genboot {mixstock}R Documentation

Generate bootstrap estimates of mixed stock analyses

Description

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

Usage

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,...)

Arguments

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

Value

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).

Examples

  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)

[Package mixstock version 0.9 Index]