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comparison survival/survival.R @ 2:ce6df2bd21cd draft

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author testtool
date Fri, 29 Sep 2017 18:41:35 -0400
parents 5b70a33bf327
children 744cf0f4d1b1
comparison
equal deleted inserted replaced
1:5b70a33bf327 2:ce6df2bd21cd
3 3
4 input =args[1] 4 input =args[1]
5 fit = args[2] 5 fit = args[2]
6 png = args[3] 6 png = args[3]
7 7
8 #fit a Kaplan-Meier and plot it 8 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))
9 input<-("test-data/input.csv")
10 fit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))
11 9
12 res <- summary(fit,times=c(1,2,3)) 10 res <- summary(tofit,times=c(1,2,3))
13 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")]) 11 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
14 write.csv(save.df, file = "survfit.csv") 12 write.csv(save.df, fit)
15 13
16 png("fit.png") 14 png(png)
17 plot(fit) 15 plot(tofit)
18 dev.off() 16 dev.off()
19 17