Reads the MCMC output (in the posteriors.sso and derived_posteriors.sso files) from a model.
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
)
Directory containing MCMC output.
TRUE/FALSE switch to get more or less information about the progress of the function.
Write key parameters and certainty nuisance quantities to a CSV file.
Name of file with parameter posteriors (default matches "posteriors.sso" used by SS, but the user could change the name)
Name of file with parameter posteriors (default matches "derived_posteriors.sso" used by SS, but the user could change the name)
First CSV file for key parameters.
Second CSV file for nuisance quantities.
Vector of strings that partially match parameter names to
write to the file csv1. This file intended to feed into
mcmc.out()
.
Vector of strings that partially match derived
quantity names to write to the file csv2. This file intended to feed into
mcmc.nuisance()
.
Optional burn-in value to apply on top of the option in the starter file.
Optional thinning value to apply on top of the option in the
starter file and in the -mcsave
runtime command.