mm.wbugs {mixstock}R Documentation

Run many-to-many model via WinBUGS

Description

Sets up the many-to-many model and passes it to WinBUGS via R2WinBUGS

Usage

mm.wbugs(x, sourcesize,
n.iter=20000,  n.burnin=floor(n.iter/2),
n.chains=x$R,
n.thin=max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
files.only = FALSE,
inittype=c("dispersed","random"),bugs.code=c("TO","BB"),
                     returntype=c("mixstock","coda","bugs"),
mixprior=1,
which.init,
debug=FALSE,...)
write.TO.bugscode(fn,MIX)

Arguments

x a mixstock data object
sourcesize Relative sizes of sources
n.iter Total length of each chain
n.burnin Number of burn-in iterations
n.chains Number of chains (default, number of sources)
n.thin thinning rate. Must be a positive integer. Set 'n.thin' > 1 to save memory and computation time if 'n.iter' is large. Default is 'max(1, floor(n.chains * (n.iter-n.burnin) / 1000))' which will only thin if there are at least 2000 simulations.
files.only (unimplemented) don't run WinBUGS, just produce input files
inittype "dispersed" or "random" depending on how you want multiple chains to be initialized
bugs.code "TO" or "BB" depending on whether you want old-style (Toshi Okuyama=TO) or more compact but possibly slower (Ben Bolker=BB) code
mixprior Dirichlet prior for contributions to mixed stocks. Should be either a vector of length (nmix+1) – one extra for the unknown stock – or a single numeric value which will be replicated
which.init for "dispersed" start with fewer chains than sources, which sources should be used as the dominant sources in the chains? (default is a random sample without replacement from the list of sources)
debug run BUGS in debug mode? (i.e. don't exit and go back to R automatically)
... other arguments to bugs
fn file name to write BUGS code to
MIX number of mixed stocks
returntype return value as a mixstock.est object, a CODA object, or a BUGS object?

Value

results of WinBUGS run, as a mixstock.est object by default: type varies according to returntype. write.TO.code produces a BUGS model file.

Note

For diagnostic purposes, it may be worth running the code initially with returntype="bugs" and using as.mcmc.bugs and as.mixstock.est.bugs to convert the result to either CODA format or mixstock format.

Author(s)

Ben Bolker


[Package mixstock version 0.9 Index]