用R作生存分析.doc

生存分析 一．Libraries and data sets library() # 查看你的系统中所有已装的libraries library(survival) # 加载一个library, 也可使用鼠标来做 library(help=survival) # see the list of available functions and data sets. data(aml) # 加载数据 aml aml # see the data # 《生存分析》需要的两个 libraries library(survival) library(KMsurv) #包含我们教材中所有的数据 # 若想使数据中的变量能够在R中作为一个变量使用，use attach(): attach(aids) infect detach(aids) 二.Survival Objects #由函数 Surv 产生一个 survival object Surv (time, time2, event, type) time: survival time time2: ending time if it is interval censored event: censoring variable. For interval censored data, 0=right censored, 1=event at time, 2=left censored, 3=interval censored. type: indicating whether it is right censored, left censored or interval censored or counting process. 默认值是右删失或 counting process #假设一个观测值为 [2, 3]，则 R 语句为 Surv(time=2,time2=3, event=3, type = interval) #右删失数据 attach(aml) Surv(time,status) detach(aml) #左截断右删失数据 data(psych) attach(psych) my.surv.object - Surv(age, age+time, death) my.surv.object [1] (51,52 ] (58,59 ] (55,57 ] (28,50 ] (21,51+] (19,47 ] (25,57 ] [22] (29,63+] (35,65+] (32,67 ] (36,76 ] (32,71+] detach(psych) 三. The Kaplan-Meier Estimates #计算生存曲线：survfitformula, conf.int, and conf.type. survfit(formula, conf.int = 0.95, conf.type = log) conf.type=”plain” #linear confidence interval in our book conf.type=”log” # 对H(t)作log transformation conf.type=”log-log” #log-transformed in our book myfit = survfit(Surv(time,status) ~ 1,data=kidney) #在新版的R里，这个~1是必要的。 attach(kidney) myfit = survfit(Surv(time,status) ~ 1) #在新版的R里，这个~1是必要的。 a=summary