[R] Problem with simple random slope in gam and bam (mgcv package)

[Simon Wood]

Martijn,

This was a problem in summary.gam handling "re" terms with largish 
datasets: I've uploaded a fix for this in mgcv_1.7-11. Hopefully on cran 
in the next few days.

best,
Simon

On 09/11/11 12:41, Martijn Wieling wrote:
> Dear useRs,
>
> This is the first time I post to this list and I would appreciate any
> help available. I've used the excellent mgcv package for a while now
> to investigate geographical patterns of language variation, and it has
> has always worked without any problems for me. The problem below
> occurs using R 2.14.0 (both 32 and 64 bit versions in Windows and the
> 64 bit version in Unix) and mgcv (both version 1.7-10 and 1.7-6).
>
> In my (simplified) model predicting pronunciation distance I'd like to
> include a random slope per Participant for a binary value (IsDem)
> which stores a word-specific characteristic. I load the data
> (available at http://www.martijnwieling.nl/dat.csv) and run the model
> as follows:
>
>> library(mgcv) # version 1.7-10, but problem also occurs with earlier versions (e.g., 1.7-6)
>> dat = read.csv('dat.csv',header=T) # data available at: http://www.martijnwieling.nl/dat.csv
>> dim(dat) # the original dataset is larger, but the problem also occurs in this subset
> [1] 20000     4
>> model = bam(PronDist ~ s(Participant,IsDem,bs="re"), data=dat)
>> print(model) # works fine
>> summary(model, freq=T) # works fine
>> summary(model) # the Bayesian p-value estimation does not work:
> Error in eigen(B, symmetric = TRUE) : infinite or missing values in 'x'
>
> I obviously am interested in more complex models, but whenever I
> include any binary value as a by-word or by-participant random slope I
> get the same error. I've tried to locate the error and it appears to
> occur in the function pinvXVX in the block which 'deals with the
> fractional part of the pinv'.
>
> Any help would be appreciated!
>
> With kind regards,
>
> Martijn Wieling
> University of Groningen
> http://www.martijnwieling.nl
>
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-- 
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603               http://people.bath.ac.uk/sw283