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 wiel...@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 <wiel...@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. >>> ______________________________________________ R-help@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.
