unmarked (version 0.8-5)

nonparboot-methods: Nonparametric bootstrapping in unmarked

Description

Call nonparboot on an unmarkedFit to obtain non-parametric bootstrap samples. These can then be used by vcov in order to get bootstrap estimates of standard errors.

Details

Calling nonparboot on an unmarkedFit returns the original unmarkedFit, with the bootstrap samples added on. Then subsequent calls to vcov with the argument method="nonparboot" will use these bootstrap samples. Additionally, standard errors of derived estimates from either linearComb or backTransform can be instructed to use bootstrap samples by providing the argument method = "nonparboot".

Examples

data(ovendata)
ovenFrame <- unmarkedFrameMPois(ovendata.list$data,
siteCovs=as.data.frame(scale(ovendata.list$covariates[,-1])), type = "removal")
(fm <- multinomPois(~ 1 ~ ufp + trba, ovenFrame))
fm <- nonparboot(fm, B = 20) # should use larger B in real life.
vcov(fm, method = "hessian")
vcov(fm, method = "nonparboot")
avg.abundance <- backTransform(linearComb(fm, type = "state", coefficients = c(1, 0, 0)))

## Bootstrap sample information propagates through to derived quantities.
vcov(avg.abundance, method = "hessian")
vcov(avg.abundance, method = "nonparboot")
SE(avg.abundance, method = "nonparboot")