Survival Analysis in Leukemia Patients Dataset in R (Practical)

 library(survival)
library(KMsurv)
library(MASS)

 setwd("C:\\Users\\LENOVO\\Desktop\\leukemia")
leukemia <- read.delim("leukemia.txt", header = TRUE, sep = " ")
leukemia

 #### KAPLAN-MEIER
km= Surv(time = leukemia$Survtime, event = leukemia$Binary)
km
km1= survfit(km~1, data = leukemia)
summary(km1)

 #### ESTIMATION OF CUMULATIVE HAZARD
Km2= survfit(coxph(km~1), type="aalen")
summary(Km2)
plot(Km2, main=expression(paste("Kaplan-Meier-estimate ", hat(Lambda)(t))), 
xlab="time(weeks)", ylab="cumulative hazard", fun="cumhaz", lwd=2)

 #### KAPLAN-MEIER for both group of the AG variables
km3= survfit(km~AG, data = leukemia)
print(km3)
summary(km3)

 ### Logrank Test
survdiff(km ~ AG,data=leukemia,rho=0)
  
### Using Cox-PH to model the survival time
fit = coxph(Surv(Survtime, Binary) ~ AG + WBC ,data=leukemia ,ties="breslow")
temp = cox.zph(fit)
print(fit)
plot(temp)

 ### Transform on a natural log scale using Cox-PH
fit1 = coxph(Surv(Survtime, Binary) ~ AG + log(WBC) ,data=leukemia ,ties="breslow")
temp1 = cox.zph(fit1)
print(fit1)
plot(temp1)


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