nimbus 2.1.0 → 2.2.0

data/lib/nimbus/forest.rb

@@ -78,7 +78,8 @@ module Nimbus
         trees.each do |t|
           individual_prediction << Nimbus::Tree.traverse(t, individual.snp_list)
         end
-        @predictions[individual.id] = Nimbus::LossFunctions.majority_class_in_list(individual_prediction, @options.tree[:classes])
+        class_sizes = Nimbus::LossFunctions.class_sizes_in_list(individual_prediction, @options.tree[:classes]).map{|p| (p/individual_prediction.size.to_f).round(3)}
+        @predictions[individual.id] = Hash[@options.tree[:classes].zip class_sizes].to_s
       }
     end
 

data/lib/nimbus/loss_functions.rb

@@ -45,7 +45,7 @@ module Nimbus
       # where Pj is the relative frequency of class j in T
       def gini_index(ids, value_table, classes)
         total_size = ids.size.to_f
-        gini = 1 - class_sizes(ids, value_table, classes).inject(0.0){|sum, size| 
+        gini = 1 - class_sizes(ids, value_table, classes).inject(0.0){|sum, size|
           sum + (size/total_size)**2}
         gini.round(5)
       end
@@ -70,6 +70,11 @@ module Nimbus
       def class_sizes(ids, value_table, classes)
         classes.map{|c| ids.count{|i| value_table[i] == c}}
       end
+
+      # Array with the list of sizes of each class in the given list of classes.
+      def class_sizes_in_list(list, classes)
+        classes.map{|c| list.count{|i| i == c}}
+      end
     end
 
   end

data/lib/nimbus/version.rb

@@ -1,3 +1,3 @@
 module Nimbus
-  VERSION = "2.1.0"
+  VERSION = "2.2.0"
 end

data/spec/forest_spec.rb

@@ -116,7 +116,8 @@ describe Nimbus::Forest do
         tree_structure.each do |t|
           individual_prediction << Nimbus::Tree.traverse(t, individual.snp_list)
         end
-        expected_predictions[individual.id] = Nimbus::LossFunctions.majority_class_in_list(individual_prediction, @config.tree[:classes])
+        class_sizes = Nimbus::LossFunctions.class_sizes_in_list(individual_prediction, @config.tree[:classes]).map{|p| (p/individual_prediction.size.to_f).round(3)}
+        expected_predictions[individual.id] = Hash[@config.tree[:classes].zip class_sizes].to_s
       }
 
       @forest.traverse

data/spec/loss_functions_spec.rb

@@ -60,6 +60,19 @@ describe Nimbus::LossFunctions do
     Nimbus::LossFunctions.majority_class_in_list(list, classes).should == 'A'
   end
 
+  it "method for class sizes" do
+    ids     = [1,2,3,4,5,7,85]
+    values  = {1 => 'B', 2 => 'C', 3 => 'A', 4 => 'A', 5 => 'C', 7 => 'B', 85 => 'C'} #2A, 2B, 3C
+    classes = ['A', 'B', 'C']
+    Nimbus::LossFunctions.class_sizes(ids, values, classes).should == [2, 2, 3]
+  end
+
+  it "method for class sizes in list" do
+    list    = %w(A A A B B B C A B C A B A)  # 6A, 5B, 2C
+    classes = ['A', 'B', 'C']
+    Nimbus::LossFunctions.class_sizes_in_list(list, classes).should == [6, 5, 2]
+  end
+
   it "Gini index" do
     ids     = [1,2,3,4,5,7]
     values  = {1 => 'B', 2 => 'C', 3 => 'A', 4 => 'A', 5 => 'C', 7 => 'C'} #3C, 2A, 1B

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nimbus
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-28 00:00:00.000000000 Z
+date: 2012-07-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2152757020 !ruby/object:Gem::Requirement
+  requirement: &2153196200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,7 +22,7 @@ dependencies:
         version: 2.11.0
   type: :development
   prerelease: false
-  version_requirements: *2152757020
+  version_requirements: *2153196200
 description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection
   context.
 email: