[Rd] long-standing documentation bug in ?anova.lme

Ben Bolker bbo|ker @end|ng |rom gm@||@com
Sun Jan 20 19:20:25 CET 2019

  Silence on this so far? Trying here one more time, otherwise I'll
submit it as a bug report ...

   Ben Bolker

On 2019-01-17 12:32 p.m., Ben Bolker wrote:
> 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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