report_CM: Conditioning model markdown report

In salmonMSE: Management Strategy Evaluation for Salmon Species

Conditioning model markdown report

Description

Generate a markdown report to plot time series and MCMC posteriors of estimates from the conditioning model. See get_report() for the various plotting functions used in the report.

Usage

report_CM(
  stanfit,
  year,
  cov1_names,
  cov_names,
  rs_names,
  name,
  filename = "CM",
  dir = tempdir(),
  open_file = TRUE,
  render_args = list(),
  ...
)

Arguments

stanfit	Output from sample_CM()
year	Optional vector of calendar years
cov1_names	Optional character vector for names of covariates that predict age-1 natural mortality
cov_names	Optional character vector for names of covariates that predict age-2+ natural mortality
rs_names	Optional character vector for names of hatchery release strategies
name	Optional character string for the model name to include in the report, e.g., model run number
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.
open_file	Logical, whether the HTML document is opened after it is rendered
render_args	List of arguments to pass to rmarkdown::render()
...	Additional arguments (not used)

Details

Report excludes MCMC values from warmup iterations

Value

Returns invisibly the output of rmarkdown::render(), typically the path of the output file

See Also

fit_CM() get_report()

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.