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survival/survival.R |
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| diff -r 5b70a33bf327 -r ce6df2bd21cd survival/survival.R --- a/survival/survival.R Fri Sep 29 18:32:23 2017 -0400 +++ b/survival/survival.R Fri Sep 29 18:41:35 2017 -0400 |
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| @@ -5,15 +5,13 @@ 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)) +tofit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input)) -res <- summary(fit,times=c(1,2,3)) +res <- summary(tofit,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") +write.csv(save.df, fit) -png("fit.png") -plot(fit) +png(png) +plot(tofit) dev.off() |