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,
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
- 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.