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.
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