gibbsC {mixstock} | R Documentation |
Runs a Gibbs sampler MCMC for mixed stock analysis, calling a routine written in C (for code). Low-level function, called by other functions.
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)
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 |
a numeric matrix containing samples from the chain: each row is a vector of estimated contribution frequencies from each rookery
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.
Ben Bolker