R/SSplotSummaryF.R

In r4ss/r4ss: R Code for Stock Synthesis

#' Plot the summary F (or harvest rate).
#'
#' Plots the summary F (or harvest rate) as set up in the starter file Needs a
#' lot of work to be generalized
#'
#' @template replist
#' @param yrs Which years to include.
#' @param Ftgt Target F where horizontal line is shown.
#' @param ylab Y-axis label.
#' @template plot
#' @template print
#' @template plotdir
#' @template verbose
#' @param uncertainty Show 95% uncertainty intervals around point estimates?
#' @param add add to existing plot
#' @template pwidth
#' @template pheight
#' @template punits
#' @template res
#' @template ptsize
#' @template mar
#' @author Allan Hicks
#' @export
#' @seealso [SSplotTimeseries()]
SSplotSummaryF <- function(
  replist,
  yrs = "all",
  Ftgt = NA,
  ylab = "Summary Fishing Mortality",
  plot = TRUE,
  print = FALSE,
  plotdir = "default",
  verbose = TRUE,
  uncertainty = TRUE,
  add = FALSE,
  pwidth = 6.5,
  pheight = 5.0,
  punits = "in",
  res = 300,
  ptsize = 10,
  mar = NULL
) {
  # plots the summary F (or harvest rate) as set up in the starter file
  # needs a lot of work to be generalized

  # table to store information on each plot
  plotinfo <- NULL

  # set default plot margins (repeated from SSplotTimeseries()
  if (is.null(mar)) {
    mar <- c(5, 4, 2, 2) + 0.1
  }

  if (plotdir == "default") {
    plotdir <- replist[["inputs"]][["dir"]]
  }

  if (yrs[1] == "all") {
    yrs <- replist[["startyr"]]:replist[["endyr"]]
  }
  Ftot <- replist[["derived_quants"]][
    match(
      paste("F_", yrs, sep = ""),
      replist[["derived_quants"]][["Label"]]
    ),
  ]
  if (all(is.na(Ftot[["Value"]]))) {
    warning(
      "Skipping SSplotSummaryF because no real values found in DERIVED_QUANTITIES\n",
      "    Values with labels like F_2012 may not be real.\n"
    )
    return()
  }
  Fmax <- max(c(Ftot[["Value"]], Ftgt + 0.01), na.rm = TRUE)
  if (uncertainty) {
    uppFtot <- Ftot[["Value"]] + 1.96 * Ftot[["StdDev"]]
    lowFtot <- Ftot[["Value"]] - 1.96 * Ftot[["StdDev"]]
    Fmax <- max(c(uppFtot, Ftgt + 0.01), na.rm = TRUE)
  }
  plotfun <- function() {
    if (!add) {
      plot(
        0,
        type = "n",
        ,
        xlab = "Year",
        ylab = ylab,
        xlim = range(yrs),
        ylim = c(0, Fmax),
        cex.lab = 1.0,
        cex.axis = 1.0,
        cex = 0.7,
        mar = mar
      )
      abline(h = 0, col = "grey")
    }
    if (uncertainty) {
      segments(
        x0 = as.numeric(substring(Ftot[["Label"]], 3, 6)),
        y0 = uppFtot,
        x1 = as.numeric(substring(Ftot[["Label"]], 3, 6)),
        y1 = lowFtot,
        col = gray(0.5)
      )
    }
    points(
      as.numeric(substring(Ftot[["Label"]], 3, 6)),
      Ftot[["Value"]],
      pch = 16,
      type = "p"
    )
    abline(h = Ftgt, col = "red")
  }
  if (plot) {
    plotfun()
  }
  if (print) {
    caption <- "Summary F (definition of F depends on setting in starter.ss)"
    file <- "ts_summaryF.png"
    plotinfo <- save_png(
      plotinfo = plotinfo,
      file = file,
      plotdir = plotdir,
      pwidth = pwidth,
      pheight = pheight,
      punits = punits,
      res = res,
      ptsize = ptsize,
      caption = caption
    )
    plotfun()
    dev.off()
    if (!is.null(plotinfo)) {
      plotinfo[["category"]] <- "Timeseries"
    }
  }
  return(invisible(plotinfo))
}