34 lines
1.0 KiB
R
34 lines
1.0 KiB
R
|
library(survival)
|
||
|
|
|
||
|
|
#
|
||
|
|
# The survival code was failing for certain data sets when called as
|
||
|
|
# survfit(Surv(time2-time1, status) ~ ......
|
||
|
|
# The issue was how tied floating point numbers are handled, and the
|
||
|
|
# fact that unique(x), factor(x) and tapply(x) are not guarranteed to
|
||
|
|
# all be the same.
|
||
|
|
# This test fails in survival 2.36-5, fixed in 2.36-6. Data sets that
|
||
|
|
# can cause it are few and far between.
|
||
|
|
#
|
||
|
|
|
||
|
|
load('ties.rda')
|
||
|
|
x <- time2 -time1
|
||
|
|
|
||
|
|
# Here is the heart of the old problem
|
||
|
|
# length(unique(x))== length(table(x))
|
||
|
|
# And the prior fix which worked ALMOST always
|
||
|
|
# x <- round(x, 15)
|
||
|
|
# length(unique(round(x,15)))== length(table(round(x,15)))
|
||
|
|
|
||
|
|
fit1 <- survfit(Surv(x) ~1)
|
||
|
|
length(fit1$time) == length(fit1$surv)
|
||
|
|
|
||
|
|
|
||
|
|
# a second test, once "rounding.R"
|
||
|
|
|
||
|
|
tdata <- data.frame(time=c(1,2, sqrt(2)^2, 2, sqrt(2)^2),
|
||
|
|
status=rep(1,5),
|
||
|
|
group=c(1,1,1,2,2))
|
||
|
|
fit <- survfit(Surv(time, status) ~ group, data=tdata)
|
||
|
|
|
||
|
|
all.equal(sum(fit$strata), length(fit$time))
|