long-standing documentation bug in ?anova.lme

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long-standing documentation bug in ?anova.lme

bbolker
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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Re: long-standing documentation bug in ?anova.lme

bbolker

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

  cheers
   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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Re: long-standing documentation bug in ?anova.lme

Martin Maechler
In reply to this post by bbolker
>>>>> 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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Re: long-standing documentation bug in ?anova.lme

bbolker

  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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