>>>>> 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/nlmein 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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