Survival_Analysis.Rmd

---
title: "Basics of Survival analysis: 
the R survival package" 
author: "D.-L. Couturier"
date: '`r format(Sys.time(), "Last modified: %d %b %Y")`'
output:
  html_document:
    theme: united 
    highlight: tango
    code_folding: show    
    toc: true           
    toc_depth: 2       
    toc_float: true     
    fig_width: 8
    fig_height: 6
---


<!--- rmarkdown::render("/Volumes/Files/courses/cruk/SurvivalAnalysis/201907/tex/sc/Survival_Analysis.Rmd") --->
<!--- rmarkdown::render("~/courses/cruk/SurvivalAnalysis/201907/tex/sc/Survival_Analysis.Rmd") --->

```{r message = FALSE, warning = FALSE, echo = FALSE} 
# change working directory: should be the directory containg the Markdown files:
#setwd("~/courses/cruk/SurvivalAnalysis/201907/tex/sc/")
#setwd("/Volumes/Files/courses/cruk/SurvivalAnalysis/201907/tex/sc")

```

# Section 0: survival package and 'aml' dataset

```{r message = FALSE, warning = FALSE, echo = TRUE} 
library(survival)
aml
```


# Section 1: Kaplan Meier plot

```{r message = FALSE, warning = FALSE, echo = TRUE} 
leukemia.surv <- survfit(Surv(time, status) ~ x, data = aml) 
plot(leukemia.surv, col=c("red","blue"), 
     mark.time=TRUE,
     conf.int=FALSE,
     axes=FALSE)
axis(1,seq(0,200,10))
axis(2,seq(0,1,.1),las=2)
legend("topright", c("Maintenance", "No Maintenance"),lty=c(1,1), col=c("red","blue")) 
title("Kaplan-Meier Curves\nfor AML Maintenance Study") 
# 
abline(h=0.5,lty=2)
```

# Section 2: Log-rank test


```{r message = FALSE, warning = FALSE, echo = TRUE} 
survdiff(Surv(time, status) ~ x, data = aml) 
```

# Section 3: Cox model

```{r message = FALSE, warning = FALSE, echo = TRUE} 
# Fit a stratified model 
fit = coxph(Surv(time, status) ~ x,data=aml)
summary(fit)
```