[R-sig-ME] a problem with lme4_0.999375-0?

[vito muggeo]

Dear Douglas,
Many thanks for finding out the error and fixing it.

Yes the results mach those from the book and the code comes from

http://www.stat.columbia.edu/~gelman/arm/examples/radon/radon_setup.R

I look forward to dowloading the new version,
many thanks again
all the best,

vito



Douglas Bates ha scritto:
> Thanks again for spotting that problem, Vito.  Because of the need for
> generality, the C code in the mer_postVar function ends up being
> fairly involved.  Once I traced through the example, however, I could
> readily spot that I was running a loop over the levels of each of the
> grouping factors but I wasn't using that loop index to change the
> input values. Therefore, the result was exactly what you observed,
> those values all ended up corresponding to the results for the first
> level of the grouping factor.
> 
> Do the results in the enclosed file look like what you expect? I
> rewrote the code that you sent because I found some aspects of that
> code to be rather frightening.  (Is that code directly from the book?)
> 
> I will commit the changes to the SVN archive on R-forge by this
> evening (North American time).  I have been tearing apart my code
> again and right now I have lmer and glmer running but nlmer is having
> problems.  I'll close out the bug report after I commit the changes.
> 
> On Jan 17, 2008 7:42 AM, Douglas Bates <bates at stat.wisc.edu> wrote:
>> Thanks for the thorough bug report, Vito.  I have added it to the bug
>> report list at http://r-forge.r-project.org/projects/lme4 (under the
>> Tracker tab).  Those with R-forge logins can add bug reports there
>> directly if they wish.  Those who do not have an R-forge login should
>> consider getting one.
>>
>> I appreciate the example.  It will make it a lot easier to isolate the problem.
>>
>>
>> On Jan 17, 2008 5:39 AM, vito muggeo <vmuggeo at dssm.unipa.it> wrote:
>>> Dear all,
>>>
>>> I'm running data from "Gelman&Hill Data Analysis Using regression..
>>> pag259-261" (you can get data by running the code below). In particular
>>> I'm interested in getting variances of the predictions of the random
>>> intercepts. I get "right" (as compared with those from the book) results
>>>   using lme 0.99875-9 (downloaded from CRAN).
>>>
>>> However using the latest lme4_0.999375-0 obtained via
>>>
>>> install.packages("lme4", repos = "http://r-forge.r-project.org")
>>>
>>> the variances of the predictions are wrong..(they are constant
>>> regardless of different cluster sizes. You can check this running the
>>> code below..
>>>
>>> Many thanks,
>>> vito
>>>
>>>
>>> srrs2 <-
>>> read.table("http://www.stat.columbia.edu/~gelman/arm/examples/radon/srrs2.dat",
>>>     header=T, sep=",")
>>>
>>> mn <- srrs2$state=="MN"
>>> radon <- srrs2$activity[mn]
>>> log.radon <- log (ifelse (radon==0, .1, radon))
>>> floor <- srrs2$floor[mn]       # 0 for basement, 1 for first floor
>>> n <- length(radon)
>>> y <- log.radon
>>> x <- floor
>>> # get county index variable
>>> county.name <- as.vector(srrs2$county[mn])
>>> uniq <- unique(county.name)
>>> J <- length(uniq)
>>> county <- rep (NA, J)
>>> for (i in 1:J){
>>>    county[county.name==uniq[i]] <- i
>>> }
>>> library(arm)
>>>
>>> M1<-lmer(y~1+x+(1|county))
>>> ranef(M1)[[1]][1:10,] #OK
>>>
>>> se.ranef(M1)[[1]][1:10,] #wrong results: they are constant!!!??!!!
>>>
>>>
>>>
>>>  > sessionInfo()
>>> R version 2.6.1 (2007-11-26)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=Italian_Italy.1252;LC_CTYPE=Italian_Italy.1252;LC_MONETARY=Italian_Italy.1252;LC_NUMERIC=C;LC_TIME=Italian_Italy.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] foreign_0.8-23    car_1.2-7         arm_1.1-1
>>> R2WinBUGS_2.1-6   coda_0.13-1       lme4_0.999375-0   Matrix_0.999375-4
>>> lattice_0.17-2
>>> [9] MASS_7.2-38
>>>
>>> loaded via a namespace (and not attached):
>>> [1] grid_2.6.1
>>>
>>>
>>> --
>>> ====================================
>>> Vito M.R. Muggeo
>>> Dip.to Sc Statist e Matem `Vianelli'
>>> Università di Palermo
>>> viale delle Scienze, edificio 13
>>> 90128 Palermo - ITALY
>>> tel: 091 6626240
>>> fax: 091 485726/485612
>>>
>>> _______________________________________________
>>> R-sig-mixed-models at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>

-- 
====================================
Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612