[R] Problem extracting enough coefs from gam (mgcv package)

[Martijn Wieling]

Dear useRs,

Just to let you know, the results using mgcv 1.7-13 are OK. @Simon:
could you perhaps still let me know if the procedure I apply w.r.t.
assigning the labels to random slopes and intercepts is correct?

With kind regards,
Martijn

--
*******************************************
Martijn Wieling
http://www.martijnwieling.nl
wieling at gmail.com
+31(0)614108622
*******************************************
University of Groningen
http://www.rug.nl/staff/m.b.wieling
*******************************************


On Tue, Apr 24, 2012 at 11:22, Martijn Wieling <wieling at gmail.com> wrote:
> Hi Simon,
>
> Thanks for your quick reply. I'm now running the model again with mgcv
> 1.7-13. This might take some time (half a day or so) as the dataset is
> quite large (112,608 rows).
> The call I've used was (I've simplified some variable names):
>
> model = bam(LingDist ~ s(Lon,Lat) + VowelRatio + IsDem + WordLength +
> SpBirthYear + IsAragon + SpBirthYear_IsAragon + PopCnt +
> s(Word,bs="re") + s(Speaker,bs="re") + s(Word,SpBirthYear,bs="re") +
> s(Word,IsAragon,bs="re") + s(Word,PopCnt,bs="re") +
> s(Speaker,VowelRatio,bs="re") + s(Speaker,IsDem,bs="re") +
> s(Speaker,WordLength,bs="re") + s(Word,Tourism,bs="re") +
> s(Word,PopAge,bs="re")+ s(Word,PopIncome,bs="re") +
> s(Word,SpEdu,bs="re") + s(Word,SpBirthYear_IsAragon,bs="re"),
> data=dat)
>
> I'll post the results w.r.t. the random slopes.
>
> My procedure to assign labels when the number of slope estimates
> equals the number of words is correct: rownames(slopes) =
> unique(dat[,c("Word")])?
>
> With kind regards,
> Martijn
>
>
> On 24/04/12 10:50, Simon Wood wrote:
>> Martijn,
>>
>> It's a bit hard to know without seeing the full model structure, but
>> it's possible that the issue is related to an undesirable side effect of
>> the handling of identifiability constraints on smooth terms, prior to
>> mgcv 1.7-13: the standard side constraint approach used for smooths
>> could lead to unexpected constraints being applied to s(...,bs="re")
>> terms in some cases.
>>
>> So, could you sent me the gam call that generates the problem, and
>> perhaps try out if it still happens in 1.7-13?
>>
>> best,
>> Simon
>>
>> On 23/04/12 18:26, Martijn Wieling wrote:
>>> Dear useRs,
>>>
>>> I have used using the excellent mgcv package (version 1.7-12) to
>>> create a generalized additive model (gam) including random effects -
>>> represented with s(...,bs="re") - on the basis of dialect data.
>>>
>>> My model contains two random-effect factors (Word and Key - the latter
>>> representing a speaker) and I have added both random intercepts and
>>> various random slopes for these random-effect factors. There is no
>>> missing data in my dataset. When I try to extract the by-word random
>>> intercepts from my model, using coef(model), I find 357 values, equal
>>> to the number of words in my dataset. Using coef(model) I get
>>> uninformative names: s(Word,1) until s(Word,357), but I'm assuming (I
>>> might be wrong though?) that I can link the labels of the words to
>>> these values by obtaining the 357 labels from the original dataset:
>>> unique(dat[,c("Word")])
>>>
>>> Unfortunately, I cannot use this procedure to label the by-word random
>>> slopes, because I find a varying number of values for these (ranging
>>> from 346 to 356) which is always less than 357. (The number of
>>> by-speaker random slopes does equal the number of speakers, though.)
>>>
>>> Does anybody i) have an idea why I obtain fewer by-word random slopes
>>> than words, and/or ii) how I can link the random slopes which are
>>> present to the correct labels of the words?
>>>
>>> (I did not include the model as it is>300 MB in size, but let me know
>>> if this is necessary.)
>>>
>>> Any help would be greatly appreciated!
>>>
>>> With kind regards,
>>> Martijn Wieling
>>> University of Groningen
>>> http://www.martijnwieling.nl
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>