[R-sig-ME] Getting each bootstrapped data frame from bootMer

Ben Bolker bbolker at gmail.com
Sun May 25 03:01:37 CEST 2014

On 14-05-22 11:26 AM, Daniel J Hocking wrote:
> I am trying to get bootstrapped predictions from a logistic glmer
> (lme4) object and compare them to the “observed” independent variable
> from each bootstrap iteration. I can use bootMer to get the
> bootstrapped predictions:
> bb <- bootMer(glmm.M35,
> FUN=function(x)predict(x,re.form=NA,newdata=df.fit,type="response"),
> nsim=10) # test with just 10 draws
> but it doesn’t appear that bootMer saves the replicate datasets. Can
> anyone help me modify the bootMer function to output the bootstrap
> data frames or at least the independent variable (y) from each? Also
> any advice on handling the occasions when an iteration fails to
> converge in bootMer would be appreciated.

  I would be tempted just to re-invent the guts of bootMer, which are
not actually very complicated -- they're just a simulate/refit loop.  So
I might do something like

nsim <- 10
bootData <- simulate(glmm.M35,nsim)  ## data frame of sim data sets
predvals <- matrix(NA,nrow=length(df.fit),ncol=nsim)
for (i  in 1:10) {
   predvals[,i] <- predict(refit(glmm.M35,bootData[[i]]),

I also suspect (although haven't tried to check) that bootMer doesn't
use any random numbers other than the ones it uses to generate the
simulations, so you would *probably* be able to retrieve the response
values used if you just did this:

bootData <- simulate(...,seed=101)

(slightly inefficient, but simulating the data is the smallest part of
the problem)

 hope that helps
    Ben Bolker


> Thanks, Dan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel
> Hocking Department of Environmental Conservation Northeast Climate
> Science Center University of Massachusetts
> http://www.danieljhocking.wordpress.com 
> dhocking at umass.edu<mailto:dhocking at umass.edu> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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