# udpateRidge.R
#
# Fitting cox model using ridge regression with factor-level covariates
# - Using chipmanj/survival github

library(devtools)

cat("\nInstalling survival from chipmanj/survival github\n\n")
devtools::install_github("chipmanj/survival")
library(survival)

# Lung dataset
cat("\nUsing lung dataset.\n")
cat("\nSetting ph.ecog and inst to factor variables.\n")
cat("\nKeeping age as numeric.\n")
# table(lung$ph.ecog)
# table(lung$ph.karno)
# table(lung$inst)

lung$ph.ecog  <- as.factor(lung$ph.ecog)
lung$inst     <- as.factor(lung$inst)

update0 <- survival::coxph(Surv(time,status)~age + ph.ecog + inst,                data = lung)
update1 <- survival::coxph(Surv(time,status)~age + ridge(ph.ecog,inst,theta=0),   data = lung)
update2 <- survival::coxph(Surv(time,status)~age + ridge(ph.ecog,inst,theta=100), data = lung)



cat("\n\n---\n\nModel 0:   Cox model adjusting for factor and non-factor covariates.\n No ridge regression.\n\n")
update0

cat("\n\n--\n\nModel 1: Cox model adjusting for factor and non-factor covariates.\n Ridge applied but with theta = 0 (should match Model 0).\n")
update1

cat("\n\n--\n\nModel 2: Cox model adjusting for factor and non-factor covariates.\n Ridge applied with theta = 100 (just for a frame of reference).\n\n")
update2