big.matrix as data.frame in R

Question

I've recently started using R for data analysis. Now I've got a problem in ranking a big query dataset (~1 GB in ASCII mode, over my laptop's 4GB RAM in binary mode). Using bigmemory::big.matrix for this dataset is a nice solution, but providing such a matrix 'm' in the gbm() or randomForest() algorithms causes the error:

cannot coerce class 'structure("big.matrix", package = "bigmemory")' into a data.frame

class(m) outputs the folowing:

[1] "big.matrix"
attr(,"package")
[1] "bigmemory"

Is there a way to correctly pass a big.matrix instance into these algorithms?

Answer 1

I obviously can't test this using data of your scale, but I can reproduce your errors by using the formula interface of each function:

require(bigmemory)
m <- matrix(sample(0:1,5000,replace = TRUE),1000,5)
colnames(m) <- paste("V",1:5,sep = "")

bm <- as.big.matrix(m,type = "integer")

require(gbm)
require(randomForest)

#Throws error you describe
rs <- randomForest(V1~.,data = bm)
#Runs without error (with a warning about the response only having two values)
rs <- randomForest(x = bm[,-1],y = bm[,1])

#Throws error you describe
rs <- gbm(V1~.,data = bm)
#Runs without error
rs <- gbm.fit(x = bm[,-1],y = bm[,1])

Not using the formula interface for randomForest is fairly common advice for large data sets; it can be quite inefficient. If you read ?gbm, you'll see a similar recommendation steering you towards gbm.fit for large data as well.

Answer 2

It is often the case that the memory occupied by numeric objects is more than the disk space. Each "double" element in a vector or matrix takes 8 bytes. When you coerce an object to a data.frame, it may need to be copied in RAM. You should avoid trying to use functions and data structures that are outside those supported by the bigmemory/big*** suite of packages. "biglm" is available, but I doubt that you can expect gbm() or randomForest() to recognize and use the facilities in the "big"-family.