[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
>>> > >>
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