R进行生存资料分析的相对优势体现在：

1、能够更加方便快捷绘制Kaplan-Meier曲线，

2、能够相对更加美观地绘制Kaplan-Meier曲线

3、相对容易给出中位生存时间及其置信区间

4、检测比例风险假设的方法更加灵活且完善

5、易于构建时间依赖模型

library(stats)

library(survival)



## Information of data



data(package = "survival")  # List datasets in survival package

help(bladder1)              # Description of data

head(bladder1)              # Show first 6 rows

str(bladder1)               # Check type of variables

summary(bladder1)           # Statistical summary



## Get the final data with nonzero follow-up

bladder1$time <- 

  as.numeric(bladder1$stop -

               bladder1$start)

summary(bladder1$time)

bladder1 <- subset(bladder1,status<=1 & time>0)





## Step1 Create Kaplan-Meier curve and estimate median survial/event time 

## The "log-log" confidence interval is preferred.

## Create overval Kaplan-Meier curve

km.as.one <- survfit(Surv(time, status) ~ 1, data = bladder1, 

                     conf.type = "log-log")



## Create Kaplan-Meier curve stratified by treatment

km.by.trt <- survfit(Surv(time, status) ~ treatment, data = bladder1, 

                     conf.type = "log-log")



## Show simple statistics of Kaplan-Meier curve

km.as.one

km.by.trt



## See survival estimates at given time (lots of outputs)

summary(km.as.one)

summary(km.by.trt)



## Plot Kaplan-Meier curve without any specification

plot(km.as.one)

plot(km.by.trt)



## Plot Kaplan-Meier curve Without confidence interval and mark of event

plot(km.as.one, conf = F, mark.time = F)

plot(km.by.trt, conf = F, mark.time = F)





## step2 Create a simple cox regression and estimate HR:

model1 <-coxph(Surv(time, status) ~ treatment + number +size, 

               data=bladder1)



## Model output

summary(model1)                    # Output summary information

confint(model1)                    # Output 95% CI for the coefficients

exp(coef(model1))                  # Output HR (exponentiated coefficients)

exp(confint(model1))               # 95% CI for exponentiated coefficients

predict(model1, type="risk")       # predicted values

residuals(model1, type="deviance") # residuals





## Step3 Check for violation of proportional hazard (constant HR over time)

model1.zph <- cox.zph(model1)

model1.zph                    

## Note: p value of treatmentthiotepa <0.05

## GLOBAL p value is more important than p values of treatmentthiotepa 

## Only GLOBAL p value <0.05 is neccesary for solution of violation

## Following steps are just for providing examples



## Displays a graph of the scaled Schoenfeld residuals, along with a smooth curve.

plot(model1.zph)



## Step4 Solution of violating of proportional hazard



## Solution 1 Stratify: create a stratified cox model,namely "contitional cox model "

model2 <-coxph(Surv(start, stop, status) ~ number +size + strata (treatment), 

               data=bladder1)

summary(model2) 

model2.zph <- cox.zph(model2)

model2.zph



## Solution 1 Create a simple time-dependent model without time-dependent variable

model3 <-coxph(Surv(start, stop, status) ~ number +size + treatment, 

               data=bladder1)

summary(model3) 



## Create a time-dependent model with time-dependent variable

bladder1$thiotepa <- 

  as.numeric (bladder1$treatment=="thiotepa")

model4 <-coxph(Surv(start, stop, status) ~ number +size + treatment

               + thiotepa:time,     ## Note: "thiotepa:time" but not "thiotepa*time"

               data=bladder1)

summary(model4) 



## Step5 Performs stepwise model selection by AIC

model5 <-step(model4)  ## Default direction is "backward"

summary(model5)





## rms::survplot() function

## Load rms package

library(rms)



## Plot Kaplan-Meier curve without any specification

fit1 <- npsurv(Surv(time, status) ~ 1, data = bladder1)

fit2 <- npsurv(Surv(time, status) ~ treatment, data = bladder1)

survplot(fit1)

survplot(fit2)



## Plot Kaplan-Meier curve Without confidence interval

survplot(fit1, conf = "none")

survplot(fit2, conf = "none")



## More options for Kaplan-Meier curve

survplot(fit2, 

         xlab = "Time, month",                  # add x-axis label

         ylab = "Survival probability, %",      # add y-axis label

         ## xlim=c(0,60),                       # add x-axis limits

         ## ylim=c(-0.1,1),                     # add y-axis limits

         ## conf.int=.95,                       # show 95% CI,

         conf='none',                           # change type of CI

         label.curves = list(keys = "lines"),   # legend instead of direct label

         levels.only  = TRUE,                   # show only levels, no label

         col=c('red','green','blue'),           # change legend color

         ## fun = function(x) {1 - x},          # Cumulative probability plot

         ## loglog   = TRUE,                    # log(-log Survival) plot

         ## logt     = TRUE,                    # log time

         time.inc = 5,                          # time increment

         ## dots     = TRUE,                    # dot grid

         n.risk   = TRUE,                       # show number at risk

         y.n.risk = 0.01,                       # Change position of number at risk

         cex.n.risk = 0.6                       # change character size for number at risk