demo/frailtypack_multivPenal.R

In frailtypack: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints

# Virginie Rondeau 2012-4-12 for optimx

options(digits=12)
if(!require("frailtypack"))stop("this test requires package frailtypack.")
if(!require("survival"))stop("this test requires survival.")
if(!require("boot"))stop("this test requires boot.")
if(!require("MASS"))stop("this test requires MASS.")
if(!require("survC1"))stop("this test requires survC1.")

cat("frailtypack test for multivariate model ...")

########################################################################
### MULTIVARIATE frailty model with gap times
########################################################################

data("dataMultiv")

modMultiv <- multivPenal(Surv(TIMEGAP,INDICREC)~ cluster(PATIENT) +
  v1 + v2 + event2(INDICMETA) + terminal(INDICDEATH),
  formula.Event2 =~ v1 + v2 + v3, formula.terminalEvent =~ v1,
  data = dataMultiv, hazard = "Weibull")

print(modMultiv, digits = 4)

########################################################################
### Figures
########################################################################
pdf(file="fig4.pdf", height = 3.6, width = 8.1)
par(mfrow = c(1, 4))
plot(modMultiv, type.plot = "Survival", event = "Recurrent1", main = "Recurrent1",
  conf.bands = TRUE, pos.legend = "topleft", cex.legend = 1.2, ylim = c(0, 1.2))
plot(modMultiv, type.plot = "Survival", event = "Recurrent2", main = "Recurrent2",
  conf.bands = TRUE, pos.legend = "topleft", cex.legend = 1.2, ylim = c(0, 1.2))
plot(modMultiv, type.plot = "Survival", event = "Terminal", main = "Terminal",
  conf.bands = TRUE, pos.legend = "topleft", cex.legend = 1.2, ylim = c(0, 1.2))
plot(modMultiv, type.plot = "Survival", event = "Both", main = "Both",
  conf.bands = TRUE, pos.legend = "topleft", cex.legend = 1, ylim = c(0, 1.2))