comparison survival/survival.R @ 1:5b70a33bf327 draft

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author testtool
date Fri, 29 Sep 2017 18:32:23 -0400
parents 6cc0c5eb71b2
children ce6df2bd21cd
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0:6cc0c5eb71b2 1:5b70a33bf327
1 require(survival, quietly = TRUE)
1 args <- commandArgs(trailingOnly = TRUE) 2 args <- commandArgs(trailingOnly = TRUE)
2 3
3 input =args[1] 4 input =args[1]
4 fit = args[2] 5 fit = args[2]
5 png = args[3] 6 png = args[3]
6 7
7 #fit a Kaplan-Meier and plot it 8 #fit a Kaplan-Meier and plot it
8 input<-("test-data/input.csv") 9 input<-("test-data/input.csv")
9 fit <- survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input)) 10 fit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))
10 11
11 res <- summary(fit,times=c(1,2,3)) 12 res <- summary(fit,times=c(1,2,3))
12 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")]) 13 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
13 write.csv(save.df, file = "survfit.csv") 14 write.csv(save.df, file = "survfit.csv")
14 15