R/15-01-01-createPUMatrix.R

In danStich/shadia: American shad dam passage performance standard model for R

#' @title Create production unit matrix
#'
#' @description Internal function to generalize creation of
#' the PU_n data structure for different PUs and fish sexes.
#' Not intended to be called directly, but visible
#' for model transparency.
#'
#' @return Matrix of fish numbers by ages in each PU following
#' execution of the upstream migration model in source code.
#'
#' @export
#'
# JMS Dec 2017
createPUMatrix <- function(isFemale, pu, isEgg = FALSE) {

  # dynamically identify the x_n dataframe, for PU n
  fishCount <- get(paste0("x_", pu), envir = .shadia)

  # dynamically identify the sp_n dataframe, for PU n
  spawnProb <- get(paste0("sp_", pu), envir = .shadia)

  if (!isEgg) {
    # for males and females
    d_pu <- spawnProb %>%
      filter(female == isFemale) %>%
      group_by(fishAges, pus) %>%
      summarize(gender = sum(surv), .groups = "keep")
  } else {
    # for eggs
    d_pu <- spawnProb %>%
      group_by(fishAges, pus) %>%
      summarize(gender = sum(fecundity * surv), .groups = "keep")
  }

  if (nrow(d_pu) == 0) {
    d_pu <- matrix(NA, 1, 3,
      dimnames = list(
        c(NULL),
        c("fishAges", "pus", "gender")
      )
    )
  }

  PUS <- merge(fishCount,
    d_pu,
    by = c("fishAges", "pus"),
    all.x = T
  )
  PUS$pus <- as.character(PUS$pus)

  return(PUS)
}