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option to set RNG seed from Philip Johnson July 2017, formerly called version 1.0-12 #4

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option to set RNG seed from Philip Johnson July 2017, formerly called version 1.0-12 #4

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1 change: 1 addition & 0 deletions R/output.R
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ print.contamMix <- function(x, tabDelim = FALSE, ...) {
if (tabDelim) {
cat(x$e, anal$MAP, anal$ci,
if (length(x$chains) > 1) coda::gelman.diag(anal$mcmcObj)$psrf else "",
x$seed,
sep="\t");
cat("\n")
} else {
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9 changes: 9 additions & 0 deletions exec/estimate.R
100755 → 100644
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Expand Up @@ -18,6 +18,7 @@ opt = getopt(rbind(
c('saveMN', NA, 0, "logical"), #save MN intermediate for debugging
c('recordAll', NA, 0, "logical"), #record *all* proportions from MCMC chain
c('tabOutput', NA, 0, "logical"), #simple tab-delimited output
c('seed', NA, 0, "integer"), #set rng seed
c('nrThreads', NA, 1, "integer")) # Number of threads to use. Defaults to 1.
)
if (is.null(opt$nIter)) opt$nIter = 50000
Expand Down Expand Up @@ -61,6 +62,14 @@ cat(paste0("Using ",used_cores, " threads.\n"), file=stderr())

## do the work
data = loadSAM(samFn=opt$samFn, malnFn=opt$malnFn, endogId=opt$consId, baseqThreshold=opt$baseq, transverOnly=opt$transverOnly, trimBases=opt$trimBases, saveMN=opt$saveMN)
## set/record RNG seed
if (is.null(opt$seed)) {
data$seed = round(runif(1,max=1e5))
} else {
data$seed = opt$seed
}
RNGkind("L'Ecuyer-CMRG")
set.seed(data$seed)
res = runChains(nChains=opt$nChains, nIter=opt$nIter, data=data, alpha=opt$alpha)

## results in text format
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