create initial versions of composition plots

NAMESPACE

@@ -12,6 +12,15 @@ export(plot_abundance_at_age)
 export(plot_biomass)
 export(plot_biomass_at_age)
 export(plot_catch_comp)
+export(plot_comp)
+export(plot_comp_andre)
+export(plot_comp_bubble)
+export(plot_comp_francis)
+export(plot_comp_residual_dist)
+export(plot_comp_residual_pattern)
+export(plot_comp_residuals)
+export(plot_comp_sample_size)
+export(plot_comp_sex_ratio)
 export(plot_discard)
 export(plot_fishing_mortality)
 export(plot_index)
@@ -24,6 +33,7 @@ export(plot_selectivity)
 export(plot_spawning_biomass)
 export(plot_stock_recruitment)
 export(plot_timeseries)
+export(prepare_comp_data)
 export(process_data)
 export(process_table)
 export(reference_line)

R/data.R

@@ -41,3 +41,65 @@
 #' }
 #'
 "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`
+#' element of `r4ss::SS_output()` with columns renamed to follow
+#' stockplotr conventions. 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 with 3626 rows and 11 variables:
+#' \describe{
+#'   \item{comp_type}{Type of composition ("length")}
+#'   \item{fleet}{Fleet name: "Fishery_current", "WCGBTS", or "Triennial"}
+#'   \item{year}{Year of the observation (`Yr` in r4ss)}
+#'   \item{month}{Month of the observation}
+#'   \item{sex}{"female" or "male"}
+#'   \item{part}{Partition: 0 = whole catch, 1 = discard, 2 = retained}
+#'   \item{bin}{Lower edge of the length bin (cm)}
+#'   \item{observed}{Observed proportion (`Obs` in r4ss)}
+#'   \item{expected}{Expected proportion (`Exp` in r4ss)}
+#'   \item{pearson}{Pearson residual reported by Stock Synthesis}
+#'   \item{n}{Adjusted input sample size (`Nsamp_adj` in r4ss)}
+#' }
+#' @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_comp_data()], [plot_comp()]
+"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` element
+#' of `r4ss::SS_output()` with columns renamed to follow stockplotr conventions.
+#' Each age composition is for one sex and one length bin, and sums to one.
+#' See `data-raw/bigskate_comps.R`.
+#'
+#' @format A tibble with 6560 rows and 12 variables:
+#' \describe{
+#'   \item{comp_type}{Type of composition ("age")}
+#'   \item{fleet}{Fleet name: "Fishery_current" or "WCGBTS"}
+#'   \item{year}{Year of the observation (`Yr` in r4ss)}
+#'   \item{month}{Month of the observation}
+#'   \item{sex}{"female" or "male"}
+#'   \item{part}{Partition: 0 = whole catch, 1 = discard, 2 = retained}
+#'   \item{length_bin}{Length bin the ages are conditioned on (`Lbin_lo` in r4ss)}
+#'   \item{bin}{Age}
+#'   \item{observed}{Observed proportion at age within the length bin}
+#'   \item{expected}{Expected proportion at age within the length bin}
+#'   \item{pearson}{Pearson residual reported by Stock Synthesis}
+#'   \item{n}{Adjusted input sample size (`Nsamp_adj` in r4ss)}
+#' }
+#' @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_comp_data()], [plot_comp_andre()]
+"bigskate_caal"