R/generate-length-to-age.R

In DanOvando/spasm: SPatial Age Structured Model (SPASM)

#' generate_length_to_age_key
#'
#' produces an age by length bins matrix with probability of being in length bin at age
#'
#' @param cv
#' @param k
#' @param linf
#' @param t0
#' @param time_step
#' @param linf_buffer
#' @param min_age
#' @param max_age
#'
#' @return a length-at-age key
#' @export
#'
generate_length_at_age_key <- function(min_age,
                                       max_age,
           cv,
           k,
           linf,
           t0,
           time_step = 1,
           linf_buffer = 10) {



    mean_length_at_age <-
      linf * (1 - exp(-k * (seq(
        min_age, max_age, by = time_step
      ) - t0)))

    length_at_age_vars <- data_frame(
      age = seq(min_age, max_age, by = time_step),
      mean_length_at_age = mean_length_at_age,
      sigma_at_age = cv * mean_length_at_age
    ) #calculate standard deviation of length at age for each age bin

    # now calculate the probability of being in each length bin at each age
    p_length_at_age <-
      expand.grid(
        age = seq(min_age, max_age, by = time_step),
        length_bin = 0:(linf_buffer * linf)
      ) %>%
      as_data_frame() %>%
      left_join(length_at_age_vars, by = 'age') %>%
      arrange(age, length_bin)

    p_length_at_age <- p_length_at_age %>%
      group_by(age) %>%
      mutate(next_length_bin = lead(length_bin, 1)) %>%
      mutate(p_bin = ifelse(
        is.na(next_length_bin) == F,
        pnorm(next_length_bin, mean_length_at_age, sigma_at_age),
        1
      ) -
        pnorm(length_bin, mean_length_at_age, sigma_at_age))

}