screechOwl screechOwl - 7 days ago 5
R Question

R is there a way to find Inf/-Inf values?

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?

Answer

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.

Comments