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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
|
4 input = args[1]
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5 type = args[2]
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|
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6 error = args[3]
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20
|
7 conf_type = args[4]
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8 conf_lower = args[5]
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4
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9 fit = args[6]
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10 png = args[7]
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0
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11
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20
|
12 tofit <- survival::survfit(Surv(obsT, status) ~ X1, type = type, error = error, conf.type = conf_type , conf.lower = conf_lower, data = read.csv(input))
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0
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13
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2
|
14 res <- summary(tofit,times=c(1,2,3))
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0
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15 save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
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2
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16 write.csv(save.df, fit)
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0
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17
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2
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18 png(png)
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31
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19 plot(tofit,xlab="Time", ylab="Survival", lwd=2,xlim=c(0,1900),ylim=c(0.3,1),col=c("red","blue"))
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4
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20 legend("topright",legend=c("low","high"),lty=c(1,1),
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|
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21 lwd=c(2.5,2.5),col=c("red","blue"))
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0
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22 dev.off()
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23
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