create initial versions of composition plots

NAMESPACE

@@ -13,6 +13,15 @@ export(plot_abundance_at_age)
 export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
+export(plot_composition_andre)
+export(plot_composition_bubble)
+export(plot_composition_distribution)
+export(plot_composition_francis)
+export(plot_composition_residual_distribution)
+export(plot_composition_residual_pattern)
+export(plot_composition_residuals)
+export(plot_composition_samples)
+export(plot_composition_sexratio)
 export(plot_discard)
 export(plot_fishing_mortality)
 export(plot_index)
@@ -23,8 +32,10 @@ export(plot_recruitment)
 export(plot_recruitment_deviations)
 export(plot_selectivity)
 export(plot_spawning_biomass)
+export(plot_spawning_potential_ratio)
 export(plot_stock_recruitment)
 export(plot_timeseries)
+export(prepare_composition_data)
 export(process_data)
 export(process_table)
 export(reference_line)

R/convert_output.R

@@ -1442,6 +1442,20 @@ convert_output <- function(
           TRUE ~ NA_character_
         )
       )
+    # Composition data by bin from r4ss (lendbase, agedbase, condbase)
+    if (!is.character(file)) {
+      comp_rows <- ss3_composition_rows(
+        dat,
+        fleet_names = fleet_names,
+        start_year = start_year,
+        end_year = end_year,
+        columns = names(out_new)
+      )
+      if (!is.null(comp_rows)) {
+        cli::cli_alert("Processing composition data (lendbase, agedbase, condbase)")
+        out_new <- rbind(out_new, comp_rows)
+      }
+    }
   } else if (model %in% c("bam", "BAM")) {
     #### BAM ####
     # Extract values from BAM output - model file after following ADMB2R

R/data.R

@@ -41,3 +41,67 @@
 #' }
 #'
 "example_data"
+
+#' Big Skate length composition data
+#'
+#' Length compositions and fits from the 2019 Big Skate stock assessment for
+#' the U.S. West Coast (`BigSkate_2019` in the Stock Synthesis test models),
+#' the model used for the r4ss example plots at
+#' \url{https://r4ss.github.io/r4ss/BigSkate/}. The data are the `lendbase`
+#' rows of [convert_output()] applied to the output of `r4ss::SS_output()`.
+#' See `data-raw/bigskate_comps.R`.
+#'
+#' Compositions are sex-specific, with female and male proportions summing to
+#' one within each year, fleet, and partition. `Fishery_current` has separate
+#' retained and discarded compositions.
+#'
+#' @format A tibble in the standard [convert_output()] format with 14504 rows
+#' and 35 columns. The columns used for compositions are:
+#' \describe{
+#'   \item{label}{"length_composition_observed", "length_composition_predicted",
+#'   "length_composition_pearson_residual" (as reported by Stock Synthesis),
+#'   or "length_composition_sample_size" (adjusted input sample size,
+#'   `Nsamp_adj` in r4ss)}
+#'   \item{estimate}{Value of the label}
+#'   \item{module_name}{`"lendbase"`}
+#'   \item{year}{Year of the observation}
+#'   \item{fleet}{Fleet name: "Fishery_current", "WCGBTS", or "Triennial"}
+#'   \item{sex}{"female" or "male"}
+#'   \item{part}{Partition: 0 = whole catch, 1 = discard, 2 = retained}
+#'   \item{length_bins}{Lower edge of the length bin (cm)}
+#' }
+#' @source Taylor, I.G., Gertseva, V., Stephens, A., and Bizzarro, J. (2019). Status of
+#' Big Skate (Beringraja binoculata) off the U.S. Pacific Coast in 2019.
+#' Pacific Fishery Management Council, Portland, OR.
+#' @seealso [bigskate_caal], [prepare_composition_data()], [plot_composition_distribution()]
+"bigskate_lencomp"
+
+#' Big Skate conditional age-at-length data
+#'
+#' Conditional age-at-length data and fits from the 2019 Big Skate stock
+#' assessment (see [bigskate_lencomp]). The data are the `condbase` rows of
+#' [convert_output()] applied to the output of `r4ss::SS_output()`. Each age
+#' composition is for one sex and one length bin, and sums to one. See
+#' `data-raw/bigskate_comps.R`.
+#'
+#' @format A tibble in the standard [convert_output()] format with 26240 rows
+#' and 35 columns. The columns used for compositions are:
+#' \describe{
+#'   \item{label}{"conditional_age_composition_observed",
+#'   "conditional_age_composition_predicted",
+#'   "conditional_age_composition_pearson_residual", or
+#'   "conditional_age_composition_sample_size"}
+#'   \item{estimate}{Value of the label}
+#'   \item{module_name}{`"condbase"`}
+#'   \item{year}{Year of the observation}
+#'   \item{fleet}{Fleet name: "Fishery_current" or "WCGBTS"}
+#'   \item{sex}{"female" or "male"}
+#'   \item{part}{Partition: 0 = whole catch, 1 = discard, 2 = retained}
+#'   \item{length_bins}{Length bin the ages are conditioned on (`Lbin_lo` in r4ss)}
+#'   \item{age}{Age}
+#' }
+#' @source Taylor, I.G., Gertseva, V., Stephens, A., and Bizzarro, J. (2019). Status of
+#' Big Skate (Beringraja binoculata) off the U.S. Pacific Coast in 2019.
+#' Pacific Fishery Management Council, Portland, OR.
+#' @seealso [bigskate_lencomp], [prepare_composition_data()], [plot_composition_andre()]
+"bigskate_caal"