1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
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)
|
