mixstock.boot {mixstock} | R Documentation

## Bootstrap samples of mixed stock analysis data

### Description

Create a bootstrap (multinomial) sample from a given set of marker data (source and mixed population genotypes), either parametric or non-parametric

### Usage

    mixstock.boot(x, param=FALSE, condense=TRUE,save.freq=FALSE,
    param.match="mean")

### Arguments

`x` | "Standard" mixstock data, a list with `mixsamp` (vector of samples in the mixed population) and `sourcesamp` (matrix of samples in the sources, rows=markers, columns=sources)
`param` | parametric bootstrapping or not?
`condense` | use `markfreq.condense` on the results?
`save.freq` | save frequencies?
`param.match` | match mean or mode of distribution when parametric bootstrapping?

### Details

Nonparametric bootstrapping just resamples the observed data from the mixed population and from each source with replacement; this is equivalent to taking a multinomial sample with the probabilities equal to the observed sample frequencies. Parametric bootstrapping takes the observed samples and resamples the probabilities themselves from a Dirichlet distribution, then takes a multinomial sample.

### Value

A bootstrapped data set, in the same format as the input data: i.e.,

`mixsamp` | samples in mixed population
`sourcesamp` | samples in sources

...

### Author(s)

Ben Bolker

### Examples

    true.freq <- matrix(c(0.65,0.33,0.01,0.01,
                           0.33,0.65,0.01,0.01),ncol=2)
    true.contrib <- c(0.9,0.1)
    x <- simmixstock0(true.freq,true.contrib,50,100,1004)
    nboot <- 1000
    boot.results.par <- matrix(NA,ncol=12,nrow=nboot)
    boot.results.npar <- matrix(NA,ncol=12,nrow=nboot)
    for (i in 1:nboot) {
      x.par  <- mixstock.boot(x,param=TRUE,condense=FALSE)
      x.npar <- mixstock.boot(x,condense=FALSE)
      boot.results.par[i,] <- c(x.par$sourcesamp,x.par$mixsamp)
      boot.results.npar[i,] <- c(x.npar$sourcesamp,x.npar$mixsamp)
    }
    summary(boot.results.par[,7:8])
    summary(boot.results.npar[,7:8])
    par(mfrow=c(1,2))
    hist(boot.results.par[,7])
    hist(boot.results.npar[,7])

[Package mixstock version 0.9.2 Index]