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@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@gmail.com>
>
>> Hi Ben:
>>
>> Thanks for your early Christmas present :)
>>
>> Best,
>> Dennis
>>
>> On Wed, Dec 22, 2010 at 5:40 AM, Ben Bolker <bbolker@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@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@gmail.com>  wrote:
>> > >>>>> On 10-12-21 12:58 PM, Dieter Menne wrote:
>> > >>>>>> Ben Bolker<bbolker@...>  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@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@r-project.org mailing list
>> > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> > >>>>>
>> > >
>> > >>
>> > _______________________________________________
>> > R-sig-mixed-models@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@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>>
>>        [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> R-sig-mixed-models@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>>
>

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