R problem with randomForest classification with raster package

Question

I am having an issue with randomForest and the raster package. First, I create the classifier:

library(raster)
library(randomForest)

# Set some user variables
fn = "image.pix"
outraster = "classified.pix"
training_band = 2
validation_band = 1
original_classes = c(125,126,136,137,151,152,159,170)
reclassd_classes = c(122,122,136,137,150,150,150,170)

# Get the training data
myraster = stack(fn)
training_class = subset(myraster, training_band)

# Reclass the training data classes as required
training_class = subs(training_class, data.frame(original_classes,reclassd_classes))

# Find pixels that have training data and prepare the data used to create the classifier
is_training = Which(training_class != 0, cells=TRUE)
training_predictors = extract(myraster, is_training)[,3:nlayers(myraster)]
training_response = as.factor(extract(training_class, is_training))
remove(is_training)

# Create and save the forest, use odd number of trees to avoid breaking ties at random
r_tree = randomForest(training_predictors, y=training_response, ntree = 201, keep.forest=TRUE) # Runs out of memory, does not allow more trees than this...
remove(training_predictors, training_response)

Up to this point, all is good. I can see that the forest was created correctly by looking at the error rates, confusion matrix, etc. When I try to classify some data, however, I run into trouble with the following, which returns all NA's in predictions:

# Classify the whole image
predictor_data = subset(myraster, 3:nlayers(myraster))
layerNames(predictor_data) = layerNames(myraster)[3:nlayers(myraster)]
predictions = predict(predictor_data, r_tree, type='response', progress='text')

And gives this warning:

Warning messages:
1: In `[<-.factor`(`*tmp*`, , value = c(1, 1, 1, 1, 1, 1,  ... :
  invalid factor level, NAs generated
(keeps going like this)...

However, calling predict.randomForest directly works fine and returns the expected predictions (this is not a good option for me because the image is large, and I cannot store the whole matrix in memory):

# Classify the whole image and write it to file
predictor_data = subset(myraster, 3:nlayers(myraster))
layerNames(predictor_data) = layerNames(myraster)[3:nlayers(myraster)]
predictor_data = extract(predictor_data, extent(predictor_data))
predictions = predict(r_tree, newdata=predictor_data)

How can I get it to work directly with the "raster" version? I know that this is possible, as shown in the examples of predict{raster}.

Answer 1

You could try nesting predict.randomForest within the writeRaster function and write the matrix as a raster in chunks as per the pdf included in the raster package. Before that, try the argument 'na.rm=TRUE' when calling predict in the raster function. You might also assign dummy values to the NAs in the predict rasters, then later rewriting them as NAs using functions in the raster package.

As for memory problems when calling RFs, I've had a plethora of memory issues dealing with BRTs. They're immense on disk and in memory! (Should a model be more complex than the data?) I've not had them run reliably on 32-bit machines (WinXp or Linux). Sometimes tweaking Windows memory allotment to applications has helped, and moving to Linux has helped more, but I get the most from 64-bit Windows or Linux machines, since they impose a higher (or no) limit on the amount of memory applications can take. You may be able to increase the number of trees you can use by doing this.