R/fish_size_comp.R

In BenWilliams-NOAA/rockfishr:

#' Fishery size composition data
#'
#' @param year assessment year
#' @param lenbins lenbin file if left NULL it looks for here::here(year, "data", "user_input", "len_bin_labels.csv")
#' @param rec_age recruitment age
#'
#' @return
#' @export fish_size_comp
#'
#' @examples
fish_size_comp <- function(YEAR, rec_age, lenbins = NULL){

    if(is.null(lenbins)){
      lenbins = read.csv(here::here(YEAR, "data", "user_input", "len_bin_labels.csv"))$len_bins
    } else {
      lenbins = read.csv(here::here(year, "data", "user_input", lenbins))$len_bins
    }

  read.csv(here::here(year, "data", "raw", "fishery_age_comp_data.csv")) %>%
    dplyr::rename_all(tolower) %>%
    dplyr::filter(!is.na(age), age>=rec_age, year>1990 & year<YEAR) %>%
    dplyr::group_by(year) %>%
    dplyr::tally(name = "age")%>%
    dplyr::filter(age>49) %>%
    dplyr::ungroup() -> ages

read.csv(here::here(year, "data", "raw", "fishery_size_comp_freq.csv"),
         colClasses = c(HAUL_JOIN = "character",
                        PORT_JOIN = "character")) %>%
    dplyr::rename_all(tolower) %>%
    dplyr::filter(!(year %in% unique(ages$year)), year>1990 & year<YEAR) %>%
    dplyr::group_by(year) %>%
    dplyr::mutate(tot = sum(frequency),
                  length = ifelse(length >= max(lenbins), max(lenbins), length),
                  n_h = length(unique(na.omit(haul_join))) + length(unique(na.omit(port_join)))) %>%
    dplyr::group_by(year, length) %>%
    dplyr::summarise(n_s = mean(tot),
              n_h = mean(n_h),
              length_tot = sum(frequency)) %>%
    dplyr::mutate(prop = length_tot / n_s) %>%
    dplyr::left_join(expand.grid(year = unique(.$year), length = lenbins), .) %>%
    tidyr::replace_na(list(prop = 0)) %>%
    dplyr::group_by(year) %>%
    dplyr::mutate(SA_Index = 1,
           n_s = mean(n_s, na.rm = T),
           n_h = mean(n_h, na.rm = T)) %>%
    dplyr::select(-length_tot) %>%
    tidyr::pivot_wider(names_from = length, values_from = prop) -> fish_size_comp

  readr::write_csv(fish_size_comp, here::here(year, "data", "output", "fish_size_comp.csv"))

  fish_size_comp

}