plot.RCModel: Plot RCM scope output

In SAMtool: Stock Assessment Methods Toolkit

Plot RCM scope output

Description

Produces HTML file (via markdown) figures of parameter estimates and output from an Assessment object. Plots histograms of operating model parameters that are updated by the RCM scoping function, as well as diagnostic plots for the fits to the RCM for each simulation. compare_RCM plots a short report that compares output from multiple RCM objects, assuming the same model structure, i.e., identical matrix and array dimensions among models, but different data weightings, data omissions, etc.

Usage

## S4 method for signature 'RCModel,missing'
plot(
  x,
  compare = FALSE,
  filename = "RCM",
  dir = tempdir(),
  sims = 1:x@OM@nsim,
  Year = NULL,
  f_name = NULL,
  s_name = NULL,
  MSY_ref = c(0.5, 1),
  bubble_adj = 1.5,
  scenario = list(),
  title = NULL,
  open_file = TRUE,
  quiet = TRUE,
  render_args,
  ...
)

compare_RCM(
  ...,
  compare = FALSE,
  filename = "compare_RCM",
  dir = tempdir(),
  Year = NULL,
  f_name = NULL,
  s_name = NULL,
  MSY_ref = c(0.5, 1),
  bubble_adj = 1.5,
  scenario = list(),
  title = NULL,
  open_file = TRUE,
  quiet = TRUE,
  render_args
)

Arguments

x	An object of class RCModel (output from RCM).
compare	Logical, if TRUE, the function will run runMSE to compare the historical period of the operating model and the RCM output.
filename	Character string for the name of the markdown and HTML files.
dir	The directory in which the markdown and HTML files will be saved.
sims	A logical vector of length x@OM@nsim or a numeric vector indicating which simulations to keep.
Year	Optional, a vector of years for the historical period for plotting.
f_name	Character vector for fleet names.
s_name	Character vector for survey names.
MSY_ref	A numeric vector for reference horizontal lines for B/BMSY plots.
bubble_adj	A number to adjust the size of bubble plots (for residuals of age and length comps).
scenario	Optional, a named list to label each simulation in the RCM for plotting, e.g.: list(names = c("low M", "high M"), col = c("blue", "red")).
title	Optional character string for an alternative title for the markdown report.
open_file	Logical, whether the HTML document is opened after it is rendered.
quiet	Logical, whether to silence the markdown rendering function.
render_args	A list of other arguments to pass to render.
...	For compare_RCM, multiple RCM objects for comparison.

Value

Returns invisibly the output from render.

See Also

RCModel RCM

SAMtool documentation built on Sept. 11, 2024, 8:07 p.m.