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R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(survival)
> #
> # A Cox model with a factor, followed by survexp.
> #
> pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
+ log(protime) + age + platelet + sex, data = pbc)
> esurv <- survexp(~ trt, ratetable = pfit2, data = pbc)
>
> temp <- pbc
> temp$sex2 <- factor(as.numeric(pbc$sex), levels=2:0,
+ labels=c("f", "m", "unknown"))
> esurv2 <- survexp(~ trt, ratetable = pfit2, data = temp,
+ rmap=list(sex=sex2))
>
> # The call components won't match, which happen to be first
> all.equal(unclass(esurv)[-1], unclass(esurv2)[-1])
[1] TRUE
>
>
> # Check that the ratetableDate function is okay
> #
> Datedate <- function(x) {
+ # Dates have an origin of 1/1/1970, dates of 1/1/1960
+ offset <- as.numeric(as.Date("1970-01-01") - as.Date("1960-01-01"))
+ y <- as.numeric(x) + offset
+ class(y) <- "date"
+ y
+ }
> as.data.frame.date <- as.data.frame.vector # needed to make the functions work
>
> n <- nrow(lung)
> tdata <- data.frame(age=lung$age + (1:n)/365.25,
+ sex = c('male', 'female')[lung$sex],
+ ph.ecog = lung$ph.ecog,
+ time = lung$time*3,
+ status = lung$status,
+ entry = as.Date("1940/01/01") + (n:1)*50)
> tdata$entry2 <- as.POSIXct(tdata$entry)
> tdata$entry3 <- Datedate(tdata$entry)
>
> p1 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
+ rmap= list(age=age*365.25, sex=sex, year=entry))
> p2 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
+ rmap= list(age=age*365.25, sex=sex, year=entry2))
> p3 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
+ rmap= list(age=age*365.25, sex=sex, year=entry3))
>
> all.equal(p1$expected, p2$expected)
[1] TRUE
> all.equal(p1$expected, p3$expected)
[1] TRUE
>
>
> # Now a ratetable with ordinary dates rather than US census style year
> trate <- survexp.us
> attr(trate, 'type') <- c(2,1,3)
> p4 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
+ rmap= list(age=age*365.25, sex=sex, year=entry))
> p5 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
+ rmap= list(age=age*365.25, sex=sex, year=entry2))
> p6 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
+ rmap= list(age=age*365.25, sex=sex, year=entry3))
>
> #all.equal(p1$expected, p4$expected) # this won't be true, US special is special
> all.equal(p4$expected, p5$expected)
[1] TRUE
> all.equal(p5$expected, p6$expected)
[1] TRUE
>
> proc.time()
user system elapsed
0.756 0.036 0.790
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