Mercurial > repos > testtool > survival
comparison survival/survival.R @ 20:b4d7a110dd32 draft
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author | testtool |
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date | Mon, 02 Oct 2017 08:51:05 -0400 |
parents | 744cf0f4d1b1 |
children | ef13fa666e0e |
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19:d95c8e3b24e7 | 20:b4d7a110dd32 |
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2 args <- commandArgs(trailingOnly = TRUE) | 2 args <- commandArgs(trailingOnly = TRUE) |
3 | 3 |
4 input = args[1] | 4 input = args[1] |
5 type = args[2] | 5 type = args[2] |
6 error = args[3] | 6 error = args[3] |
7 conf.type = args[4] | 7 conf_type = args[4] |
8 conf.lower = args[5] | 8 conf_lower = args[5] |
9 fit = args[6] | 9 fit = args[6] |
10 png = args[7] | 10 png = args[7] |
11 | 11 |
12 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type = type, error = error, conf.type = conf.type , conf.lower = conf.lower, data = read.csv(input)) | 12 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type = type, error = error, conf.type = conf_type , conf.lower = conf_lower, data = read.csv(input)) |
13 | 13 |
14 res <- summary(tofit,times=c(1,2,3)) | 14 res <- summary(tofit,times=c(1,2,3)) |
15 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")]) | 15 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")]) |
16 write.csv(save.df, fit) | 16 write.csv(save.df, fit) |
17 | 17 |