plot_bam: Plot results from Beaufort Assessment Model

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

Plot results from Beaufort Assessment Model

Description

A generic plotting function that calls plotting functions from FishGraph and bamExtras.

Usage

plot_bam(
  spp = NULL,
  graphics.type = "pdf",
  draft = FALSE,
  use.color = TRUE,
  years_plot = NULL,
  FGPlot_args = list(x = quote(spp), DataName = "spp", draft = draft, use.color =
    use.color, graphics.type = graphics.type),
  windows_args = list(),
  Bound.vec.plots.args = list(),
  BSR.time.plots.args = list(BSR.references = list("Bmsy", "SSBmsy", "Rmsy")),
  CLD.total.plots.args = list(CLD.w.references = list("msy.klb", "msy.klb", "Dmsy.klb"),
    CLD.n.references = list("msy.num", "msy.num", "Dmsy.num"), units.CLD.w =
    x$info$units.landings),
  Cohort.plots.args = list(),
  Comp.plots.args = list(),
  Comp.yearly.plots.args = list(print.neff = TRUE, print.n = TRUE),
  Eq.plots.args = list(F.references = list("Fmsy", "F30"), user.Eq =
    list("L.eq.wholeklb", "L.eq.knum", "D.eq.knum")),
  F.time.plots.args = list(F.references = list("Fmsy", "F30"), F.additional =
    c("F.F30.ratio")),
  Growth.plots.args = list(plot.all = TRUE),
  Index.plots.args = list(),
  Landings.plots.args = list(),
  NFZ.age.plots.args = list(user.plots = "N.age.mdyr"),
  Parm.plots.args = list(),
  PerRec.plots.args = list(user.PR = list("SPR", "ypr.lb.whole"), F.references =
    list("Fmsy", "F30")),
  Phase.plots.args = list(Xaxis.F = FALSE),
  Selectivity.plots.args = list(compact = TRUE),
  StockRec.plots.args = list()
)

Arguments

spp	bam output rdat object
graphics.type	from FishGraph help: 'a vector of graphics file types to which graphics are saved. When NULL, no plots are saved.'
draft	from FishGraph help: 'modifies plots for use in a report. When FALSE main titles are omitted.'
use.color	from FishGraph help: 'plots are made in grayscale when FALSE'
years_plot	vector of years to plot in time series. If NULL, all years are plotted
FGPlot_args	set of arguments to pass to all FishGraph plotting functions

Examples

## Not run: 
# Make plots
plot_bam(rdat_BlackSeaBass)

## End(Not run)

nikolaifish/bamExtras documentation built on July 21, 2023, 8:26 a.m.