[R] Problems with generating F-distr from lme()

[Andreas Nord]

Dear all, 

Using the data set and code below, I am interested in modelling how egg
temperature (egg.temp) 
is related to energy expenditure (kjday) and clutch size (treat) in
incubating birds using the
lme-function. I wish to generate the F-distribution for my model, and have
tried to do so using 
the anova()-function. However, in the resulting anova-table, the parameter
kjday has gone from 
being highly non-signiicant in the lme-expression, to all of a sudden being
significant at the 
0.05 level. At the same time, "treat" retains its original p-value. I've
tried to understand why,
but can't really figure it out. So, what has happened and why? How to best
interpret it?

Further, any advice on how to best generate F-distributions from the
lme-function is most appreciated.

Many thanks in advance, 
Andreas Nord
Sweden


  ind treat egg.temp  kjday
   79     2 27.33241 42.048
   42     2 30.73269 41.760
   10     2 29.54986 38.304
  206     2 31.78947 45.216
   23     2 29.69114 40.896
   24     2 36.48199 46.944
   45     2 29.76454 44.064
   29     2 30.56510 42.912
   78     2 27.71468 43.200
   79     3 25.88227 45.216
   42     3 30.95983 44.640
   10     3 28.13296 45.216
  206     3 31.77147 45.216
   23     3 27.50000 42.336
    5     3 28.16205 51.264
   24     3 34.69391 48.960
   45     3 28.79778 46.368
  368     3 26.18006 45.792
   29     3 29.75208 45.216
   78     3 25.28393 43.200
   44     3 23.32825 44.640


# lme-model with "individual" as random factor
> incub.lme2<-lme(egg.temp~kjday+treat,random=~1|ind,data=incub.df)

Fixed effects: egg.temp ~ kjday + treat 
                Value Std.Error DF   t-value p-value
(Intercept) 24.937897  6.662475 11  3.743038  0.0032
kjday        0.108143  0.152540  7  0.708945  0.5013
treat3      -1.506605  0.485336  7 -3.104254  0.0172


#generating an anova table to get the F-distribution
> anova(incub.lme2)
            numDF denDF   F-value p-value
(Intercept)     1    11 1176.6686  <.0001
kjday           1     7    5.7060  0.0483
treat           1     7    9.6364  0.0172
> 

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