64 lines
2.4 KiB
R
64 lines
2.4 KiB
R
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library(survival)
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#
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# A Cox model with a factor, followed by survexp.
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#
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pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
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log(protime) + age + platelet + sex, data = pbc)
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esurv <- survexp(~ trt, ratetable = pfit2, data = pbc)
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temp <- pbc
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temp$sex2 <- factor(as.numeric(pbc$sex), levels=2:0,
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labels=c("f", "m", "unknown"))
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esurv2 <- survexp(~ trt, ratetable = pfit2, data = temp,
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rmap=list(sex=sex2))
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# The call components won't match, which happen to be first
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all.equal(unclass(esurv)[-1], unclass(esurv2)[-1])
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# Check that the ratetableDate function is okay
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#
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Datedate <- function(x) {
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# Dates have an origin of 1/1/1970, dates of 1/1/1960
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offset <- as.numeric(as.Date("1970-01-01") - as.Date("1960-01-01"))
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y <- as.numeric(x) + offset
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class(y) <- "date"
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y
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}
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as.data.frame.date <- as.data.frame.vector # needed to make the functions work
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n <- nrow(lung)
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tdata <- data.frame(age=lung$age + (1:n)/365.25,
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sex = c('male', 'female')[lung$sex],
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ph.ecog = lung$ph.ecog,
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time = lung$time*3,
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status = lung$status,
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entry = as.Date("1940/01/01") + (n:1)*50)
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tdata$entry2 <- as.POSIXct(tdata$entry)
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tdata$entry3 <- Datedate(tdata$entry)
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p1 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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rmap= list(age=age*365.25, sex=sex, year=entry))
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p2 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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rmap= list(age=age*365.25, sex=sex, year=entry2))
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p3 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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rmap= list(age=age*365.25, sex=sex, year=entry3))
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all.equal(p1$expected, p2$expected)
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all.equal(p1$expected, p3$expected)
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# Now a ratetable with ordinary dates rather than US census style year
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trate <- survexp.us
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attr(trate, 'type') <- c(2,1,3)
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p4 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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rmap= list(age=age*365.25, sex=sex, year=entry))
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p5 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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rmap= list(age=age*365.25, sex=sex, year=entry2))
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p6 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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rmap= list(age=age*365.25, sex=sex, year=entry3))
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#all.equal(p1$expected, p4$expected) # this won't be true, US special is special
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all.equal(p4$expected, p5$expected)
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all.equal(p5$expected, p6$expected)
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