[R-lang] Re: comparisons in lmer

[Marina Sherkina-Lieber]

Thank you, Andy!
What is the difference between lmer and glmer?
And it would help if you decipher parts of the command for the Tukey test.
Marina

Quoting Andy Fugard <andyfugard@gmail.com>:

> 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
>



-- 
Marina Sherkina-Lieber
Ph.D. candidate
Dept. of Linguistics
University of Toronto