Nothing
the data
data(Kidney, package='INLA') head(Kidney)
scale the response variable
Kidney$years = Kidney$time / 365.25
run the model
library("INLA") mod = inla( inla.surv(years, event) ~ age * sex + f(ID, model="iid", prior='pc.prec', param=c(0.5, 0.1)), family="weibullsurv", control.family = list(hyper=list( 'log alpha' = list( prior='loggamma', param=c(1,1))) ), data=Kidney, control.inla=list(h=0.001, int.strategy='grid'), control.compute = list(config=TRUE), verbose=FALSE)
results
knitr::kable(mod$summary.fixed, digits=3) knitr::kable(mod$summary.hyper, digits=3)
standard deviation
modSd = Pmisc::priorPost(mod) knitr::kable(modSd$summary, digits=3)
for(D in grep('^sd', names(modSd), value=TRUE)) { do.call(matplot, modSd[[D]]$matplot) do.call(legend, modSd$legend) }
do.call(matplot, modSd$alpha$matplot) do.call(legend, modSd$legend)
xSeq = seq(0,1/12,len=1000) myDens = Pmisc::sampleDensHaz(mod, xSeq, n=25) matplot(xSeq*365.25, myDens[,'dens',]/365.25, type='l', col = '#00000020', lty=1, xlab='days', ylab='dens')
data('meuse', package='sp') distBreaks = seq(0, 1, len=101) meuse$distCut = cut(meuse$dist, breaks=distBreaks, right=FALSE) meuse$soilFac = factor(meuse$soil, levels=1:3, labels=c('Calcerous','Non-Calcerous','Red Brick')) meuse[1:4,c('cadmium','elev','dist','distCut', 'soilFac')]
library("INLA", quietly=TRUE) mod = inla( cadmium ~ elev + soilFac + f(distCut, model='rw2', prior = 'pc.prec', param = c(0.01, 0.5), values = levels(distCut), constr=FALSE, extraconstr = list( A = model.matrix(~0+cut(0.25, distBreaks)), e=0 )), data = meuse, family = 'gamma', control.family = list(hyper=list( prec=list(prior = 'pc.prec', param = c(0.1, 0.5)))), verbose=FALSE )
standard deviation
mod$summary.random$distCut[is.na(mod$summary.random$distCut$mean),-1] = 0 matplot(distBreaks[-length(distBreaks)], exp(mod$summary.random$distCut[,paste0(c('0.5','0.025','0.975'), 'quant')]), ylab = 'relative rate', xlab='distance', type='l', lty=c(1,2,2), col='black', log='y') legend("bottomleft", lty=c(1,2), legend=c('median','95% CI'), bty='n')
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