>>>>> Ben Bolker
>>>>> on Thu, 17 Jan 2019 12:32:20 -0500 writes:
> 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.
We'd be grateful for patches, thank you Ben!
Notably for 'nlme' and 'foreign', both of which are maintained
by R-core (rather than individual R core or R Foundation
members) we've also encouraged that R's bugzilla be used for
non-trivial bug reports as that allows attached patches and
simple references too.
> Is there a publicly accessible SVN server for recommended packages (in
> general) and nlme (in particular) anywhere?
nlme's SVN is physically at the same place as the R sources
(here at ETH Zurich), with URL
https://svn.r-project.org/R-packages/trunk/nlme
in addition to 'nlme', at least 'foreign', 'mgcv' and
'cluster' are also maintained there.
Thank you for the question:
I do think "we" should add the corresponding svn URL to the
respective DESCRIPTION file.
OTOH, 'Matrix' has moved to R-forge a while ago .. and I'm
currently also not sure about the other Recommended packages
such as 'KernSmooth' or 'boot' .
Best,
Martin
Martin Maechler
ETH Zurich and R core team
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