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.

# S4 method for 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),
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),
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.

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.