importMCMC: Import Coleraine MCMC Results

Description

Import Coleraine MCMC traces for likelihoods, parameters, spawning biomass, and recruitment.

Usage

importMCMC(dir, coda=FALSE, quiet=TRUE, pretty.labels=FALSE,
           l.choose=NULL, p.choose=NULL)

Value

A list containing:

L: likelihoods
P: parameters
B: biomass by year
R: recruitment by year

as data frames, or mcmc objects if coda=TRUE.

Arguments

dir: directory containing the files mcmclike.out, params.pst, spawbiom.pst and recruits.pst.
coda: whether data frames should be coerced to class mcmc using the coda package.
quiet: whether to report progress while parsing files in directory.
pretty.labels: whether likelihood and parameter columns should be renamed
l.choose: vector of strings, indicating which likelihood components to import, or NULL to import all.
p.choose: vector of strings, indicating which parameters to import, or NULL to import all.

References

Hilborn, R., Maunder, M., Parma, A., Ernst, B., Payne, J., and Starr, P. (2003). Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116.

Examples

Run this code

path <- system.file("example/mcmc", package="scape")
mcmc <- importMCMC(path)  # or rename and select particular elements:
mcmc <- importMCMC(path, pretty.labels=TRUE,
                   l.choose=c("CAc","CAs","Survey","Prior","Total"),
                   p.choose=c("R0","Rinit","uinit","cSleft","cSfull",
                              "sSleft","sSfull","logq"))

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