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author testtool
date Fri, 29 Sep 2017 18:32:23 -0400
parents 6cc0c5eb71b2
children ce6df2bd21cd
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require(survival, quietly = TRUE)
args <- commandArgs(trailingOnly = TRUE)

input =args[1]
fit = args[2]
png = args[3]

#fit a Kaplan-Meier and plot it
input<-("test-data/input.csv")
fit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))

res <- summary(fit,times=c(1,2,3))
save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
write.csv(save.df, file = "survfit.csv")

png("fit.png")
plot(fit)
dev.off()