R Under development (unstable) (2023-07-03 r84633 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (.Platform$OS.type != "windows") { + + library(lme4) + + mySumm <- function(.) { + s <- sigma(.) + c(beta =getME(., "beta"), + sigma = s, + sig01 = unname(s * getME(., "theta"))) + } + + fm1 <- lmer(Yield ~ 1|Batch, Dyestuff) + boo01 <- bootMer(fm1, mySumm, nsim = 10) + boo02 <- bootMer(fm1, mySumm, nsim = 10, use.u = TRUE) + + ## boo02 <- bootMer(fm1, mySumm, nsim = 500, use.u = TRUE) + if (require(boot)) { + boot.ci(boo02,index=2,type="perc") + } + + fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) + boo03 <- bootMer(fm2, mySumm, nsim = 10) + boo04 <- bootMer(fm2, mySumm, nsim = 10, use.u = TRUE) + + if (lme4:::testLevel() > 1) { + gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), + data = cbpp, family = binomial) + boo05 <- bootMer(gm1, mySumm, nsim = 10) + boo06 <- bootMer(gm1, mySumm, nsim = 10, use.u = TRUE) + + cbpp$obs <- factor(seq(nrow(cbpp))) + gm2 <- glmer(cbind(incidence, size - incidence) ~ period + + (1 | herd) + (1|obs), + family = binomial, data = cbpp) + boo03 <- bootMer(gm2, mySumm, nsim = 10) + boo04 <- bootMer(gm2, mySumm, nsim = 10, use.u = TRUE) + } + load(system.file("testdata","culcita_dat.RData",package="lme4")) + cmod <- glmer(predation~ttt+(1|block),family=binomial,data=culcita_dat) + set.seed(101) + ## FIXME: sensitive to step-halving PIRLS tests + ## expect_warning(cc <- confint(cmod,method="boot",nsim=10,quiet=TRUE, + ## .progress="txt",PBargs=list(style=3)),"some bootstrap runs failed") + + + library(parallel) + if (detectCores()>1) { + ## http://stackoverflow.com/questions/12983137/how-do-detect-if-travis-ci-or-not + travis <- nchar(Sys.getenv("TRAVIS"))>0 + if(.Platform$OS.type != "windows" && !travis) { + boo01P <- bootMer(fm1, mySumm, nsim = 10, parallel="multicore", ncpus=2) + } + + ## works in Solaris from an interactive console but not ??? + ## via R CMD BATCH + if (Sys.info()["sysname"] != "SunOS") + boo01P.snow <- bootMer(fm1, mySumm, nsim = 10, parallel="snow", ncpus=2) + } + + set.seed(101) + dd <- data.frame(x=runif(200), + f=rep(1:20,each=10), + o=rnorm(200,mean=2)) + dd$y <- suppressMessages(simulate(~x+(1|f)+offset(o), + family="poisson", + newdata=dd, + newparams=list(theta=1,beta=c(0,2)))[[1]]) + + ## fails under flexLambda + dd$y2 <- suppressMessages(simulate(~x+(1|f)+offset(o), + family="gaussian", + newdata=dd, + newparams=list(theta=1,beta=c(0,2),sigma=1))[[1]]) + + fm3 <- glmer(y~x+(1|f)+offset(o), + data=dd,family="poisson") + + fm4 <- lmer(y2~x+(1|f)+offset(o), + data=dd) + + mySumm2 <- function(fit) return(c(fixef(fit),getME(fit,'theta'))) + ## still some issues to fix here + bb <- bootMer(fm3,mySumm2,nsim=10) + attr(bb,"boot.fail.msgs") + bb2 <- bootMer(fm4,mySumm2,nsim=10) + + } ## skip on windows (for speed) > > proc.time() user system elapsed 0.12 0.03 0.14