[R-sig-ME] getME function crashes

[lancelot]

everything's fine for me with the development version of lme4 (github)

 > library(arm)
Le chargement a nécessité le package : MASS
Le chargement a nécessité le package : Matrix
Le chargement a nécessité le package : lme4
Le chargement a nécessité le package : lattice

arm (Version 1.6-09, built: 2013-9-23)

Working directory is D:/Analyses

 > library(lme4)
 > set.seed (1)
 > J <- 15
 > n <- J*(J+1)/2
 > group <- rep (1:J, 1:J)
 > mu.a <- 5
 > sigma.a <- 2
 > a <- rnorm (J, mu.a, sigma.a)
 > b <- -3
 > x <- rnorm (n, 2, 1)
 > y <- rbinom (n, 1, invlogit (a[group] + b*x))
 > mod <- glmer (y ~ x + (1 | group), family=binomial(link="logit"))
 > getME(mod, "L")
'MatrixFactorization' of Formal class 'dCHMsimpl' [package "Matrix"] 
with 10 slots
   ..@ x       : num [1:15] 1.22 1.22 1.1 1.44 1.74 ...
   ..@ p       : int [1:16] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ i       : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ nz      : int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
   ..@ nxt     : int [1:17] 1 2 3 4 5 6 7 8 9 10 ...
   ..@ prv     : int [1:17] 16 0 1 2 3 4 5 6 7 8 ...
   ..@ colcount: int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
   ..@ perm    : int [1:15] 0 1 2 3 4 5 6 7 8 9 ...
   ..@ type    : int [1:4] 2 1 0 1
   ..@ Dim     : int [1:2] 15 15
 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arm_1.6-09      lme4_1.1-1      lattice_0.20-25 Matrix_1.1-0 
MASS_7.3-29

loaded via a namespace (and not attached):
[1] abind_1.4-1    coda_0.16-1    fortunes_1.5-1 grid_3.0.2 
minqa_1.2.1    nlme_3.1-111
[7] splines_3.0.2  tools_3.0.2


Idem with the 64-bit version of R

Renaud




Le 07/11/2013 17:31, Johannes Radinger a écrit :
> Hi,
>
> Actually I tried to use the sim function from the package "arm" to get
> posterior simulations of beta from a merMod.
> But somehow this function crashed and I could trace the problem back to the
> function getME(model,"L") which is
> the cause for the crash.
> For example here an example dataset for a binomial model (glmer) from the
> sim function in the 'arm'-package:
>
> set.seed (1)
> J<- 15
> n<- J*(J+1)/2
> group<- rep (1:J, 1:J)
> mu.a<- 5
> sigma.a<- 2
> a<- rnorm (J, mu.a, sigma.a)
> b<- -3
> x<- rnorm (n, 2, 1)
> y<- rbinom (n, 1, invlogit (a[group] + b*x))
>
> mod<- glmer (y ~ x + (1 | group), family=binomial(link="logit"))
>
> When I now run getME(mod, "L") my R session completely crashes with
> following error:
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
>
> Traceback:
>   1: .Call(merPredDL, ptr())
>   2: PR$L()
>   3: getME(mod, "L")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> I am running following setup:
>
> R version 3.0.2 (2013-09-25)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] arm_1.6-09      lme4_1.0-5      lattice_0.20-24 Matrix_1.1-0
> MASS_7.3-29
>
> loaded via a namespace (and not attached):
> [1] abind_1.4-0   coda_0.16-1   grid_3.0.2    minqa_1.2.1   nlme_3.1-111
> splines_3.0.2 tools_3.0.2
>
> Can anyone reproduce this problem?
>
> /Johannes
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>

-- 
Renaud Lancelot
Directeur adjoint / Deputy director
http://umr-cmaee.cirad.fr/
http://formation-elevage-suds.cirad.fr/
CIRAD, UMR CMAEE, Campus International de Baillarguet TA A-DIR / B
F34398 Montpellier

Head of epidemiology team
EDENext Project, coordinator: http://www.edenext.eu/

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