mm.wbugs {mixstock} | R Documentation |
Sets up the many-to-many model and passes it to WinBUGS via R2WinBUGS
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)
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? |
results of WinBUGS run, as a mixstock.est
object
by default: type varies according to returntype
.
write.TO.code
produces a BUGS model file.
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.
Ben Bolker