Plot RCM scope output

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 class 'RCModel,missing'
plot(
  x,
  compare = FALSE,
  filename = "RCM",
  dir = tempdir(),
  sims = 1:x@OM@nsim,
  Year = NULL,
  Age = 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,
  Age = 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. Useful if seasonal time steps are used.
Age: Optional, a vector of ages for plotting. Useful if seasonal time steps are used.
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.

Usage

Arguments

Value

See also