[R-sig-ME] lme4 broken ?

[Martin Maechler]

>>>>> "l" == lancelot  <renaud.lancelot at cirad.fr>
>>>>>     on Fri, 13 Apr 2012 08:55:24 +0200 writes:

    > I re-installed the previous version of Matrix (Matrix_1.0-5.tar.gz 
    > available on CRAN) from source, and it now works (see below).

    > I confirm there is a problem - at least on Windows - between lme4
    > and R-Forge present versions) and the present version of
    > Matrix 1.0-6.

Hmm, I very much doubt this, at it least in this generality.
Other people have seen similar problems (not involving lme4 at
all), on R-help or R-devel, and the solution has been to
re-install packages (or R!) only.

The mismatch of number of arguments of .Internal(identical)
is really from using packages that were *built* with one version
of R, in a different version of *R*.

So, in principle

    update.packages(checkBuilt = TRUE)

should get you there.

Regards,
Martin Maechler


    > All the best,

    > Renaud

    >> sessionInfo()
    > R version 2.15.0 (2012-03-30)
    > Platform: i386-pc-mingw32/i386 (32-bit)

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

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

    > other attached packages:
    > [1] lme4_0.999902344-0 Matrix_1.0-5       lattice_0.20-6

    > loaded via a namespace (and not attached):
    > [1] grid_2.15.0    MASS_7.3-17    minqa_1.2.0    nlme_3.1-103 
    > splines_2.15.0 tools_2.15.0


    >> library(lme4)
    > Le chargement a nécessité le package : lattice
    > Le chargement a nécessité le package : Matrix
    >> example(lmer)

    lmer> ## linear mixed models - reference values from older code
    lmer> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
    > Linear mixed model fit by REML ['lmerMod']
    > Formula: Reaction ~ Days + (Days | Subject)
    > Data: sleepstudy

    > REML criterion at convergence: 1743.628

    > Random effects:
    > Groups   Name        Variance Std.Dev. Corr
    > Subject  (Intercept) 612.10   24.741
    > Days         35.07    5.922   0.066
    > Residual             654.94   25.592
    > Number of obs: 180, groups: Subject, 18

    > Fixed effects:
    > Estimate Std. Error t value
    > (Intercept)  251.405      6.825   36.84
    > Days          10.467      1.546    6.77

    > Correlation of Fixed Effects:
    > (Intr)
    > Days -0.138

    lmer> (fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), 
    > sleepstudy))
    > Linear mixed model fit by REML ['lmerMod']
    > Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
    > Data: sleepstudy

    > REML criterion at convergence: 1743.669

    > Random effects:
    > Groups   Name        Variance Std.Dev.
    > Subject  (Intercept) 627.58   25.052
    > Subject  Days         35.86    5.988
    > Residual             653.58   25.565
    > Number of obs: 180, groups: Subject, 18

    > Fixed effects:
    > Estimate Std. Error t value
    > (Intercept)  251.405      6.885   36.51
    > Days          10.467      1.560    6.71

    > Correlation of Fixed Effects:
    > (Intr)
    > Days -0.184

    lmer> anova(fm1, fm2)
    > Data: sleepstudy
    > Models:
    > fm2: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
    > fm1: Reaction ~ Days + (Days | Subject)
    > Df    AIC    BIC  logLik deviance  Chisq Chi Df Pr(>Chisq)
    > fm2  5 1762.0 1778.0 -876.00   1752.0
    > fm1  6 1763.9 1783.1 -875.97   1751.9 0.0639      1     0.8004



    > Le 12/04/2012 20:11, Joehanes, Roby (NIH/NHLBI) [F] a écrit :
    >> Hi Renaud,
    >> 
    >> It works okay in my computer (Linux). Maybe you want to update all
    >> underlying libraries?
    >> 
    >> Hope this helps, Roby
    >> 
    >> (fm1<- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
    >> 
    >> _______________________________________________
    >> R-sig-mixed-models at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
    >> 

    > -- 
    > Renaud Lancelot
    > EDENext Project, coordinator: http://www.edenext.eu/

    > CIRAD, UMR15, Campus International de Baillarguet TA A-DIR / B
    > F34398 Montpellier

    > Tel.  +33 4 67 59 37 17  -  Fax  +33 4 67 59 37 98
    > Secr. +33 4 67 59 37 37  - Cell. +33 6 77 52 08 69

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