importMCMC {scapeMCMC}R Documentation

Import Coleraine MCMC Results

Description

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

Usage

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

Arguments

dir directory containing the files ‘mcmclike.out’, ‘params.pst’, ‘spawbiom.pst’ and ‘recruits.pst’.
info optional string containing information to store with MCMC results.
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.

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.

Note

The example dataset xmcmc was generated using importMCMC.

The functions ll (package gdata) and head are recommended for browsing MCMC results, e.g. ll(xmcmc); ll(xmcmc$P); head(xmcmc$P).

Author(s)

Arni Magnusson arnima@u.washington.edu.

References

Hilborn, R., M. Maunder, A. Parma, B. Ernst, J. Payne, and P. Starr. 2003. Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116. Available at http://fish.washington.edu/research/coleraine/coleraine.pdf.

See Also

importProj, read.table, readLines, scan, xmcmc.

scapeMCMC-package gives an overview of the package.

Examples

## Not run: 
path <- paste(.find.package("scapeMCMC"), "/example", sep="")
xmcmc <- importMCMC(path)  # or rename and select particular elements:
xmcmc <- importMCMC(path, pretty.labels=TRUE,
                    l.choose=c("CAc","CAs","Survey","Prior","Total"),
                    p.choose=c("R0","Rinit","uinit","cSleft","cSfull",
                               "sSleft","sSfull","logq"))
## End(Not run)

[Package scapeMCMC version 1.0-3 Index]