In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)

base_model <- readRDS("/srv/hake/models/2025/02-version/01-base-models/01-base/01-base.rds")
end_yr <- 2025

devtools::load_all("~/github/pacific-hake/hake-assessment/")
source("~/github/pacific-hake/hake-assessment/beamer/jmc/presentation/table-cohorts-by-country.R")

# Get ratios of biomass
prop_biomass_df <- table_survey_by_country(survey_by_country_df, ret_df = T) |>
  select(year, canada.prop, us.prop) |>
  rename(Year = year) |>
  mutate(canada.prop = as.numeric(canada.prop)) |>
  mutate(us.prop = as.numeric(us.prop))

# Get biomass at age combined
biomass_at_age_df <- table_at_age(
  base_model,
  type = "baa",
  end_yr = end_yr,
  ret_df = TRUE) |>
  mutate(Year = as.numeric(Year))

j <- biomass_at_age_df |>
  right_join(prop_biomass_df, by = "Year")

can_baa <- j |>
  mutate(across(!Year & !canada.prop & !us.prop, ~{.x * canada.prop})) |>
  select(-canada.prop, -us.prop)

us_baa <- j |>
  mutate(across(!Year & !canada.prop & !us.prop, ~{.x * us.prop})) |>
  select(-canada.prop, -us.prop)

table_cohort_by_country(
  base_model,
  cohorts = c(1999, 2010, 2014, 2016, 2020, 2021),
  cohort_bold = TRUE,
  cohort_italics = TRUE,
  cohort_underline = TRUE,
  cohort_line_above = TRUE,
  cohort_line_below = FALSE,
  reverse_cohorts = TRUE,
  caption = paste0("Select values for Cohorts-at-age, for large cohorts. ",
                   "The biomass by country was calculated by taking the ",
                   "survey biomass proportions by country from Table 13 and the biomass-",
                   "at-age from Table 18 and multiplying. Blank values represent ",
                   "years for which there was no survey. Dashes are shown for age 0 and 1 values ",
                   "for Canada ans US biomasses because the survey biomass index ",
                   "representsa age 2+ only. ",
                   "The Canada and US biomasses, when added together equal the ",
                   "Start biomass. ",
                   "\\textbf{Note that a single proportion for each year is being ",
                   "used for all ages in the given year. A future improvement would ",
                   "be using survey biomass-at-age data to generate this table}"),
  font_size = 8,
  header_font_size = 9,
  longtable = TRUE,
  can_baa_df = can_baa,
  us_baa_df = us_baa)