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R code for chapter 7

Section 7.3

Create of a dummy day variable.

dummies <- c(1:20, rep(20, max(my.sir.data$time) - 20))

Then, we extend the data set.

sir.data.ext <- by(my.sir.data, my.sir.data$id, function(x) {
    temp <- x[rep(1, x$time), ]
    temp$day <- dummies[1:nrow(temp)]
    status <- c(rep("cens", nrow(temp) - 1),
                as.character(temp$to[1]))
    temp$status <- factor(ifelse(status == "cens", 0, status),
                          levels = c(0, 1, 2))
    temp
    })
sir.data.ext <- do.call(rbind, sir.data.ext)

head(sir.data.ext, 4L)

Fit of a multinomial logit model using the nnet package

require(nnet)
fit.multinom <- multinom(status ~ pneu + factor(day),
                         sir.data.ext)
coef(fit.multinom)[, "pneu"]