Plot fishing mortality time series from an IAMSE MSE

`plotiamse.f()` produces time-series plots of fishing mortality for each harvest control rule (HCR) evaluated in an IAMSE management strategy evaluation. The function aggregates results across replicates and can display median trajectories, uncertainty envelopes, and optional smoothed trend lines.

Usage

plotiamse.f(
  dat,
  set,
  resMSE,
  trendline = TRUE,
  uncert = TRUE,
  med = TRUE,
  hcrs = NA,
  ylim = NULL,
  plot.legend = TRUE,
  ylab = "Fishing mortality",
  xlab = ""
)

Arguments

dat: Data object as returned by [check.dat()], containing life-history and reference-point information used in the MSE.
set: Settings list as returned by [check.set()] and modified for the MSE run (e.g. containing `nysim`, `nrep`, and `hcr`).
resMSE: Result object returned by [run.mse()], containing simulated time series for each HCR and replicate.
trendline: Logical; if `TRUE`, draw a smoothed trend or additional line highlighting the general trajectory of fishing mortality over time (e.g. using a smoother or running mean). Default is `TRUE`.
uncert: Logical; if `TRUE`, display uncertainty across replicates, typically in the form of quantile bands or envelopes around the median. Default is `TRUE`.
med: Logical; if `TRUE`, draw the median fishing mortality trajectory across replicates for each HCR. If `FALSE`, only uncertainty or other summaries are shown, depending on the internal implementation. Default is `TRUE`.
hcrs: Optional character vector or indices specifying which HCRs to plot. If `NA` (default), all HCRs present in `set$hcr` (and `resMSE`) are plotted.
ylim: Optional numeric vector of length two giving the y-axis limits. If `NULL` (default), limits are chosen automatically to encompass the plotted fishing mortality values.
plot.legend: Logical; if `TRUE` (default), add a legend identifying the plotted HCRs.
ylab: Character string specifying the y-axis label. Default is `"Fishing mortality"`.
xlab: Character string specifying the x-axis label. Default is an empty string `""`. Often set to `"Year"` or similar by the user.

Value

This function is called for its side effect of producing a plot. Invisibly returns `NULL`.

Details

By default, one line per HCR is drawn, and uncertainty across stochastic replicates is indicated (for example, by plotting quantile bands; the exact representation depends on the internal implementation). The function uses base R graphics.