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
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 >
>>>>> 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
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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