Dear Prof. Wood, Thank you for your reply!
Best, Fotis On Wed, May 18, 2016 at 12:05 PM, Simon Wood <simon.w...@bath.edu> wrote: > Dear Fotis, > > The test is a randomization test, based on comparing differences of > residuals, ordered with respect to the covariate of the smooth, to > differences of residuals in randomized order. Random effect terms are > excluded because there is not basis size to choose. Currently smooths with > factor by variables are also excluded for reasons of maintainer laziness, > as this would require special case code to exclude the covariate values > that are irrelevant given the factor level. Sorry about that. > > My guess is that you don't have a problem here anyway, given the fairly > low edfs relative to the basis dimension. In general as a double check I > would plot the residuals against ctrial, colour coded by level of igc, just > to check that there doesn't seem to be missed pattern in them. However with > binary residuals you are unlikely to see much. > > best, > Simon > > > On 17/05/16 20:39, Fotis Fotiadis wrote: > >> Hello all >> >> I am using bam for a mixec-effects logistic regression model: >> >> b0<-bam(acc~ 1 + igc + s(ctrial, by=igc) + s(sbj, bs="re") + s(ctrial, >> sbj, >> bs="re") , data=data, family=binomial) >> >> summary(b0) >>> >> Family: binomial >> Link function: logit >> >> Formula: >> acc ~ 1 + igc + s(ctrial, by = igc) + s(sbj, bs = "re") + s(ctrial, >> sbj, bs = "re") >> >> Parametric coefficients: >> Estimate Std. Error z value Pr(>|z|) >> (Intercept) 2.8334 0.2030 13.955 < 2e-16 *** >> igcPA.pseudo 0.4692 0.1285 3.650 0.000262 *** >> igcCAT.ideo 0.3276 0.2906 1.127 0.259734 >> igcCAT.pseudo 0.6701 0.2945 2.275 0.022888 * >> --- >> 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):igcPA.ideo 3.827 4.733 295.0 < 2e-16 *** >> s(ctrial):igcPA.pseudo 3.317 4.110 356.1 < 2e-16 *** >> s(ctrial):igcCAT.ideo 3.979 4.911 308.6 < 2e-16 *** >> s(ctrial):igcCAT.pseudo 4.937 5.974 383.8 < 2e-16 *** >> s(sbj) 54.326 62.000 3032.8 < 2e-16 *** >> s(ctrial,sbj) 43.045 62.000 2706.6 1.31e-08 *** >> --- >> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 >> >> R-sq.(adj) = 0.362 Deviance explained = 38.9% >> fREML = 25436 Scale est. = 1 n = 18417 >> >> >> I want to know if the wigglyness of the smooths [s(ctrial, by=igc)] is >> appropriate, so I used the gam.check() function. The values though for >> k-index and p-value are NAs: >> >> gam.check(b0) >>> >> Method: fREML Optimizer: perf newton >> full convergence after 5 iterations. >> Gradient range [-7.60152e-08,8.12795e-06] >> (score 25436.12 & scale 1). >> Hessian positive definite, eigenvalue range [0.6271375,24.46625]. >> Model rank = 168 / 168 >> >> Basis dimension (k) checking results. Low p-value (k-index<1) may >> indicate that k is too low, especially if edf is close to k'. >> >> k' edf k-index p-value >> s(ctrial):igcPA.ideo 9.00 3.83 NA NA >> s(ctrial):igcPA.pseudo 9.00 3.32 NA NA >> s(ctrial):igcCAT.ideo 9.00 3.98 NA NA >> s(ctrial):igcCAT.pseudo 9.00 4.94 NA NA >> s(sbj) 64.00 54.33 NA NA >> s(ctrial,sbj) 64.00 43.04 NA NA >> >> Does anyone know why is this? >> >> Thank you in advance for your time, >> Fotis >> >> P.S. I am using RStudio Version 0.99.896, R 3.3.0, and mgcv package >> version >> 1.8.12. >> -- >> 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. >> >> < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > >> Απαλλαγμένο >> από ιούς. www.avast.com >> < >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail >> > >> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> [[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. >> > > > -- > 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. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Απαλλαγμένο από ιούς. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2> [[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.