[R] anova statistics in lmer

From: Diego Vázquez <dvazquez_at_lab.cricyt.edu.ar>
Date: Tue 16 May 2006 - 01:52:52 EST


Dear list members,

I am new to R and to the R-help list. I am trying to perform a mixed-model analysis using the lmer() function. I have a problem with the output anova table when using the anova() function on the lmer output object: I only get the numerator d.f., the sum of squares and the mean squares, but not the denominator d.f., F statistics and P values. Below is a sample output, following D. Bates' SASmixed example in his paper "Fitting linear mixed models in R" (R-News 5: 27-30).

By reading the R-help archive, I see that this problem has come up before (e.g., http://tolstoy.newcastle.edu.au/R/help/06/04/25013.html). What I understand from the replies to this message is that this incomplete output results from some unresolved issues with lmer, and that it is currently not possible to use it to obtain full anova statistics. Is this correct? And is this still unresolved? If so, what is the best current alternative to conduct a mixed model analysis, other than going back to SAS?

I would greatly appreciate some help.

Diego


Example using SASmixed "HR" data (see D. Bates, "Fitting linear mixed models in R", R-News 5: 27-30)

> data("HR",package="SASmixed")
> library(lme4)

Loading required package: Matrix
Loading required package: lattice

Attaching package: 'lattice'

        The following object(s) are masked from package:Matrix :

         qqmath

> (fm1<-lmer(HR~baseHR+Time*Drug+(1|Patient),HR))
Linear mixed-effects model fit by REML
Formula: HR ~ baseHR + Time * Drug + (1 | Patient)

          Data: HR
      AIC      BIC    logLik MLdeviance REMLdeviance
 788.6769 810.9768 -386.3384   791.8952     772.6769
Random effects:
 Groups   Name        Variance Std.Dev.
 Patient  (Intercept) 44.541   6.6739
 Residual             29.780   5.4571

number of obs: 120, groups: Patient, 24

Fixed effects:

             Estimate Std. Error t value

(Intercept)  33.96209    9.93059  3.4199
baseHR        0.58819    0.11846  4.9653
Time        -10.69835    2.42079 -4.4194
Drugb         3.38013    3.78372  0.8933
Drugp        -3.77824    3.80176 -0.9938
Time:Drugb    3.51189    3.42352  1.0258
Time:Drugp    7.50131    3.42352  2.1911

Correlation of Fixed Effects:
           (Intr) baseHR Time   Drugb  Drugp  Tm:Drgb
baseHR     -0.963
Time       -0.090  0.000
Drugb      -0.114 -0.078  0.237
Drugp      -0.068 -0.125  0.236  0.504

Time:Drugb 0.064 0.000 -0.707 -0.335 -0.167 Time:Drugp 0.064 0.000 -0.707 -0.167 -0.333 0.500
> anova(fm1)

Analysis of Variance Table
          Df Sum Sq Mean Sq
baseHR     1 745.99  745.99
Time       1 752.86  752.86
Drug       2  86.80   43.40

Time:Drug 2 143.17 71.58
-- 
Diego Vázquez
Instituto Argentino de Investigaciones de las Zonas Áridas
Centro Regional de Investigaciones Científicas y Tecnológicas
CC 507, (5500) Mendoza, Argentina
http://www.cricyt.edu.ar/interactio/dvazquez/

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Received on Tue May 16 01:59:35 2006

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