# A short example of use of Addregmc:
# <harald.fekjar@basalmed.uio.no>, 2001-12-01

# 1) Install "addreg version 2" (beta)
# 2) Use source("path/addregmc.R") to read 
#    the source code for Addregmc
#    (where "path" is the path to the folder that contains the downloaded file)

# Example of analysis as given in:
# Odd Aalen, Ørnulf Borgan and Harald Fekjær (2001)
# "Covariate adjustment of event histories estimated from Markov chains: The additive approach"
# Biometric, vol. 57, 108-116


# Run Additive hazard regression on each transition:
overg01 <- addreg(Surv(TPu,DP)~Z10+newZ1+newZ2+newZ1Z2,testobs=F,estcovar=T,data=bmtdata)
overg12 <- addreg(Surv(TPu,T2u,D3)~low+high+Z8+newZ1+newZ2,testobs=F,estcovar=T,data=bmtdata[bmtdata$DP==1,])
overg02 <- addreg(Surv(t02,s02)~1,testobs=F,estcovar=T,data=bmtdata)

# Define each transition:
overg01.mce <- addregmce(overg01,from=1,to=2)
overg12.mce <- addregmce(overg12,from=2,to=3)
overg02.mce <- addregmce(overg02,from=1,to=3)

# Choose covariates:
covardata <- data.frame(Z10=1,low=0,high=1,Z8=0,newZ1=0,newZ2=0,newZ1Z2=0)

# Run addregmc / estimate:
addregmc.res <- addregmc(list(overg01.mce,overg12.mce,overg02.mce),covardata,estcovar=F)

# Check the transitions:
addregmc.res

# Get estimates:
summary(addregmc.res)
summary(addregmc.res,esttime=12,confint=T)

# Plot results:
plot(addregmc.res)
plot(addregmc.res,fromto=c(1,2),stoptime=55)