Two fixes related to transformation and model building

train() failure for censoring predictions (algorithm.rb),
transformation log for creating n_prop and q_prop fixed (transform.rb)

2 files changed, 5 insertions, 6 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index c026c56..9dcf6a8 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -381,10 +381,10 @@ module OpenTox
         else
           #LOGGER.debug gram_matrix.to_yaml
           @r = RinRuby.new(false,false) # global R instance leads to Socket errors after a large number of requests
-          @r.eval "set.seed(1)"
           @r.eval "suppressPackageStartupMessages(library('caret'))" # requires R packages "caret" and "kernlab"
           @r.eval "suppressPackageStartupMessages(library('doMC'))" # requires R packages "multicore"
           @r.eval "registerDoMC()" # switch on parallel processing
+          @r.eval "set.seed(1)"
           begin
 
             # set data
@@ -417,7 +417,7 @@ module OpenTox
 
             # model + support vectors
             LOGGER.debug "Creating R SVM model ..."
-            @r.eval <<-EOR
+            train_success = @r.eval <<-EOR
               model = train(prop_matrix,y,method="svmradial",tuneLength=8,trControl=trainControl(method="LGOCV",number=10),preProcess=c("center", "scale"))
               perf = ifelse ( class(y)!='numeric', max(model$results$Accuracy), model$results[which.min(model$results$RMSE),]$Rsquared )
             EOR
@@ -431,6 +431,7 @@ module OpenTox
 
             # censoring
             prediction = nil if ( @r.perf.nan? || @r.perf < min_train_performance )
+            prediction = nil unless train_success
             LOGGER.debug "Performance: #{sprintf("%.2f", @r.perf)}"
           rescue Exception => e
             LOGGER.debug "#{e.class}: #{e.message}"
@@ -459,12 +460,12 @@ module OpenTox
         
         # need packs 'randomForest', 'RANN'
         @r.eval <<-EOR
-          set.seed(1)
           suppressPackageStartupMessages(library('caret'))
           suppressPackageStartupMessages(library('randomForest'))
           suppressPackageStartupMessages(library('RANN'))
           suppressPackageStartupMessages(library('doMC'))
           registerDoMC()
+          set.seed(1)
           
           acts = read.csv(ds_csv_file, check.names=F)
           feats = read.csv(fds_csv_file, check.names=F)
diff --git a/lib/transform.rb b/lib/transform.rb
index 5c485fb..f6f769d 100644
--- a/lib/transform.rb
+++ b/lib/transform.rb
@@ -396,9 +396,7 @@ module OpenTox
             @q_prop = gsl_q_prop_orig.row(0).to_a
           end
 
-         if (@n_prop && @q_prop)
-            LOGGER.debug "F: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}" 
-          end
+          LOGGER.debug "F: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}"  if (@n_prop && @n_prop[0] && @q_prop)
           LOGGER.debug "Sims: #{@sims.size}, Acts: #{@acts.size}" if (@sims && @acts)
 
           @sims = [ gram_matrix, @sims ]