genboot: Generate bootstrap estimates of mixed stock analyses

In bbolker/mixstock: Functions for Mixed Stock Analysis

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, pb=TRUE, 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
pb	(logical) draw progress bar?
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)

bbolker/mixstock documentation built on July 23, 2024, 12:18 p.m.