From bbo|ker @end|ng |rom gm@||@com  Mon Jan 21 20:26:16 2019
From: bbo|ker @end|ng |rom gm@||@com (Ben Bolker)
Date: Mon, 21 Jan 2019 14:26:16 -0500
Subject: [Rd] long-standing documentation bug in ?anova.lme
In-Reply-To: <23621.38614.877168.877150@stat.math.ethz.ch>
References: <75c1ba9b-eec3-3beb-5c8f-f7f4cc445449@gmail.com>
 <23621.38614.877168.877150@stat.math.ethz.ch>
Message-ID: <a394bfaf-b391-aa65-a1f0-7da49f3b85f2@gmail.com>


  Here are relevant patches to address the various issues described
below.  Thanks for the SVN info!

  cheers
    Ben Bolker


On 2019-01-21 4:54 a.m., Martin Maechler wrote:
>>>>>> 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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[Rd] long-standing documentation bug in ?anova.lme
Ben Bolker