1 files changed, 0 insertions, 82 deletions
diff --git a/lib/r-util.rb b/lib/r-util.rb
deleted file mode 100644
index 0d58389..0000000
--- a/lib/r-util.rb
+++ /dev/null
@@ -1,82 +0,0 @@
-# pending: package dir hack ---------
-# CONFIG[:base_dir] = "/home/<user>/opentox-ruby/www"
-# PACKAGE_DIR = "/home/<user>/opentox-ruby/r-packages"
-package_dir = CONFIG[:base_dir].split("/")
-package_dir[-1] = "r-packages"
-package_dir = package_dir.join("/")
-PACKAGE_DIR = package_dir
-
-
-
-module Lib
-  
-  module RUtil
-    
-    def self.dataset_to_dataframe( dataset )
-      LOGGER.debug "convert dataset to dataframe #{dataset.uri}"
-      all_features = []
-      dataset.features.each do |f|
-        feat_name = "feature_#{f[0].split("/")[-1]}"
-        LOGGER.debug "- adding feature: #{feat_name}"
-        feat = OpenTox::Feature.find(f[0])
-        nominal = feat.metadata[RDF.type].to_a.flatten.include?(OT.NominalFeature)
-        values = []
-        dataset.compounds.each do |c|
-          val = dataset.data_entries[c][f[0]]
-          raise "not yet implemented" if val!=nil && val.size>1
-          v = val==nil ? "" : val[0].to_s
-          v = "NA" if v.size()==0
-          values << v
-        end
-        all_features << feat_name
-        @@r.assign feat_name,values
-        @@r.eval "#{feat_name} <- as.numeric(#{feat_name})" unless nominal
-      end
-      df_name = "df_#{dataset.uri.split("/")[-1].split("?")[0]}"
-      cmd =  "#{df_name} <- data.frame(#{all_features.join(",")})"
-      @@r.eval cmd
-      #@@r.eval "head(#{df_name})"
-      df_name
-    end
-    
-    def self.stratified_split( dataframe, pct=0.3, seed=42 )
-      @@r.eval "set.seed(#{seed})"
-      @@r.eval "split <- stratified_split(#{dataframe}, ratio=#{pct})"
-      split = @@r.pull 'split'
-      split.collect{|s| s.to_i}
-    end
-    
-    def self.package_installed?( package )
-      @@r.eval ".libPaths(\"#{PACKAGE_DIR}\")"
-      p = @@r.pull "installed.packages()[,1]"
-      p.include?(package) 
-    end
-    
-    def self.install_packages( package )
-      unless package_installed? package
-        @@r.eval "install.packages(\"#{package}\", repos=\"http://cran.r-project.org\", dependencies=T, lib=\"#{PACKAGE_DIR}\")"
-      end
-    end
-    
-    def self.library( package )
-      install_packages( package )
-      @@r.eval "library(\"#{package}\")"
-    end
-    
-    def self.init_r
-      @@r = RinRuby.new(true,false) unless defined?(@@r) and @@r
-      library("sampling")
-      library("gam")
-      @@r.eval "source(\"#{PACKAGE_DIR}/stratification.R\")"
-    end
-    
-    def self.quit_r
-      begin
-        @@r.quit
-        @@r = nil
-      rescue
-      end
-    end
-    
-  end
-end