Dear Prof. Wood Thank you, again, for your immediate response.
Best, Fotis On Mon, May 23, 2016 at 4:32 PM, Simon Wood <simon.w...@bath.edu> wrote: > Q1: It looks like the model is not fully identifiably given the data and > as a result igcCAT.ideo has been set to zero - there is no sensible test to > conduct with such a term, hence the NAs in the test stat an p-value fields. > > Q2: A separate (centred) smooth is estimated for each level of igc. If you > want a baseline (igcCAT.pseudo) smooth, and difference smooths for the rest > of the levels of igc then you need to set igc to be an ordered factor, and > use something like... > ~ igc + s(ctrial) + s(ctrial,by=igc) > - see section on `by' variables in ?gam.models. > > best, > Simon > > > On 22/05/16 23:29, Fotis Fotiadis wrote: > >> Hallo all >> >> I am using a gam model for my data. >> >> m2.4<-bam(acc~ 1 + igc + s(ctrial, by=igc) + shape + s(ctrial, by=shape) + >> s(ctrial, sbj, bs = "fs", m = 1) , data=data, family=binomial) >> >> igc codes condition and there are four levels (CAT.pseudo, >> CAT.ideo,PA.pseudo, PA.ideo), and shape is a factor (that cannot be >> considered random effect) with four levels too (rand21, rand22, rand23, >> rand30). >> >> Here is the summary of the model >> >>> summary(m2.4) >>> >> Family: binomial >> Link function: logit >> >> Formula: >> acc ~ 1 + igc + s(ctrial, by = igc) + shape + s(ctrial, by = shape) + >> s(ctrial, sbj, bs = "fs", m = 1) >> >> Parametric coefficients: >> Estimate Std. Error z value Pr(>|z|) >> (Intercept) 3.5321 0.1930 18.302 < 2e-16 *** >> igcCAT.ideo 0.0000 0.0000 NA NA >> igcPA.ideo -0.3650 0.2441 -1.495 0.1348 >> igcPA.pseudo -0.2708 0.2574 -1.052 0.2928 >> shaperand22 -0.1390 0.1548 -0.898 0.3693 >> shaperand23 0.3046 0.1670 1.823 0.0682 . >> shaperand30 -0.5839 0.1163 -5.020 5.16e-07 *** >> --- >> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 >> >> Approximate significance of smooth terms: >> edf Ref.df Chi.sq p-value >> s(ctrial):igcCAT.pseudo 3.902 4.853 74.787 1.07e-14 *** >> s(ctrial):igcCAT.ideo 2.293 2.702 13.794 0.001750 ** >> s(ctrial):igcPA.ideo 1.000 1.000 11.391 0.000738 *** >> s(ctrial):igcPA.pseudo 3.158 3.815 20.411 0.000413 *** >> s(ctrial):shaperand21 2.556 3.316 31.387 1.46e-06 *** >> s(ctrial):shaperand22 1.000 1.000 0.898 0.343381 >> s(ctrial):shaperand23 2.304 2.850 6.144 0.118531 >> s(ctrial):shaperand30 4.952 5.947 27.806 0.000144 *** >> s(ctrial,sbj) 221.476 574.000 1502.779 < 2e-16 *** >> --- >> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 >> >> Rank: 652/655 >> R-sq.(adj) = 0.405 Deviance explained = 43.9% >> fREML = 24003 Scale est. = 1 n = 18417 >> >> >> I am not sure how this model works, but I guess it creates four smooths >> for >> each level of condition, and four smooths for each level of shape. >> >> There is also the intercept of the model, set at the reference level of >> condition (CAT.pseudo) and at the reference level of shape (rand21). Each >> parametric term represents the difference of each level of each of the two >> factors from the intercept. >> >> I have two questions >> >> Q1: >> Does anyone now why I get NA results in the second line of the parametric >> terms? >> >> Q2: >> The term igcCAT.ideo denotes the difference in the intercept between >> (A): condition=igcCAT.ideo, and >> (B): (condition=igcCATpseudo ) &(shape=rand21). >> But what is the value (level) of shape for (A)? >> Is it the reference level? Or is it, perhaps, the "grand mean" of the >> shape >> variable? >> >> >> Thank you in advance for your time, >> Fotis >> >> >> > > -- > Simon Wood, School of Mathematics, University of Bristol BS8 1TW UK > +44 (0)117 33 18273 http://www.maths.bris.ac.uk/~sw15190 > > -- PhD Candidate Department of Philosophy and History of Science University of Athens, Greece. http://users.uoa.gr/~aprotopapas/LLL/en/members.html#fotisfotiadis Notice: Please do not use this account for social networks invitations, for sending chain-mails to me, or as it were a facebook account. Thank you for respecting my privacy. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
