salmonMSE (version 0.1.0)

report_CM: Conditioning model markdown report

Description

Generate a markdown report to plot time series and MCMC posteriors of estimates from the conditioning model

Usage

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

Value

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

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

See Also

fit_CM()