[R-sig-ME] lmer() - no applicable method for 'profile'

Douglas Bates bates at stat.wisc.edu
Wed Dec 29 02:03:43 CET 2010


Thanks for checking that out, Dennis.  I will produce updated scripts
etc. if I ever finish my grading of project reports.  (Well I have to
finish them because the grades are due tomorrow.)

The env stuff has gone away to be replaced by reference classes,
something that John Chambers added to R-2.12.0.  They are based on
environments but indirectly.

On Tue, Dec 28, 2010 at 6:20 PM, Dennis Murphy <djmuser at gmail.com> wrote:
> Hi:
>
> I decided to check Sam's claims but couldn't reproduce them, at least in
> Chapter 1. Sam, please check out the sessionInfo() and see if you have the
> same packages loaded with the same versions. [I autoload ggplot2, lattice
> and sos; of these, only lattice is relevant to lme4(a).]
>
> OTOH, some glitches did appear when I ran the code chunks from Chapter 1 of
> the draft book:
>
> (i) env() could not be found (missing package, maybe?);
> (ii) running splom() opens up the browser.
>
> Abridged transcript:
>
> ####### Chunk 16, Ch. 1:
>
> env(fm1ML)$Lambda
> Error: could not find function "env"
>
> ####### Chunk 17 (ditto 18)...which makes sense given the result of 16:
>
>> print(image(env(fm1)$Lambda, sub=NULL, xlab=NULL, ylab=NULL))
> Error in print(image(env(fm1)$Lambda, sub = NULL, xlab = NULL, ylab = NULL))
> :
>  error in evaluating the argument 'x' in selecting a method for function
> 'print'
>
>
> ####### Chunks 19 and 20 work, as does everything through chunk 26:
>> pr1 <- profile(fm1ML)
>> print(xyplot(pr1, aspect = 1.3))
>
>
> ####### Chunk 27 (and by extension, 28):
> ####### calling splom() opens up the browser
> ####### the plot seems to render correctly, though
>
>> print(splom(pr1))
> Called from: function (x, y, groups, subscripts, i, j, ...)
> {
>    tr <- traces[[j]][[i]]
>    browser()
>    grid::pushViewport(viewport(xscale = c(-1.07, 1.07) * mlev,
>        yscale = c(-1.07, 1.07) * mlev))
>    dd <- sapply(current.panel.limits(), diff)/50
>    psij <- predict(tr$sij)
>    ll <- tr$ll
>    panel.grid(h = -1, v = -1)
>    llines(psij$y, psij$x, ...)
>    llines(predict(tr$sji), ...)
>    with(ll$tki, lsegments(y - dd[1], x, y + dd[1], x, ...))
>    with(ll$tkj, lsegments(x, y - dd[2], x, y + dd[2], ...))
>    for (k in seq_along(levels)) llines(ll$pts[k, , ], ...)
>    grid::popViewport(1)
> }(x = c(3.51976904877845, 4.41462262361588), y = c(0, 145.71944617029
> ), groups = NULL, subscripts = 1:2, i = 1L, j = 2L)
> Browse[1]>
>
>  <message iterates three times as I hit CRs to advance the browser and then
> exits without error>
>
> Everything else in Chapter 1 seems to work fine, though, including profile()
> and its plots.
>
>> sessionInfo()
> R version 2.12.1 Patched (2010-12-18 r53869)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  grid
> methods
> [9] base
>
> other attached packages:
>  [1] lme4a_0.999375-59  MatrixModels_0.2-1 minqa_1.1.13
> Rcpp_0.9.0
>  [5] Matrix_0.999375-46 sos_1.3-0          brew_1.0-4
> lattice_0.19-13
>  [9] ggplot2_0.8.9      proto_0.3-8        reshape_0.8.3
> plyr_1.2.1
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-6 nlme_3.1-97     stats4_2.12.1   tools_2.12.1
>
> Hope this is of some help.
> Dennis
>
> On Tue, Dec 28, 2010 at 9:22 AM, sam steyaert <samsteyaert at gmail.com> wrote:
>
>> Dear all,
>>
>> I am relatively new to this list. I would like to use the 'profile'
>> function of the lme4a package. I followed the instructions by Ben Bolker.
>>
>> "Yes.  For now I think
>>
>> install.packages("lme4a",repos="http://www.math.mcmaster.ca/bolker/R")
>>
>> or
>> manually getting
>> <
>> http://www.math.mcmaster.ca/bolker/R/bin/windows/contrib/2.12/lme4a_0.999375-59.zip
>> >
>>  should work. "
>>
>> I still get the error message as mentioned before:
>>
>> "Error in UseMethod("profile") :
>>   no applicable method for 'profile' applied to an object of class "mer" "
>>
>> ...even if lme4a was already installed:
>>
>> " install.packages("lme4a",repos="http://www.math.mcmaster.ca/bolker/R")
>> Installing package(s) into ‘d:\Documents and Settings\samst\My
>> Documents/R/win-library/2.12’
>> (as ‘lib’ is unspecified)
>> Warning: package 'lme4a' is in use and will not be installed"
>>
>> Can anyone help me further with this?
>>
>> Kind regards,
>>
>> Sam Steyaert
>>
>>
>>
>> 2010/12/22 Dennis Murphy <djmuser at gmail.com>
>>
>>> Hi Ben:
>>>
>>> Thanks for your early Christmas present :)
>>>
>>> Best,
>>> Dennis
>>>
>>> On Wed, Dec 22, 2010 at 5:40 AM, Ben Bolker <bbolker at gmail.com> wrote:
>>>
>>> > -----BEGIN PGP SIGNED MESSAGE-----
>>> > Hash: SHA1
>>> >
>>> >   Yes.  For now I think
>>> >
>>> > install.packages("lme4a",repos="http://www.math.mcmaster.ca/bolker/R")
>>> >
>>> > or
>>> >
>>> > manually getting
>>> >
>>> > <
>>> >
>>> http://www.math.mcmaster.ca/bolker/R/bin/windows/contrib/2.12/lme4a_0.999375-59.zip
>>> > >
>>> >
>>> >  should work.
>>> >
>>> >
>>> >
>>> >
>>> > On 10-12-22 03:56 AM, lancelot wrote:
>>> > > I have a "page not found" message for this URL.
>>> > >
>>> > > Renaud
>>> > >
>>> > > Le 21/12/2010 19:26, Ben Bolker a écrit :
>>> > > On 10-12-21 01:25 PM, Andrew Dolman wrote:
>>> > >>>> That's an lme4 binary that you linked to on r-forge. Your hosted
>>> > >>>> binary work though cheers.
>>> > >>>>
>>> > >>>> Andy.
>>> > >>>>
>>> > >>>>
>>> > >>>> andydolman at gmail.com
>>> > >>>>
>>> > >
>>> > >   Oops.  How about
>>> > >
>>> > > <
>>> >
>>> https://r-forge.r-project.org/bin/windows/contrib/latest/lme4a_0.999375-59.zip
>>> > >
>>> > >
>>> > >
>>> > >    ?
>>> > >
>>> > >
>>> > >>>>
>>> > >>>>
>>> > >>>> On 21 December 2010 19:11, Ben Bolker<bbolker at gmail.com>  wrote:
>>> > >>>>> On 10-12-21 12:58 PM, Dieter Menne wrote:
>>> > >>>>>> Ben Bolker<bbolker at ...>  writes:
>>> > >>>>>>
>>> > >>>>>>>
>>> > >>>>>>>    You need to be using the development version (lme4a).
>>> > >>>>>>>    install.packages("lme4a",repos="http://r-forge.r-project.org
>>> ")
>>> > >>>>>>>    if that fails, try posting sessionInfo()
>>> > >>>>>>
>>> > >>>>>> This fails on Windows, and has been reported several times
>>> already
>>> > >>>>>> and confirmed
>>> > >>>>>> as "temporary broken".
>>> > >>>>>>
>>> > >>>>>> Is there a way to get the Windows build updated?
>>> > >>>>>>
>>> > >>>>>> Dieter
>>> > >>>>>>
>>> > >>>>>> _______________________________________________
>>> > >>>>>> R-sig-mixed-models at r-project.org mailing list
>>> > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> > >>>>>
>>> > >>>>>   (Resending to list)
>>> > >>>>>
>>> > >>>>>   I've put up a recent binary (32-bit Windows, R 2.12.x): try
>>> > >>>>>
>>> > >>>>> install.packages("lme4a",repos="
>>> http://www.math.mcmaster.ca/bolker/R
>>> > ")
>>> > >>>>>
>>> > >>>>> and let me know if it works.
>>> > >>>>>
>>> > >>>>> I'm a little puzzled that install.packages() doesn't work from
>>> > R-forge,
>>> > >>>>> there seems to be a binary version there: can you download
>>> > >>>>> <
>>> >
>>> https://r-forge.r-project.org/bin/windows/contrib/latest/lme4_0.999375-37.zip
>>> > >
>>> > >>>>>
>>> > >>>>>   ... ?
>>> > >>>>>
>>> > >>>>>   Ben
>>> > >>>>>
>>> > >>>>> _______________________________________________
>>> > >>>>> R-sig-mixed-models at r-project.org mailing list
>>> > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> > >>>>>
>>> > >
>>> > >>
>>> > _______________________________________________
>>> > R-sig-mixed-models at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> > >>
>>> >
>>> > -----BEGIN PGP SIGNATURE-----
>>> > Version: GnuPG v1.4.10 (GNU/Linux)
>>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>> >
>>> > iEYEARECAAYFAk0R/+sACgkQc5UpGjwzenOqoACghl1TkqQiCjctGxzN8OyirM2+
>>> > LqEAoIgEVJYyxpXkWonqgKaA7DC34P6G
>>> > =S50A
>>> > -----END PGP SIGNATURE-----
>>> >
>>> > _______________________________________________
>>> > R-sig-mixed-models at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> >
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
>>>
>>> _______________________________________________
>>> R-sig-mixed-models at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>
>>>
>>
>
>        [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>




More information about the R-sig-mixed-models mailing list