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

[lbaril at montana.edu]

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.

> 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