From bbo|ker @end|ng |rom gm@||@com  Thu Jan 17 18:32:20 2019
From: bbo|ker @end|ng |rom gm@||@com (Ben Bolker)
Date: Thu, 17 Jan 2019 12:32:20 -0500
Subject: [Rd] long-standing documentation bug in ?anova.lme
Message-ID: <75c1ba9b-eec3-3beb-5c8f-f7f4cc445449@gmail.com>

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



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