[R] dispcrepancy between aov F test and tukey contrasts results with mixed effects model

[lbaril at montana.edu]

Thanks Peter for the advice and quick response.  I just want to clarify
what you suggest.  I should average values within a site then do a one-way
anova to test for differnces between sites based on the 2 to 3 new samples
per stand type -- and not use random effects for site?  Or, because I've
reduced the data I've 'corrected' the problem with the glht multiple
comparisons and can use the p-values from that summary if I include site
as a random effect?   Thanks again for your advice.



> lbaril at montana.edu wrote:
>> Hello,
>> I have some conflicting output from an aov summary and tukey contrasts
with a mixed effects model I was hoping someone could clarify.  I am
comparing the abundance of a species across three willow stand types.
Since I have 2 or 3 sites within a habitat I have included site as a
random effect in the lme model.  My confusion is that the F test given by
>> aov(model) indicates there is no difference between habitats, but the
tukey contrasts using the multcomp package shows that one pair of
habits
>> is significantly different from each other.  Why is there a
discrepancy?
>> Have I specified my model correctly?  I included the code and output
below.  Thank you.
>
> Looks like glht() is ignoring degrees of freedom. So what it does is
wrong but it is not easy to do it right (whatever "right" is in these
cases). If I understand correctly, what you have is that "stand" is
strictly coarser than "site", presumably the stands representing each 2,
2, and 3 sites, with a varying number of replications within each site.
Since the between-site variation is considered random, you end up with a
comparison of stands based on essentially only 7 pieces of information.
(The latter statement requires some qualification, but let's not go there
to day.)
>
> If you have roughly equal replications within each site, I'd be strongly
tempted to reduce the analysis to a simple 1-way ANOVA of the site averages.
>
>>> co.lme=lme(coye~stand,data=t,random=~1|site)
>>> summary (co.lme)
>> Linear mixed-effects model fit by REML
>>  Data: R
>>        AIC      BIC    logLik
>>   53.76606 64.56047 -21.88303
>> Random effects:
>>  Formula: ~1 | site
>>         (Intercept)  Residual
>> StdDev:   0.3122146 0.2944667
>> Fixed effects: coye ~ stand
>>                  Value Std.Error DF    t-value p-value
>> (Intercept)  0.4936837 0.2305072 60  2.1417277  0.0363
>> stand2       0.4853222 0.3003745  4  1.6157240  0.1815
>> stand3      -0.3159230 0.3251201  4 -0.9717117  0.3862
>>  Correlation:
>>        (Intr) stand2
>> stand2 -0.767
>> stand3 -0.709  0.544
>> Standardized Within-Group Residuals:
>>        Min         Q1        Med         Q3        Max
>> -2.4545673 -0.5495609 -0.3148274  0.7527378  2.5151476
>> Number of Observations: 67
>> Number of Groups: 7
>>> anova(co.lme)
>>             numDF denDF   F-value p-value
>> (Intercept)     1    60 23.552098  <.0001
>> stand           2     4  3.738199  0.1215
>>> summary(glht(co.lme,linfct=mcp(stand="Tukey")))
>>          Simultaneous Tests for General Linear Hypotheses
>> Multiple Comparisons of Means: Tukey Contrasts
>> Fit: lme.formula(fixed = coye ~ stand, data = R, random = ~1 | site)
Linear Hypotheses:
>>            Estimate Std. Error z value Pr(>|z|)
>> 2 - 1 == 0   0.4853     0.3004   1.616   0.2385
>> 3 - 1 == 0  -0.3159     0.3251  -0.972   0.5943
>> 3 - 2 == 0  -0.8012     0.2994  -2.676   0.0202 *
>> ---
>> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>> (Adjusted p values reported -- single-step method)
>> Lisa Baril
>> Masters Candidate
>> Department of Ecology
>> Montana State University - Bozeman
>> 406.994.2670
>> ______________________________________________
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>
>
> --
>     O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
>    c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>   (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45)
35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
>
>


Lisa Baril
Masters Candidate
Department of Ecology
Montana State University - Bozeman
406.994.2670