[R] Individual log likelihoods of nlsList objects.

Martin Maechler maechler at stat.math.ethz.ch
Thu Jul 1 23:12:31 CEST 2004

>>>>> "Ken" == Ken Kelley <kkelley at nd.edu>
>>>>>     on Thu, 1 Jul 2004 14:23:16 -0500 writes:

    Ken> Hello all.
    Ken> I was wondering if the logLike.nls() and logLike.nlme() functions are still
    Ken> being used. 
no, but the correctly spelled ones,   logLik.nls and logLik.nlme

    Ken> Neither function seems to be available in the most recent
    Ken> release of R (1.9.1). 

how do you know?

    Ken> The following is contained in the help file for
    Ken> logLik(): "classes which already have methods for this
    Ken> function include: 'glm', 'lm', 'nls' and 'gls', 'lme'
    Ken> and others in package 'nlme'." 

Hence do rather believe the documentation ....

    Ken> Thus, I was expecting
    Ken> that logLik.nls() and logLik.nlme() could be used for
    Ken> objects of the nls and nlme class, respectively. 

They *are* used whenever you (or your code indirectly) call
logLik(.) on  "nls" or "nlme" objects respectively.

You were never to call these directly, and you this has been
discouraged a bit more as a side effect of the introduction of
name spaces for all "core" and recommended (and quite a few more
CRAN and bioconductor) packages.

You definitely need to learn about Classes and Methods
("S3" in this case) in R {or the S language in general},
and read the article about "Namespaces" in R-news, or (more
technical), Luke Tierney's pages on this.

If you want to see them use, e.g.,


    Ken> Are these functions no longer needed because logLike()
    Ken> subsumes logLike.nls() and logLike.nlme() as special
    Ken> cases? Did/does logLike.nls() and logLike.nlme() have
    Ken> any advantages above and beyond logLike() when applying
    Ken> them to nls and nlme objects?

    Ken> On a related note, is there a way to get the log likelihoods of each
    Ken> individual from an nlsList object? 

    Ken> On p. 349 of Pinheiro and Bates (2000) the logLik() function is said to give
    Ken> the sum of the individual nls log-likelihoods. However,
    Ken> logLike(some.nlsList.object) does not work for me (even when there are no
    Ken> NAs). Any ideas?

if you are insisting on typo-ing you will have more problems
with all versions of S  ;-)
or did you try logLik( <...> ) ?

In any case use, (small) reproducible examples for these.
Have you read the posting guide, mentioned at the tail of this message?


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