# R - Survival Analysis

The R package named

**survival**is used to carry out survival analysis. This package contains the function

**Surv()**which takes the input data as a R formula and creates a survival object among the chosen variables for analysis. Then we use the function

**survfit()**to create a plot for the analysis.

## Install Package

install.packages("survival")

### Syntax

The basic syntax for creating survival analysis in R is −Surv(time,event) survfit(formula)Following is the description of the parameters used −

**time**is the follow up time until the event occurs.**event**indicates the status of occurrence of the expected event.**formula**is the relationship between the predictor variables.

### Example

We will consider the data set named "pbc" present in the survival packages installed above. It describes the survival data points about people affected with primary biliary cirrhosis (PBC) of the liver. Among the many columns present in the data set we are primarily concerned with the fields "time" and "status". Time represents the number of days between registration of the patient and earlier of the event between the patient receiving a liver transplant or death of the patient.# Load the library. library("survival") # Print first few rows. print(head(pbc))When we execute the above code, it produces the following result and chart −

id time status trt age sex ascites hepato spiders edema bili chol 1 1 400 2 1 58.76523 f 1 1 1 1.0 14.5 261 2 2 4500 0 1 56.44627 f 0 1 1 0.0 1.1 302 3 3 1012 2 1 70.07255 m 0 0 0 0.5 1.4 176 4 4 1925 2 1 54.74059 f 0 1 1 0.5 1.8 244 5 5 1504 1 2 38.10541 f 0 1 1 0.0 3.4 279 6 6 2503 2 2 66.25873 f 0 1 0 0.0 0.8 248 albumin copper alk.phos ast trig platelet protime stage 1 2.60 156 1718.0 137.95 172 190 12.2 4 2 4.14 54 7394.8 113.52 88 221 10.6 3 3 3.48 210 516.0 96.10 55 151 12.0 4 4 2.54 64 6121.8 60.63 92 183 10.3 4 5 3.53 143 671.0 113.15 72 136 10.9 3 6 3.98 50 944.0 93.00 63 NA 11.0 3From the above data we are considering time and status for our analysis.

### Applying Surv() and survfit() Function

Now we proceed to apply the**Surv()**function to the above data set and create a plot that will show the trend.

# Load the library. library("survival") # Create the survival object. survfit(Surv(pbc$time,pbc$status == 2)~1) # Give the chart file a name. png(file = "survival.png") # Plot the graph. plot(survfit(Surv(pbc$time,pbc$status == 2)~1)) # Save the file. dev.off()When we execute the above code, it produces the following result and chart −

Call: survfit(formula = Surv(pbc$time, pbc$status == 2) ~ 1) n events median 0.95LCL 0.95UCL 418 161 3395 3090 3853

The trend in the above graph helps us predicting the probability of survival at the end of a certain number of days.

*Table of contents:*1. R - Overview

2. R - Environment Setup

3. R - Basic Syntax

4. R - Data Types

5. R - Variables

6. R - Operators

7. R - Decision Making

8. R - Loops

9. R - Functions

10. R - Strings

11. R - Vectors

12. R - Matrices

13. R - Arrays

14. R - Factors

15. R - Data Frames

16. R - Packages

17. R - Data Reshaping

18. R - CSV Files

19. R - Excel Files

20. R - Binary Files

21. R - XML Files

22. R - JSON Files

23. R - Web Data

24. R - Database

25. R - Pie Charts

26. R - Bar Charts

27. R - Boxplots

28. R - Histograms

29. R - Line Graphs

30. R - Scatterplots

31. R - Mean, Median and Mode

32. R - Linear Regression

33. R - Multiple Regression

34. R - Logistic Regression

35. R - Normal Distribution

36. R - Binomial Distribution

37. R - Poisson Regression

38. R - Analysis of Covariance

39. R - Time Series Analysis

40. R - Nonlinear Least Square

41. R - Decision Tree

42. R - Random Forest

43. R - Survival Analysis

44. R - Chi Square Tests

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