%load_ext rpy2.ipython

%%R
library(survival)

addicts <- read.csv("demo_surv/addicts.csv", head=TRUE)

Y <- with(addicts, Surv(survtime, status == 1))

model_coxph <- coxph(Y ~ strata(clinic) + prison + mdosedata, data=addicts)
print(summary(model_coxph))

%%R
library(ggplot2)
library(data.table)

source('demo_surv/myggsurv.R')
model_clinic <- with(addicts, Surv(survtime, status==1) ~ clinic)
g_dose <- myggsurv(
  survfit(model_clinic),
  xlab='Time stay in the experiement (days)', ylab='Survival probability'
) + theme_classic(18)

g <- g_dose + theme(legend.position=c(0, 0), legend.justification=c(0, 0)) + 
  labs(title='KM curves', color='Categories') +
  scale_color_brewer(palette='Paired')
show(g)