1 files changed, 82 insertions, 0 deletions
diff --git a/lib/r-util.rb b/lib/r-util.rb
new file mode 100644
index 0000000..0d58389
--- /dev/null
+++ b/lib/r-util.rb
@@ -0,0 +1,82 @@
+# 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