# load data bissau <- read.table("http://publicifsv.sund.ku.dk/~pka/epidata/bissau.txt", header = TRUE) library(survival) # new variables: binary variable for dtp, variable for age at exit, and log(time) bissau$dtpany <- 1 bissau$dtpany[bissau$dtp == 0] <- 2 bissau$outage <- bissau$age+bissau$fuptime bissau$logtime <- log(bissau$fuptime) # 1.: slide 32 fit <- coxph(Surv(fuptime, dead != 0) ~ (bcg == 1) + factor(agem), data = bissau) summary(fit) # 2.: slide 32 fit2 <- glm(dead ~ (bcg==1) + factor(agem), family = "poisson", offset = logtime, data = bissau) summary(fit2) exp(fit2$coefficients) # 3.: include DTP instead of BCG fit3 <- coxph(Surv(fuptime, dead != 0) ~ factor(dtpany) + factor(agem), data = bissau) summary(fit3) # 4.: add BCG fit4 <- coxph(Surv(fuptime, dead != 0) ~ (bcg == 1) + factor(dtpany) + factor(agem), data = bissau) summary(fit4) # 5.: age as time variable # use alternative formula for Surv: time, time2, event fit5 <- coxph(Surv(age, outage, dead != 0) ~ (bcg == 1) + factor(dtpany), data = bissau) summary(fit5)