[R] summary.lme and anova question

[Christoph Scherber]

Dear all,

When analyzing data from a climate change experiment using linear mixed-effects models, I recently
came across a situation where:

- the summary(model) showed a significant difference between the levels of a two-level factor,
- while the anova(model) showed no significance for that factor (see below).

My question now is: Is the anova.lme() approach correct for that model? And why does the F-test for 
CO2 yield a non-significant P-value, while the t-test in the summary.lme() is significant?

Many thanks for your help!

Best wishes
Christoph

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mod11=lme(log(ind1+1) ~ CO2*DROUGHT*TEMP, random=~1|B/C,na.action=na.exclude)

summary(mod11)
Linear mixed-effects model fit by REML
Data: NULL
      AIC      BIC    logLik
  97.3077 115.6069 -37.65385

Random effects:
Formula: ~1 | B
         (Intercept)
StdDev: 1.303146e-05

Formula: ~1 | C %in% B
        (Intercept)  Residual
StdDev:   0.2466839 0.4846578

Fixed effects: log(ind1 + 1) ~ CO2 * DROUGHT * TEMP
                      Value Std.Error DF   t-value p-value
(Intercept)       1.9981490 0.2220158 29  9.000030  0.0000
CO2              -1.0308687 0.3139778  5 -3.283254  0.0219
DROUGHT          -0.9715216 0.2798173 29 -3.471986  0.0016
TEMP             -0.5592615 0.2954130 29 -1.893151  0.0684
CO2:DROUGHT       1.2196261 0.3957214 29  3.082032  0.0045
CO2:TEMP          0.9791044 0.4068987 29  2.406261  0.0227
DROUGHT:TEMP      0.6413038 0.4068987 29  1.576077  0.1259
CO2:DROUGHT:TEMP -1.1448624 0.5675932 29 -2.017047  0.0530
Correlation:
                 (Intr) CO2    DROUGHT TEMP   CO2:DROUGHT CO2:TE DROUGHT:
CO2              -0.707                                                 DROUGHT          -0.630 
0.446                                          TEMP             -0.597  0.422  0.474 
                    CO2:DROUGHT       0.446 -0.630 -0.707  -0.335                           CO2:TEMP 
          0.433 -0.613 -0.344  -0.726  0.486                    DROUGHT:TEMP      0.433 -0.306 
-0.688  -0.726  0.486       0.527        CO2:DROUGHT:TEMP -0.311  0.439  0.493   0.520 -0.697 
-0.717 -0.717
Standardized Within-Group Residuals:
       Min         Q1        Med         Q3        Max
-1.4631313 -0.5715171 -0.2024273  0.4592221  1.9568914

Number of Observations: 47
Number of Groups:
       B C %in% B
       6       12

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anova(mod11)
                 numDF denDF   F-value p-value
(Intercept)          1    29 162.95719  <.0001
CO2                  1     5   1.15108  0.3324
DROUGHT              1    29   5.53240  0.0257
TEMP                 1    29   0.04519  0.8331
CO2:DROUGHT          1    29   5.66686  0.0241
CO2:TEMP             1    29   1.88455  0.1803
DROUGHT:TEMP         1    29   0.03481  0.8533
CO2:DROUGHT:TEMP     1    29   4.06848  0.0530


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