[R-lang] Re: comparisons in lmer

[Andy Fugard]

On Wed, Jan 12, 2011 at 6:06 PM, Maureen Gillespie <
gillespie.maureen@gmail.com> wrote:

> What if you DO want to do a bunch of paired tests and your coding scheme
> isn't going to get at them all in one go? What is the best way of doing
> this? Run multiple models on subsets of the data, then adjust/correct for
> multiple comparisons?



You could use Tukey's all-pairwise comparisons via glht in the multcomp
package.  For instance:

>
> require(languageR)
> require(multcomp)
>
>
> M1 = glmer(CaseMarking ~ WordOrder * AgeGroup +
+   AnimacyOfSubject + Text + (1|Speaker),
+   family = "binomial", data = warlpiri)
> M1
Generalized linear mixed model fit by the Laplace approximation
Formula: CaseMarking ~ WordOrder * AgeGroup + AnimacyOfSubject + Text +
(1 | Speaker)
   Data: warlpiri
   AIC BIC logLik deviance
 296.2 327 -140.1    280.2
Random effects:
 Groups  Name        Variance Std.Dev.
 Speaker (Intercept) 0.46023  0.6784
Number of obs: 347, groups: Speaker, 27

Fixed effects:
                                     Estimate Std. Error z value Pr(>|z|)

(Intercept)                           -2.7731     0.4659  -5.952 2.65e-09
***
WordOrdersubNotInitial                 0.2731     0.5025   0.543   0.5868

AgeGroupchild                          1.2059     0.4726   2.552   0.0107 *

AnimacyOfSubjectinanimate              0.6406     0.3822   1.676   0.0938 .

Texttextb                              0.2887     0.4833   0.597   0.5503

Texttextc                              0.7376     0.4237   1.741   0.0817 .

WordOrdersubNotInitial:AgeGroupchild  -1.8233     0.7382  -2.470   0.0135 *

---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
            (Intr) WrdONI AgGrpc AnmcOS Txttxtb Txttxtc
WrdOrdrsbNI -0.341
AgeGropchld -0.594  0.371
AnmcyOfSbjc -0.031 -0.052  0.041
Texttextb   -0.478 -0.040 -0.039 -0.137
Texttextc   -0.568 -0.033 -0.009 -0.311  0.606
WrdOrdNI:AG  0.249 -0.674 -0.434 -0.069  0.053   0.026
>
> summary(glht(M1, linfct=mcp(Text="Tukey")))

         Simultaneous Tests for General Linear Hypotheses

Multiple Comparisons of Means: Tukey Contrasts


Fit: glmer(formula = CaseMarking ~ WordOrder * AgeGroup + AnimacyOfSubject +

    Text + (1 | Speaker), data = warlpiri, family = "binomial")

Linear Hypotheses:
                   Estimate Std. Error z value Pr(>|z|)
textb - texta == 0   0.2887     0.4833   0.597    0.821
textc - texta == 0   0.7376     0.4237   1.741    0.188
textc - textb == 0   0.4490     0.4063   1.105    0.509
(Adjusted p values reported -- single-step method)

Cheers,

Andy

-- 
Dr Andy Fugard
http://www.andyfugard.info
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