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1
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1 require(survival, quietly = TRUE)
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0
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2 args <- commandArgs(trailingOnly = TRUE)
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3
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4 input =args[1]
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5 fit = args[2]
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6 png = args[3]
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7
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8 #fit a Kaplan-Meier and plot it
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9 input<-("test-data/input.csv")
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1
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10 fit <- survival::survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))
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0
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11
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12 res <- summary(fit,times=c(1,2,3))
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13 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
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14 write.csv(save.df, file = "survfit.csv")
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15
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16 png("fit.png")
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17 plot(fit)
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18 dev.off()
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19
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