plot_MCBE: Plot results from MCBE uncertainty analysis

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Plot results from MCBE uncertainty analysis

Description

Plot results from MCBE uncertainty analysis

Usage

plot_MCBE(
  sim_summary = NULL,
  dir_figs = "figs",
  fileName = "bam",
  dir_bam_base = NULL,
  filter_MCBE_args = list(filter_info = list(gradient.max = c(0, 0.01), Fref = c(0, 5),
    F.Fref = c(0, 5), R.sigma.par = c(0.2, 1), R0_prob = c(0.005, 0.995), avoid_bounds =
    TRUE), nm_rp = list(parms = c(Fref = "Fmsy", F.Fref = "Fend.Fmsy.mean"))),
  tseries_plot_args = list(),
  aseries_plot_args = list(),
  base_tseries_args = list(type = "o", lty = 1, lwd = 2, pch = 16, col = "black"),
  base_aseries_args = list(type = "o", lty = 1, lwd = 2, pch = 16, col = "black"),
  nm_rp = list(parms = c(Fref = "Fmsy", F.Fref = "Fend.Fmsy.mean", Sref = "msst", S.Sref
    = "SSBend.MSST", Lref = "msy.klb", Bref = "Bmsy"), t.series = c(F = "F.full", F.Fref
    = "F.Fmsy", S = "SSB", S.Sref = "SSB.msst")),
  plot2pdf = TRUE,
  sc_pdf = list(w = 1, h = 1)
)

Arguments

sim_summary	Output object from summarize_MCBE
dir_figs	name of directory that will be created to store figures
fileName	Name of BAM base files in dir_bam_base, not including file extensions.
dir_bam_base	Name of directory where the bam base model is located relative to the working directory, for adding base model results to plots (optional).
tseries_plot_args	List of arguments to pass to bamExtras::plot_boot_vec when plotting time series.
aseries_plot_args	List of arguments to pass to bamExtras::plot_boot_vec when plotting age series.
base_tseries_args	List of arguments to add to plotting functions (e.g. points()) that add base results to time series plots
base_aseries_args	List of arguments to add to plotting functions (e.g. points()) that add base results to age series plots
nm_rp	list specifying names of reference points to include in plots.
plot2pdf	If plot2pdf = TRUE, each plot will be written to a pdf in dir_figs. If false, figures will be plotted to the active graphic device.
sc_pdf	Optional scalars for pdf width and height. Multiplied by defaults pdf width and height. Defaults to 1 which has no effect.
filter_info	list of ranges used to filter out MCBE results. set to NULL to retain all results.

Examples

## Not run: 
# Run MCBE, writing files to dir_bam_sim
run_MCBE("GrayTriggerfish", dir_bam_sim="sim_GrTr")
# Summarize results of MCBE and assign to object
MCBE_GrTr <- summarize_MCBE(dir_bam_sim="sim_GrTr")
# Plot MCBE results

## End(Not run)

nikolaifish/bamExtras documentation built on April 17, 2025, 9:44 p.m.