Competing Risks - Predicting on dataset without response can crash R

[jatherrien]

Hello, I've noticed that with competing risk data if I first predict on a dataset that has a response, and then predict next on a dataset without one, that R crashes entirely. Here's a script that can reliably trigger it. The script causes a crash on the three computers I tested it on, but they're all Linux so I don't know if it's cross-platform or not.

set.seed(500)

n = 1500

data <- data.frame(x=rnorm(n), delta=sample(1:2, replace=TRUE, size=n))
data$T <- rexp(n, rate=ifelse(data$delta==1, 1/10, 1/15))

censorTimes <- rexp(n, rate=1/9)
data$delta = ifelse(data$T < censorTimes, 0, data$delta)
data$T = pmin(data$T, censorTimes)

trainingData <- data[1:1000,]
testData <- data[1001:1500,]

newData <- data.frame(x=rnorm(20))

library(randomForestSRC)

# Log-rank split rule is only used for speed; it still crashes on default splitrule
modelRfsrc = rfsrc(Surv(T, delta) ~ x, trainingData, 
                   ntree=1000, nodesize=10, mtry=1, 
                   nsplit=0, splitrule = "logrank")


testSetPredictions <- predict(modelRfsrc, testData)

# This line triggers the crash. I've tried sometimes running it before the predictions for testData
# and often it then *won't* crash, but it sometimes still does. It always triggers a crash though if
# I've run the predictions for testData before, even if before that I had successfully run this line.
newDataPredictions <- predict(modelRfsrc, newData)

Here's my sessionInfo():

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] randomForestSRC_2.8.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4 parallel_3.4.4 tools_3.4.4    yaml_2.2.0   

[kogalur]

Thank you for the excellent example. There was indeed a bug w.r.t. the absence of responses in a competing risk scenario. You can find a beta build with the fix here, if it's convenient:

https://www.dropbox.com/s/4esx9qvft9ah6fb/randomForestSRC_2.8.0.11.tar.gz?dl=0

We'll likely push a new build up to CRAN in a couple of weeks.

[skvempati]

Hi, I am having the same issue but I don't see a new build on CRAN (v. 2.8.0 is up and able to be installed). Are there still plans for a new build to be pushed to CRAN or should I use the beta build?

Thanks!

[kogalur]

Sorry, I shouldn't closed this issue until we updated CRAN. We got delayed but we're very close, maybe a few days away, from posting. If you need it immediately, I'd use the beta build.