tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And
some names are misspelled in ?lme. I can submit all this stuff as a bug
report if that's preferred.
?anova.lme says:
When only one fitted model object is present, a data frame with
the sums of squares, numerator degrees of freedom, denominator
degrees of freedom, F-values, and P-values
The output of
fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
anova(fm1)
gives columns
numDF denDF F-value p-value
-- i.e. the sums of squares aren't there! (For fairly good reasons; lme
doesn't actually compute them internally, and it might not always be
straightforward to compute them, for more complex models. They would
mostly be useful for comparison with simpler, method-of-moments based
approaches like aov()). Federico Calboli pointed this out on r-help in
2004: https://stat.ethz.ch/pipermail/r-help/2004-May/051444.html
Two more points:
* the last sentence of the Description might need one fewer comma
[after "statistic"] or one more [after "p-value"].
* in ?lme, Littell's name is misspelled at least twice and Reinsel's
at least once.
Is there a publicly accessible SVN server for recommended packages (in
general) and nlme (in particular) anywhere?
cheers
Ben Bolker
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