genboot {mixstock} | R Documentation |
Given a data set or simulated data set (in the usual format of a list of source samples and samples from the mixed stock), generate bootstrap-resampled data sets (either parametrically or nonparametrically) and a vector of estimates from the resampled data sets
genboot(x, method="cml", nboot=1000, rseed=1001, verbose=FALSE, fuzz=0.001, maxfail=100, rpt=20, start.type="lsolve", param=FALSE,param.match="mean",ndepfac=10000,save.boot=FALSE, print.boot=FALSE,...)
x |
A mixed stock data set: a list with elements sourcesamp (a
matrix, with sources as columns and markers as rows, of samples
in the sources) and mixsamp (a vector of markers sampled
in the mixed stock) |
method |
"cml" for conditional max. likelihood or "uml" for unconditional max. likelihood |
nboot |
number of bootstrap samples |
rseed |
random-number seed |
verbose |
produce verbose output? |
fuzz |
small value for keeping estimated frequencies away from 0/1 |
maxfail |
number of consecutive fitting tries before entering NAs for a given simulation |
rpt |
frequency with which to report progress |
start.type |
starting conditions for fitting procedure (see
startvec and/or startvec0 ) |
param |
Do parametric bootstrapping? |
param.match |
match mean or mode of resampled frequencies? |
ndepfac |
scaling factor for CML fit |
save.boot |
save bootstrap replicates? |
print.boot |
verbose output from bootstrap? |
... |
additional arguments to cml |
An object of type mixstock.est
with element resample
as a matrix of bootstrap results (where the columns
are the parameters, the negative log-likelihood of the fit, and a code
for convergence).
data(simex) x <- genboot(simex,method="cml",nboot=100) r <- x$resample r.ok <- r[!is.na(r[,"Convergence"]) & r[,"Convergence"]==0,] old.par <- par(no.readonly=TRUE) par(mfrow=c(2,2)) hist(r.ok[,1],main="Contrib. A") hist(r.ok[,2],main="Contrib. B") hist(r.ok[,3],main="Neg. log likelihoods") plot(r.ok[,1],r.ok[,3], xlab="Contrib. A",ylab="NLL") par(old.par)