I'm trying to run a randomForest on a large-ish data set (5000x300). Unfortunately I'm getting an error message as follows:
> RF <- randomForest(prePrior1, postPrior1[,6]
+ ,,do.trace=TRUE,importance=TRUE,ntree=100,,forest=TRUE)
Error in randomForest.default(prePrior1, postPrior1[, 6], , do.trace = TRUE, :
NA/NaN/Inf in foreign function call (arg 1)
So I try to find any NA's using :
> df2 <- prePrior1[is.na(prePrior1)]
> df2
character(0)
> df2 <- postPrior1[is.na(postPrior1[,6])]
> df2
numeric(0)
which leads me to believe that it's Inf's that are the problem as there don't seem to be any NA's.
Any suggestions for how to root out Inf's?
You're probably looking for is.finite, though I'm not 100% certain that the problem is Infs in your input data.
Be sure to read the help for is.finite carefully about which combinations of missing, infinite, etc. it picks out. Specifically, this:
> is.finite(c(1,NA,-Inf,NaN))
[1] TRUE FALSE FALSE FALSE
> is.infinite(c(1,NA,-Inf,NaN))
[1] FALSE FALSE TRUE FALSE
One of these things is not like the others. Not surprisingly, there's an is.nan function as well.
randomForest's 'NA/NaN/Inf in foreign function call' is often a false warning, and really irritating:
- you will get this if any of the variables passed is character
- actual NaNs and Infs almost never happen in clean data
Fast and dirty trick to narrow things down, do a binary-search on your variable list, and use token parameters like ntree=2 to get an instant pass/fail on the subset of variables:
RF <- randomForest(prePrior1[m:n],ntree=2,...)
In analogy to is.na, you can use is.infinite to find occurrences of infinites.
Take a look at with, e.g.:
> with(df, df == Inf)
foo bar baz abc ...
[1,] FALSE FALSE TRUE FALSE ...
[2,] FALSE TRUE FALSE FALSE ...
...
joran's answer is what you want and informative. For more details about is.na() and is.infinite(), you should check out https://stat.ethz.ch/R-manual/R-devel/library/Matrix/html/is.na-methods.html
and besides, after you get the logical vector which says whether each element of the original vector is NA/Inf, you can use the which() function to get the indices, just like this:
> v1 <- c(1, Inf, 2, NaN, Inf, 3, NaN, Inf)
> is.infinite(v1)
[1] FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE
> which(is.infinite(v1))
[1] 2 5 8
> is.na(v1)
[1] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
> which(is.na(v1))
[1] 4 7
the document for which() is here https://stat.ethz.ch/R-manual/R-devel/library/base/html/any.html
