R help - Sep 2013 - Bug in Survival - predict.coxph with collapse? (related to question "censor=FALSE and id options in survfit.coxph")

Hello everyone, Hello Terry, 

 

Trying to find workarounds for the bug described in
http://r.789695.n4.nabble.com/censor-FALSE-and-id-options-in-survfit-coxph
-td4670320.html,

I found another issue which might or might not be related and which I
think is a bug - unless I got the usage of the collapse argument in
predict.coxph totally wrong. 

 

Using predict.coxph with a collapse vector, it gives the error the
collapse-vector has the wrong length.

Using the example data given in
http://r.789695.n4.nabble.com/censor-FALSE-and-id-options-in-survfit-coxph
-td4670320.html:

predict = predict(mod, newdata=datnew, collapse=datnew$id)

Error in predict.coxph(mod, newdata = datnew, collapse = datnew$id) : 

  Collapse vector is the wrong length

 

all the best 

 

Julian

 

 

########### CODE #############

# create data

 

set.seed(20130625)

n <- 100 # sample size

x <- rbinom(n, 1, 0.5) # covariate

z <- rep(0, n) # start time

y <- rexp(n, exp(x)) # event time

e <- y < 2 # censor at 2

y <- pmin(y, 2) # observation time

dat <- data.frame(x,z,y,e)

rm(x,z,y,e)

 

# fit cox model with start/stop format

library(survival)

mod <- coxph(Surv(z, y, e)~x, data=dat)

summary(mod)

 

plot(survfit(mod))

 

# create prediction dataset with 3 individuals with

# x = 0 on (0,2)

# x = 1 on (0,2)

# x = 0 on (0,1) and x = 1 on (1,2)

datnew <- data.frame(x=c(0,1,0,1), z=c(0,0,0,1), y=c(2,2,1,2), e=rep(0,4),
id=c(1,2,3,3))

datnew

 

 

#### Prediction ######

 

predict(mod, newdata=datnew)                    ## works

predict(mod, newdata=datnew, collapse=datnew$id) ##error

predict(mod, newdata=dat[1:5,], collapse=c(1,2,3,4))  ## error


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