[Rd] new behavior of model.response

[Therneau, Terry M., Ph.D. via R-devel]

I am getting some unexplained changes in the latest version of survival, and 
finally 
traced it down to this: model.response acts differently for Surv objects.
Here is a closed form example using a made up class Durv = diagnose survival.   
I tracked 
it down by removing methods one by one from Surv; I had just added some new 
ones so they 
were my suspects.

test <- data.frame(time=1:8, status=rep(0:1, 4), age=60:67)
row.names(test) <- letters[1:8]

Durv <- function(...) {
     temp <- cbind(...)
     class(temp) <- "Durv"
     temp
}
mf1 <- model.frame(Durv(time, status) ~ age, data=test)
names(model.response(mf1))
#  NULL

length.Durv <- function(x) nrow(x)
names(model.response(mf1))
#  [1] "a" "b" "c" "d" "e" "f" "g" "h" NA  NA  NA  NA  NA  NA NA  NA

The length method for Surv objects has been around for some while, this 
behavior is new.  
It caused the 'time' component of survfit objects to suddenly have names and so 
was 
discovered in my test suite.  I had planned to submit an update today, but now 
need to 
delay it.

The length of the Surv (Durv) object above is 8, BTW; the fact that it's 
representation 
requires either 16 elements (right censored) or 24 (interval censored) is a 
footnote.

Terry Therneau

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] new behavior of model.response

[Therneau, Terry M., Ph.D. via R-devel]

Charles Berry pointed out an error in my reasoning.   In the current survival I 
forgot the 
S3method line for length in the NAMESPACE file, so the behavior is really not 
new.  
Nonetheless it remains surprising and non-intuitive.  Why does model.response 
sometimes 
attach spurious names, when the Surv object itself does not have them?

Terry


tmt% R --vanilla
R version 3.4.2 (2017-09-28) -- "Short Summer"

test <- data.frame(time=1:8, status=rep(0:1, 4), age=60:67)
row.names(test) <- letters[1:8]

library(survival)

mf2 <- model.frame(Surv(time, status) ~ age, data=test)
names(mf2[[1]])
# NULL
names(model.response(mf2))
# NULL

length.Surv <- survival:::length.Surv

names(model.response(mf2))
  # [1] "a" "b" "c" "d" "e" "f" "g" "h" NA  NA  NA  NA  NA  NA  NA NA


[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel