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comparison survival/survival.R @ 4:744cf0f4d1b1 draft

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author testtool
date Mon, 02 Oct 2017 07:54:25 -0400
parents ce6df2bd21cd
children b4d7a110dd32
comparison
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3:e31c47bf46a4 4:744cf0f4d1b1
1 require(survival, quietly = TRUE) 1 require(survival, quietly = TRUE)
2 args <- commandArgs(trailingOnly = TRUE) 2 args <- commandArgs(trailingOnly = TRUE)
3 3
4 input =args[1] 4 input = args[1]
5 fit = args[2] 5 type = args[2]
6 png = args[3] 6 error = args[3]
7 conf.type = args[4]
8 conf.lower = args[5]
9 fit = args[6]
10 png = args[7]
7 11
8 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input)) 12 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type = type, error = error, conf.type = conf.type , conf.lower = conf.lower, data = read.csv(input))
9 13
10 res <- summary(tofit,times=c(1,2,3)) 14 res <- summary(tofit,times=c(1,2,3))
11 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")]) 15 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
12 write.csv(save.df, fit) 16 write.csv(save.df, fit)
13 17
14 png(png) 18 png(png)
15 plot(tofit) 19 plot(tofit,xlab="Survival (days)", ylab="Survival", lwd=2,xlim=c(0,1900),ylim=c(0.3,1),col=c("red","blue"))
20 legend("topright",legend=c("low","high"),lty=c(1,1),
21 lwd=c(2.5,2.5),col=c("red","blue"))
16 dev.off() 22 dev.off()
17 23