diff options
| author | davor <vorgrimmlerdavid@gmx.de> | 2012-03-06 15:41:00 +0100 |
|---|---|---|
| committer | davor <vorgrimmlerdavid@gmx.de> | 2012-03-06 15:41:00 +0100 |
| commit | 90c012d4567da61758d43616a18c4fe306bbdf39 (patch) | |
| tree | ddec0c913ea6146943d35ee2473794d96455d5c7 | |
| parent | c765cce75bd7d4ede144ff7b3634ed666238f273 (diff) | |
Adjusted rfe settings and fixed minor bug.
| -rw-r--r-- | lib/algorithm.rb | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/lib/algorithm.rb b/lib/algorithm.rb index d2a1843..40cbc84 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -443,7 +443,7 @@ module OpenTox end - module FeatureSelection + module FeatureSelection include Algorithm # Recursive Feature Elimination using caret # @param [Hash] required keys: ds_csv_file, prediction_feature, fds_csv_file (dataset CSV file, prediction feature column name, and feature dataset CSV file), optional: del_missing (delete rows with missing values). @@ -487,7 +487,7 @@ module OpenTox # features with zero variance removed zero_var = names ( which ( apply ( features, 2, function(x) var(x, na.rm=T) ) == 0 ) ) features = features[,!names(features) %in% zero_var] - + pp = NULL if (del_missing) { # needed if rows should be removed @@ -514,13 +514,13 @@ module OpenTox subsets = subsets[subsets>1] # Recursive feature elimination - rfProfile = rfe( x=features, y=y, rfeControl=rfeControl(functions=rfFuncs, number=250), sizes=subsets) + rfProfile = rfe( x=features, y=y, rfeControl=rfeControl(functions=rfFuncs, method='cv'), sizes=subsets) optVar = rfProfile$optVariables if (rfProfile$bestSubset == dim(features)[2]) { newRMSE = rfProfile$results$RMSE newRMSE[which.min(rfProfile$results$RMSE)] = Inf newOptSize = rfProfile$results[which.min(newRMSE),]$Variables - optVar = rfProfile$Variables(1:newOptSize) + optVar = rfProfile$optVariables[1:newOptSize] } # read existing dataset and select most useful features |