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
>
Index: nlme/DESCRIPTION
===================================================================
--- nlme/DESCRIPTION (revision 7616)
+++ nlme/DESCRIPTION (working copy)
@@ -21,3 +21,4 @@
Encoding: UTF-8
License: GPL (>= 2) | file LICENCE
BugReports: https://bugs.r-project.org
+URL: https://svn.r-project.org/R-packages/trunk/nlme
\ No newline at end of file
Index: nlme/man/anova.lme.Rd
===================================================================
--- nlme/man/anova.lme.Rd (revision 7616)
+++ nlme/man/anova.lme.Rd (working copy)
@@ -61,7 +61,7 @@
}
\description{
When only one fitted model object is present, a data frame with the
- sums of squares, numerator degrees of freedom, denominator degrees of
+ numerator degrees of freedom, denominator degrees of
freedom, F-values, and P-values for Wald tests for the terms in the
model (when \code{Terms} and \code{L} are \code{NULL}), a combination
of model terms (when \code{Terms} in not \code{NULL}), or linear
@@ -71,7 +71,7 @@
log-likelihood, the Akaike Information Criterion (AIC), and the
Bayesian Information Criterion (BIC) of each object is returned. If
\code{test=TRUE}, whenever two consecutive objects have different
- number of degrees of freedom, a likelihood ratio statistic, with the
+ number of degrees of freedom, a likelihood ratio statistic with the
associated p-value is included in the returned data frame.
}
\value{
Index: nlme/man/lme.Rd
===================================================================
--- nlme/man/lme.Rd (revision 7616)
+++ nlme/man/lme.Rd (working copy)
@@ -117,8 +117,8 @@
(1982). The variance-covariance parametrizations are described in
Pinheiro and Bates (1996). The different correlation structures
available for the \code{correlation} argument are described in Box,
- Jenkins and Reinse (1994), Littel \emph{et al} (1996), and Venables and
- Ripley, (2002). The use of variance functions for linear and nonlinear
+ Jenkins and Reinsel (1994), Littell \emph{et al} (1996), and Venables and
+ Ripley (2002). The use of variance functions for linear and nonlinear
mixed effects models is presented in detail in Davidian and Giltinan
(1995).
@@ -136,7 +136,7 @@
Data", Journal of the American Statistical Association, 83,
1014--1022.
- Littel, R.C., Milliken, G.A., Stroup, W.W., and Wolfinger, R.D. (1996)
+ Littell, R.C., Milliken, G.A., Stroup, W.W., and Wolfinger, R.D. (1996)
"SAS Systems for Mixed Models", SAS Institute.
Pinheiro, J.C. and Bates., D.M. (1996) "Unconstrained
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