtain relevant key quantities for captions/alt text
pop.baa.start.year <- min(data$year)
pop.baa.end.year <- max(data$year)
pop.baa.age.min <- min(data$age)
pop.baa.age.max <- max(data$age)
pop.baa.fish.min <- min(data$estimate)
pop.baa.fish.max <- max(data$estimate)

# calculate & export key quantities
export_kqs(pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max)

# Add key quantities to captions/alt text
insert_kqs(pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max)

create_rda(
object = plot,
# get name of function and remove "plot_" from it
Expand Down
22 changes: 22 additions & 0 deletions R/plot_fishing_mortality.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,28 @@ plot_fishing_mortality <- function(

### Make RDA ----
if (make_rda) {

# Obtain relevant key quantities for captions/alt text
F.ref.pt <- as.character(ref_line)
F.start.year <- min(prepared_data$year)
F.end.year <- max(prepared_data$year)
F.min <- min(prepared_data$estimate)
F.max <- max(prepared_data$estimate)

# calculate & export key quantities
export_kqs(F.ref.pt,
F.start.year,
F.end.year,
F.min,
F.max)

# Add key quantities to captions/alt text
insert_kqs(F.ref.pt,
F.start.year,
F.end.year,
F.min,
F.max)

create_rda(
object = final,
topic_label = ifelse(relative, "relative_fishing_mortality", "fishing_mortality"),
Expand Down
26 changes: 25 additions & 1 deletion R/plot_indices.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ plot_indices <- function(
module = NULL,
focus = NULL,
make_rda = FALSE,
figures_dir = NULL,
figures_dir = getwd(),
...
) {
# Set cpue unit label for plot
Expand Down Expand Up @@ -114,6 +114,30 @@ plot_indices <- function(

### Make RDA ----
if (make_rda) {

# Obtain relevant key quantities for captions/alt text
cpue.start.year <- min(prepared_data$year)
cpue.end.year <- max(prepared_data$year)
cpue.min <- min(prepared_data$estimate)
cpue.max <- max(prepared_data$estimate)
cpue.units <- ifelse(unit_label == "",
"an estimated index ratio", # default if empty
unit_label)

# calculate & export key quantities
export_kqs(cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units)

# Add key quantities to captions/alt text
insert_kqs(cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units)

create_rda(
object = plt,
# get name of function and remove "plot_" from it
Expand Down
22 changes: 22 additions & 0 deletions R/plot_landings.R
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,28 @@ plot_landings <- function(

### Make RDA ----
if (make_rda) {

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@Schiano-NOAA Schiano-NOAA Mar 16, 2026

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Is this chunk going to be unique to all plots? Like we won't be able to generalize this and make it more concise?

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@Schiano-NOAA Schiano-NOAA Mar 16, 2026

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Line 102-108

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@sbreitbart-NOAA sbreitbart-NOAA Mar 16, 2026

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Lines 102-108 are where key quantities are calculated for this plot (and I'd expect this is where each plot/table's KQs will be calculated too). The next couple of functions are where the generalization happens: in the exporting of the KQs into a csv, and the insertion of the KQs into the alt text/captions csv.

# Obtain relevant key quantities for captions/alt text
landings.start.year <- min(prepared_data$year)
landings.end.year <- max(prepared_data$year)
landings.min <- min(prepared_data$estimate)
landings.max <- max(prepared_data$estimate)
landings.units <- unit_label

# calculate & export key quantities
export_kqs(landings.start.year,
landings.end.year,
landings.min,
landings.max,
landings.units)

# Add key quantities to captions/alt text
insert_kqs(landings.start.year,
landings.end.year,
landings.min,
landings.max,
landings.units)

create_rda(
object = plt,
# get name of function and remove "plot_" from it
Expand Down
19 changes: 19 additions & 0 deletions R/plot_recruitment_deviations.R
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Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,25 @@ plot_recruitment_deviations <- function(
} else {
selected_dat <- dat
}

# Obtain relevant key quantities for captions/alt text
recruit.dev.start.year <- min(filter_data$year)
recruit.dev.end.year <- max(filter_data$year)
recruit.dev.min <- min(filter_data$estimate)
recruit.dev.max <- max(filter_data$estimate)

# calculate & export key quantities
export_kqs(recruit.dev.start.year,
recruit.dev.end.year,
recruit.dev.min,
recruit.dev.max)

# Add key quantities to captions/alt text
insert_kqs(recruit.dev.start.year,
recruit.dev.end.year,
recruit.dev.min,
recruit.dev.max)

create_rda(
object = final,
# get name of function and remove "plot_" from it
Expand Down
32 changes: 32 additions & 0 deletions R/plot_stock_recruitment.R
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,38 @@ plot_stock_recruitment <- function(

# Make RDA
if (make_rda) {

# Obtain relevant key quantities for captions/alt text
sr.age.min <- dat |>
dplyr::filter(!is.na(year) & !is.na(age)) |>
dplyr::slice(which.min(age)) |>
dplyr::select(age) |>
as.numeric()
sr.ssb.units <- spawning_biomass_label
sr.ssb.min <- min(sr$spawning_biomass, na.rm = TRUE)
sr.ssb.max <- max(sr$spawning_biomass, na.rm = TRUE)
sr.min <- min(sr$predicted_recruitment, na.rm = TRUE)
sr.max <- max(sr$predicted_recruitment, na.rm = TRUE)
sr.units <- recruitment_label

# calculate & export key quantities
export_kqs(sr.age.min,
sr.ssb.units,
sr.ssb.min,
sr.ssb.max,
sr.min,
sr.max,
sr.units)

# Add key quantities to captions/alt text
insert_kqs(sr.age.min,
sr.ssb.units,
sr.ssb.min,
sr.ssb.max,
sr.min,
sr.max,
sr.units)

create_rda(
object = final,
# get name of function and remove "plot_" from it
Expand Down
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