In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

this_spp <- "walleye pollock"
# this_spp <- "pacific hake"

title: `r paste0("4B data availability for ", this_spp)`

data_cache <- here::here("report", "data-cache-april-2022")
survey_cols <- c(
  RColorBrewer::brewer.pal(5L, "Set1"),
  RColorBrewer::brewer.pal(8L, "Set1")[7:8],
  "#303030", "#a8a8a8", "#a8a8a8", "#a8a8a8"
)
this_spp_hyphens <- gsub(" ", "-", this_spp)
dat <- readRDS(paste0(file.path(data_cache, this_spp_hyphens), ".rds"))
library(dplyr)
library(ggplot2)
theme_set(gfplot::theme_pbs())

dat$catch |>
  filter(grepl("4B", major_stat_area_name)) |>
  gfplot::tidy_catch() |>
  gfplot::plot_catch()

Commercial

dat$commercial_samples |>
  filter(grepl("4B", major_stat_area_name)) |>
  gfplot::tidy_sample_avail() |>
  gfplot::plot_sample_avail() +
  scale_fill_viridis_c(option = "D", end = 0.82, na.value = "transparent") +
  ggtitle("Commercial")

Survey

dat$survey_samples |>
  filter(grepl("4B", major_stat_area_name)) |>
  gfplot::tidy_sample_avail() |>
  gfplot::plot_sample_avail() +
  scale_fill_viridis_c(option = "C", end = 0.82, na.value = "transparent") +
  ggtitle("Survey")

Commercial

dat$commercial_samples |>
  filter(grepl("4B", major_stat_area_name)) |>
  group_by(year, gear_desc) |>
  summarize(
    n_length = sum(!is.na(length)),
    n_age = sum(!is.na(age)),
    n_weight = sum(!is.na(weight)),
    n_structure = sum(age_specimen_collected == 1)
  ) |> 
  mutate(gear_desc = stringr::str_to_title(gear_desc)) |> 
  knitr::kable(format = "pandoc")

Survey

dat$survey_samples |>
  filter(grepl("4B", major_stat_area_name)) |>
  group_by(year, survey_series_desc) |>
  summarize(
    n_length = sum(!is.na(length)),
    n_age = sum(!is.na(age)),
    n_weight = sum(!is.na(weight)),
    n_structure = sum(age_specimen_collected == 1)
  ) |> 
  knitr::kable(format = "pandoc")

Commercial lengths

dat$commercial_samples |>
  filter(grepl("4B", major_stat_area_name)) |> 
  ggplot(aes(x = length, fill = gear_desc)) +
  geom_histogram(alpha = 0.65, position = "identity", colour = "grey70") +
  facet_wrap(~year, ncol = 3, dir="v", scales = "free_y") +
  scale_fill_brewer(palette = "Set2")

Survey lengths

dat$survey_samples |>
  filter(grepl("4B", major_stat_area_name)) |> 
  ggplot(aes(x = length, fill = survey_series_desc)) +
  geom_histogram(alpha = 0.65, position = "identity", colour = "grey70") +
  facet_wrap(~year, ncol = 3, dir="v", scales = "free_y") +
  scale_fill_brewer(palette = "Set2")

Commercial ages

dat$commercial_samples |>
  filter(grepl("4B", major_stat_area_name)) |> 
  ggplot(aes(x = age, fill = gear_desc)) +
  geom_histogram(alpha = 0.65, position = "identity", colour = "grey70") +
  facet_wrap(~year, ncol = 3, dir="v", scales = "free_y") +
  scale_fill_brewer(palette = "Set2")

Survey ages

dat$survey_samples |>
  filter(grepl("4B", major_stat_area_name)) |> 
  ggplot(aes(x = age, fill = survey_series_desc)) +
  geom_histogram(alpha = 0.65, position = "identity", colour = "grey70") +
  facet_wrap(~year, ncol = 3, dir="v", scales = "free_y") +
  scale_fill_brewer(palette = "Set2")