gibbsC {mixstock}R Documentation

Run mixed stock analysis Gibbs sampler, in C

Description

Runs a Gibbs sampler MCMC for mixed stock analysis, calling a routine written in C (for code). Low-level function, called by other functions.

Usage

gibbsC(a=1, startiter, maxiter, data, mixsamp=NULL, sourcesamp=NULL,
startfval=NULL, thin=1, fprior=NULL, outfile=FALSE,
outfn="mixstock-gibbs", randseed=1001, rptiter=-1, debug=FALSE,
contrun=FALSE,contrib.start=NULL,sourcefreq.start=NULL)

Arguments

a Prior strength parameter
startiter Number of iterations to discard (burn-in)
maxiter Total number of chain steps
data A mixstock.data object
mixsamp Marker sample from mixed populations
sourcesamp Marker samples from sources
startfval Where to start the chain: 0=
thin thinning factor
fprior Bayesian prior
outfile send data to an output file?
outfn name of output file
randseed random-number seed
rptiter frequency for sending reports to screen
debug debug?
contrun continuation run? set fval and sourcefreq directly
contrib.start vector of starting contributions
sourcefreq.start matrix of starting source freqs

Value

a numeric matrix containing samples from the chain: each row is a vector of estimated contribution frequencies from each rookery

Note

gibbsC calls C code to generate multinomial deviates derived from the randlib.c library (version 1.3: http://odin.mdacc.tmc.edu/anonftp/), written by Barry W. Brown, James Lovato, Kathy Russell, and John Venier, derived in turn from page 559 of: Devroye, Luc, Non-Uniform Random Variate Generation. Springer-Verlag, New York, 1986.

Author(s)

Ben Bolker


[Package mixstock version 0.9 Index]