bug in confint with boot method and several random terms ?
On 14-01-12 10:10 AM, espesser wrote:
Dear all, Here is a reproducible example of a possible bug concerning confint.merMod with method="boot", when more than a single random term is specified. The problem does not concern the bootstrapping itself, but the external function bootFun. Unhappily, I'm not skill enough to fix it. I did not found previous mention of this , but apologizes if I'm missing something. Thank you for your help R. espesser
This was fixed recently (11 days ago) in the development version. I will work on putting the latest version (just bumped to 1.1-4) on http://lme4.r-forge.r-project.org/repos . In the meantime, if you have development tools installed (which has gotten to be relatively easy, even on Windows ...) you can always install the latest version via library("devtools"); install_github("lme4","lme4") We are hoping for another CRAN release fairly soon, but holding your breath might be dangerous. Ben Bolker
library(lme4)
data(Penicillin)
fm2 <- lmer(diameter ~ 1 + (1|plate) + (1|sample), Penicillin)
summary(fm2)
Linear mixed model fit by REML ['lmerMod']
Formula: diameter ~ 1 + (1 | plate) + (1 | sample)
Data: Penicillin
REML criterion at convergence: 330.8606
Random effects:
Groups Name Variance Std.Dev.
plate (Intercept) 0.7169 0.8467
sample (Intercept) 3.7309 1.9316
Residual 0.3024 0.5499
Number of obs: 144, groups: plate, 24; sample, 6
Fixed effects:
Estimate Std. Error t value
(Intercept) 22.9722 0.8086 28.41
confint(fm2, method="boot",nsim=100)
Computing bootstrap confidence intervals ...
Error in setNames(Cv_to_Sv(th, s = sigma(x)), c(tnames(x, old = FALSE, :
'names' attribute [3] must be the same length as the vector [2]
In addition: Warning message:
In m0[lower.tri(m0, diag = TRUE)] <- x :
number of items to replace is not a multiple of replacement length
# It is OK with only one random intercept:
fm2_single <- lmer(diameter ~ 1 + (1|plate) , Penicillin)
confint(fm2_single, method="boot",nsim=100)
Computing bootstrap confidence intervals ...
2.5 % 97.5 %
sd_(Intercept)|plate 0.000000 0.7437895
sigma 1.751577 2.1949818
(Intercept) 22.606299 23.3667589
I
##########################
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] boot_1.3-9 lme4_1.0-5 Matrix_1.1-0 lattice_0.20-23
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4
ggplot2_0.9.3.1 grid_3.0.2
[6] gtable_0.1.2 labeling_0.2 MASS_7.3-29
minqa_1.2.1 munsell_0.4.2
[11] nlme_3.1-111 plyr_1.8 proto_0.3-10
RColorBrewer_1.0-5 reshape2_1.2.2
[16] scales_0.2.3 splines_3.0.2 stringr_0.6.2 tools_3.0.2