Error when using knnImpute pre-processing option for dataset containing factor

[saviola777]

Hello,

here is a reproducible example:

library(caret)
library(mlbench)
data("PimaIndiansDiabetes2")
pp <- preProcess(PimaIndiansDiabetes2, method = "knnImpute")
PimaIndiansDiabetes2pp <- predict(pp, newdata = PimaIndiansDiabetes2)

This does not produce errors when using "medianImpute". When I remove the only factor from the data, it works as expected:

PimaIndiansDiabetes2$diabetes <- NULL
pp <- preProcess(PimaIndiansDiabetes2, method = "knnImpute")
PimaIndiansDiabetes2pp <- predict(pp, newdata = PimaIndiansDiabetes2)

my session info is attached below. I already dug through the code for a bit and it seems that the old data used by the nnimp function (stored in pp$data) does not contain the factor columns and the function then tries to select all non-NA columns of the new data from the old data (old[, non_missing_cols, drop = FALSE]), which fails because the factors are not NA but not in the old data.

Is this a bug, or am I missing something when it comes to using the "knnImpute" option?

R version 3.2.4 (2016-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Gentoo/Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C              LC_TIME=en_US.UTF8       
 [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8   
 [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C             
[10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] caret_6.0-64    ggplot2_2.0.0   lattice_0.20-33 mlbench_2.1-1

[topepo]

You aren't missing anything; it is a bug and you are correct about the issue. I checked in code to fix the issue.

Thanks,

Max