Redesign key quantity extraction/insertion pipeline

CODE_OF_CONDUCT.md

@@ -47,7 +47,7 @@ Examples of representing our community include using an official e-mail address,
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement anonymously using this [form](https://forms.gle/MVNesUbP15bHei1J7).
 
-Reports will be reviewed by a member of the NOAA Fisheries Office of Science and Technology who is not participating in the `stockplotr` project [Patrick Lynch] but has the full support of `stockplotr` Community Leaders. All reports will be reviewed promptly and fairly.
+Reports will be reviewed by a member of the NOAA Fisheries Office of Science and Technology who is not participating in the {stockplotr} project [Patrick Lynch] but has the full support of {stockplotr} Community Leaders. All reports will be reviewed promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the reporter of any incident whenever possible; however, please note behaviors that meet the official criteria for harrassment must be reported by supervisors under NOAA policy.
 
@@ -103,4 +103,4 @@ Community Impact Guidelines were inspired by
 For answers to common questions about this code of conduct, see the FAQ at
 <https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
 
-[homepage]: https://www.contributor-covenant.org
+[homepage]: https://www.contributor-covenant.org

CONTRIBUTING.md

@@ -1,14 +1,14 @@
-# Contributing to `stockplotr`
+# Contributing to {stockplotr}
 
-Do you have an idea that would improve `stockplotr`? *Consider making a contribution!* We welcome ideas for improving not only our code, but also our documentation, tutorial, and any other material associated with `stockplotr`. Here are some options and tips for doing so.
+Do you have an idea that would improve {stockplotr}? *Consider making a contribution!* We welcome ideas for improving not only our code, but also our documentation, tutorial, and any other material associated with {stockplotr}. Here are some options and tips for doing so.
 
 Note: To make any contribution, you must agree to abide by the [Code of Conduct](https://github.com/nmfs-ost/stockplotr/blob/main/CODE_OF_CONDUCT.md).
 
 ## Contributing ideas: code, documentation, etc.
 
 ### Recommended workflow: fork & submit a pull request
 
-The most efficient way to contribute an idea is to fork `stockplotr`, make your suggested changes on a local branch, and then submit a pull request. This will allow the developers to easily evaluate your suggested changes. Please see the [GitHub Docs' "Contributing to a project" page](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project) for step-by-step guidance in using this workflow.
+The most efficient way to contribute an idea is to fork {stockplotr}, make your suggested changes on a local branch, and then submit a pull request. This will allow the developers to easily evaluate your suggested changes. Please see the [GitHub Docs' "Contributing to a project" page](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project) for step-by-step guidance in using this workflow.
 
 ### Recommended practices
 
@@ -26,4 +26,4 @@ If possible, please submit a reproducible example ([reprex](https://reprex.tidyv
 
 ## Contributing questions
 
-Have a question? Ask it in our [Discussions page](https://github.com/nmfs-ost/stockplotr/discussions). You can categorize it under General, Ideas, Q&A, and more.
+Have a question? Ask it in our [Discussions page](https://github.com/nmfs-ost/stockplotr/discussions). You can categorize it under General, Ideas, Q&A, and more.

DESCRIPTION

@@ -20,7 +20,7 @@ Description: Creates exploratory and finished tables and figures for stock
     interprets outputs of stock assessment models as well as allows the
     analyst to create report ready tables and figures, reducing the need
     to create their own and format then when adding into a report. This
-    package is intended to be used in conjuction with `asar`, a partially
+    package is intended to be used in conjuction with {asar}, a partially
     automated template for writing various stock assessment reports.
     Throughout development, we will be creating a set of standardized
     figures and tables for a stock assessment report, developing functions
@@ -48,6 +48,7 @@ Imports:
     naniar,
     prodlim,
     quarto,
+    rlang,
     scales,
     stats,
     stringr,

NAMESPACE

@@ -28,4 +28,3 @@ export(reference_line)
 export(save_all_plots)
 export(table_landings)
 export(theme_noaa)
-export(write_captions)

R/plot_abundance_at_age.R

@@ -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
   )
@@ -97,6 +97,9 @@ plot_abundance_at_age <- function(
       ggplot2::ggplot()
     )
   }
+
+  data <- data |>
+    dplyr::mutate(age = as.numeric(age))
 
   # Plot data
   plot <- plot_aa(
@@ -111,6 +114,31 @@ 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$estimate) |> round(digits = 3)
+    pop.naa.fish.max <- max(data$estimate) |> round(digits = 3)
+
+    # 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

R/plot_biomass.R

@@ -149,6 +149,47 @@ plot_biomass <- function(
 
   ### Make RDA ----
   if (make_rda) {
+
+    if (relative){
+      # pulling out the 2nd df in 'data' works for several datasets
+      rel.B.min <- ggplot2::ggplot_build(final)@data[[2]] |>
+        as.data.frame() |>
+        dplyr::pull(y) |>
+        min()
+      rel.B.max <- ggplot2::ggplot_build(final)@data[[2]] |>
+        as.data.frame() |>
+        dplyr::pull(y) |>
+        max()
+
+      # calculate & export key quantities
+      export_kqs(rel.B.min, rel.B.max)
+
+      # Add key quantities to captions/alt text
+      insert_kqs(rel.B.min, rel.B.max)
+
+    } else {
+      B.min <- min(prepared_data$estimate)
+      B.max <- max(prepared_data$estimate)
+
+      export_kqs(B.min, B.max)
+      insert_kqs(B.min, B.max)
+    }
+
+    B.ref.pt <- as.character(ref_line)
+    B.units <- as.character(unit_label)
+    B.start.year <- min(prepared_data$year) |> round(digits = 3)
+    B.end.year <- max(prepared_data$year) |> round(digits = 3)
+
+    export_kqs(B.ref.pt,
+               B.units,
+               B.start.year,
+               B.end.year)
+
+    insert_kqs(B.ref.pt,
+               B.units,
+               B.start.year,
+               B.end.year)
+
     create_rda(
       object = final,
       topic_label = ifelse(relative, "relative_biomass", "biomass"),

R/plot_biomass_at_age.R

@@ -82,6 +82,9 @@ plot_biomass_at_age <- function(
     )
   }
 
+  data <- data |>
+    dplyr::mutate(age = as.numeric(age))
+
   # Plot data
   plot <- plot_aa(
     dat = data,
@@ -95,6 +98,31 @@ 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$estimate) |> round(digits = 3)
+    pop.baa.fish.max <- max(data$estimate) |> round(digits = 3)
+
+    # 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

R/plot_catch_comp.R

@@ -100,6 +100,10 @@ plot_catch_comp <- function(
     group <- processed_data[[2]]
     facet <- processed_data[[3]]
   }
+
+  data <- data |>
+    dplyr::mutate(age = as.numeric(age))
+
   # Plot data
   plot <- plot_aa(
     dat = data,
@@ -111,6 +115,31 @@ plot_catch_comp <- function(
 
   # export figure to rda if argument = T
   if (make_rda == TRUE) {
+
+    # Obtain relevant key quantities for captions/alt text
+    caa.start.year <- min(data$year)
+    caa.end.year <- max(data$year)
+    caa.age.min <- min(data$age)
+    caa.age.max <- max(data$age)
+    tot.catch.min <- min(data$estimate) |> round(digits = 3)
+    tot.catch.max <- max(data$estimate) |> round(digits = 3)
+
+    # calculate & export key quantities
+    export_kqs(caa.start.year,
+               caa.end.year,
+               caa.age.min,
+               caa.age.max,
+               tot.catch.min,
+               tot.catch.max)
+
+    # Add key quantities to captions/alt text
+    insert_kqs(caa.start.year,
+               caa.end.year,
+               caa.age.min,
+               caa.age.max,
+               tot.catch.min,
+               tot.catch.max)
+
     create_rda(
       object = plot,
       # get name of function and remove "plot_" from it

R/plot_fishing_mortality.R

@@ -95,6 +95,47 @@ plot_fishing_mortality <- function(
 
   ### Make RDA ----
   if (make_rda) {
+
+    if (relative){
+    # Obtain relevant key quantities for captions/alt text
+      # pulling out the 2nd df in 'data' works for several datasets
+      rel.F.min <- ggplot2::ggplot_build(final)@data[[2]] |>
+        as.data.frame() |>
+        dplyr::pull(y) |>
+        min() |>
+        round(digits = 2)
+      rel.F.max <- ggplot2::ggplot_build(final)@data[[2]] |>
+        as.data.frame() |>
+        dplyr::pull(y) |>
+        max() |>
+        round(digits = 2)
+
+      # calculate & export key quantities
+      export_kqs(rel.F.min, rel.F.max)
+
+      # Add key quantities to captions/alt text
+      insert_kqs(rel.F.min, rel.F.max)
+
+    } else {
+      F.min <- min(prepared_data$estimate) |> round(digits = 3)
+      F.max <- max(prepared_data$estimate) |> round(digits = 3)
+
+      export_kqs(F.min, F.max)
+      insert_kqs(F.min, F.max)
+    }
+
+    F.ref.pt <- as.character(ref_line)
+    F.start.year <- min(prepared_data$year)
+    F.end.year <- max(prepared_data$year)
+
+    export_kqs(F.ref.pt,
+               F.start.year,
+               F.end.year)
+
+    insert_kqs(F.ref.pt,
+               F.start.year,
+               F.end.year)
+
     create_rda(
       object = final,
       topic_label = ifelse(relative, "relative_fishing_mortality", "fishing_mortality"),

R/plot_indices.R

@@ -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
@@ -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$estimate) |> round(digits = 3)
+    cpue.max <- max(prepared_data$estimate) |> round(digits = 3)
+    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

R/plot_landings.R

@@ -99,6 +99,28 @@ plot_landings <- function(
 
   ### Make RDA ----
   if (make_rda) {
+
+    # 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$estimate) |> round(digits = 3)
+    landings.max <- max(prepared_data$estimate) |> round(digits = 3)
+    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