Error message using mstate::msprep ??bug? - r

Question

I have had a problem with an error abend using mstate::msprep to prepare my data for a pretty classical 3 state problem. I can run the code from the mstate package vignette with no difficulty. My problem is entirely parallel to the vignette example. Subjects receive an islet transplant, then may achieve insulin independence. Whether they do or do not, they may have islet graft failure (or loss of insulin independence if it was achieved.) The vignette example works with included covariates (retained by the keep = parameter). My version works fine if I don't include the keep parameter but fails consistently if I use the keep parameter. Since my example works perfectly well without the keep variable, I very much doubt that there is a problem with my main data. It must be some problem with the “keep” data. See below for the session output.
Neither data set has any missing data. I tried the vignette data limiting it to three covariates -- one categorical, one continuous, and the third with one of the event-time variables, exactly parallel to my three covariates. The vignette still works perfectly, but mine doesn’t. Both covariate "keep" lists are character vectors. In sum, I can't imagine a more parallel "real" question to the vignette example.
I have tracked the problem to a subroutine of msprep "msprepEngine" at line 85 at the second time through the processing loop, but I haven't been able to figure out what the problem is. I suspect that it is a bug, but since I can't identify it, I can't be sure.
I would be very grateful for anyone that can help me with this issue. The vignette code is available with the package. Unfortunately I am not free to share my problem's data, but as I said above, the program works perfectly without the keep parameter. There must be something about my "keep" covariates that is giving the system indigestion.
Thanks in advance for any suggestions.
Larry Hunsicker
> library(magrittr)
> library(survival)
> library(mstate)
>
> #Three state tmat:
> data(ebmt3)
> names(msbmt)
[1] "id" "from" "to" "trans" "Tstart" "Tstop" "time" "status" "dissub" "age"
[11] "prtime"
> dim(msbmt)
[1] 5577 11
> tmat <- trans.illdeath(names = c("Tx", "PR", "RelDeath"))
> covs <- c('dissub', 'age', 'drmatch', 'tcd', 'prtime')
> class(covs)
[1] "character"
> msbmt <- msprep(time = c(NA, "prtime", "rfstime"),
+ status = c(NA, "prstat", "rfsstat"),
+ data = ebmt3, trans = tmat, id = 'id', keep = covs)
>
> names(insfree3)
[1] "PatientID" "YrFree" "Free" "YrLossFail" "LossFail" "StudyID" "IEQ_kg"
> tmat3 <- trans.illdeath(names = c("Tx", "II", "LossFail"))
> IImt <- msprep(time = c(NA, 'YrFree', 'YrLossFail'),
+ status = c(NA, 'Free', 'LossFail'),
+ data = insfree3, trans = tmat3, id = 'PatientID')
>
> tmat3 <- trans.illdeath(names = c("Tx", "II", "LossFail"))
> covs <- c('StudyID', 'IEQ_kg', 'YrFree')
> class(covs)
[1] "character"
> IImt <- msprep(time = c(NA, 'YrFree', 'YrLossFail'),
+ status = c(NA, 'Free', 'LossFail'),
+ data = insfree3, trans = tmat3, id = 'PatientID', keep = covs)
Error in rep(keep[, i], tbl) : invalid 'times' argument

Answer 1

I found the problem, and it is a bug. I just don't know whose bug it is. msprep() works when data is a data.frame, but not when it is a tibble. My repro example:
> library(survival)
> library(mstate)
> library(dplyr)
> data(ebmt3)
> class(ebmt3)
[1] "data.frame"
> tmat <- transMat(x = list(c(2, 3), c(3), c()), names = c("Tx",
+ "PR", "RelDeath"))
> ebmt3$prtime <- ebmt3$prtime/365.25
> ebmt3$rfstime <- ebmt3$rfstime/365.25
> covs <- c("dissub", "age", "drmatch", "tcd", "prtime")
> msbmt <- msprep(time = c(NA, "prtime", "rfstime"),
+ status = c(NA, "prstat", "rfsstat"), data = ebmt3,
+ trans = tmat, keep = covs)
> ebmt3 <- as_tibble(ebmt3)
> class(ebmt3)
[1] "tbl_df" "tbl" "data.frame"
> msbmt <- msprep(time = c(NA, "prtime", "rfstime"),
+ status = c(NA, "prstat", "rfsstat"), data = ebmt3,
+ trans = tmat, keep = covs)
Error in rep(keep[, i], tbl) : invalid 'times' argument
I tracked the error down to line 157 in msprep()
ddcovs <- lapply(1:nkeep, function(i) rep(keep[, i], tbl))
When data is a data.frame, this line works. When it is a tibble, it abends with the above error message.
It was my impression that things that work with a data.frame should also work with a tibble, since a tibble is a data.frame. So I'm not sure whether this is a bug in msprep() or in the code for a tibble. But the way to avoid the error is to be sure that the data parameter in the call to msprep() is a data.frame, but not a tibble.
Larry Hunsicker