Reads the MCMC output (in the posteriors.sso and derived_posteriors.sso files) from a model.
Usage
SSgetMCMC(
dir = NULL,
verbose = TRUE,
writecsv = FALSE,
postname = "posteriors.sso",
derpostname = "derived_posteriors.sso",
csv1 = "keyposteriors.csv",
csv2 = "nuisanceposteriors.csv",
keystrings = c("NatM", "R0", "steep", "RecrDev_2008", "Q_extraSD"),
nuisancestrings = c("Objective_function", "SSB_", "InitAge", "RecrDev"),
burnin = 0,
thin = 1
)Arguments
- dir
A file path to the directory of interest. The default value is
dir = NULL, which leads to using the current working directory.- verbose
A logical value specifying if output should be printed to the screen.
- writecsv
Write key parameters and certainty nuisance quantities to a CSV file.
- postname
Name of file with parameter posteriors (default matches "posteriors.sso" used by SS, but the user could change the name)
- derpostname
Name of file with parameter posteriors (default matches "derived_posteriors.sso" used by SS, but the user could change the name)
- csv1
First CSV file for key parameters.
- csv2
Second CSV file for nuisance quantities.
- keystrings
Vector of strings that partially match parameter names to write to the file csv1. This file intended to feed into
mcmc.out().- nuisancestrings
Vector of strings that partially match derived quantity names to write to the file csv2. This file intended to feed into
mcmc.nuisance().- burnin
Optional burn-in value to apply on top of the option in the starter file.
- thin
Optional thinning value to apply on top of the option in the starter file and in the
-mcsaveruntime command.