diff survival/survival.R @ 0:6cc0c5eb71b2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/survival/survival.R	Fri Sep 29 18:11:27 2017 -0400
@@ -0,0 +1,18 @@
+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 <- 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()
+