nimbus 0.5 → 0.6

data/lib/nimbus/configuration.rb

@@ -8,7 +8,6 @@ module Nimbus
       :forest_size,
       :tree_SNP_sample_size,
       :tree_SNP_total_count,
-      :tree_max_branches,
       :tree_node_min_size,
       :loss_function_discrete,
       :loss_function_continuous,
@@ -24,7 +23,6 @@ module Nimbus
       :forest_size          => 500,
       :tree_SNP_sample_size => 60,
       :tree_SNP_total_count => 200,
-      :tree_max_branches    => 2000,
       :tree_node_min_size   => 5,
       
       :loss_function_discrete   => 'majority_class',
@@ -48,7 +46,6 @@ module Nimbus
       @forest_size              = DEFAULTS[:forest_size]
       @tree_SNP_sample_size     = DEFAULTS[:tree_SNP_sample_size]
       @tree_SNP_total_count     = DEFAULTS[:tree_SNP_total_count]
-      @tree_max_branches        = DEFAULTS[:tree_max_branches]
       @tree_node_min_size       = DEFAULTS[:tree_node_min_size]
       @loss_function_discrete   = DEFAULTS[:loss_function_discrete]
       @loss_function_continuous = DEFAULTS[:loss_function_continuous]
@@ -62,7 +59,6 @@ module Nimbus
       { 
         :snp_sample_size => @tree_SNP_sample_size,
         :snp_total_count => @tree_SNP_total_count,
-        :tree_max_branches => @tree_max_branches,
         :tree_node_min_size => @tree_node_min_size
       }
     end
@@ -98,7 +94,6 @@ module Nimbus
         @forest_size          = user_config_params['forest']['forest_size'].to_i if user_config_params['forest']['forest_size']
         @tree_SNP_total_count = user_config_params['forest']['SNP_total_count'].to_i if user_config_params['forest']['SNP_total_count']
         @tree_SNP_sample_size = user_config_params['forest']['SNP_sample_size_mtry'].to_i  if user_config_params['forest']['SNP_sample_size_mtry']
-        @tree_max_branches    = user_config_params['forest']['max_branches'].to_i  if user_config_params['forest']['max_branches']
         @tree_node_min_size   = user_config_params['forest']['node_min_size'].to_i if user_config_params['forest']['node_min_size']
       end
 
@@ -169,7 +164,6 @@ module Nimbus
       Nimbus.message "*   Forest size: #{@forest_size} trees"
       Nimbus.message "*   Total SNP count: #{@tree_SNP_total_count}"
       Nimbus.message "*   SNPs sample size (mtry): #{@tree_SNP_sample_size}"
-      Nimbus.message "*   Maximum number of branches per tree: #{@tree_max_branches}"
       Nimbus.message "*   Minimun node size in tree: #{@tree_node_min_size}"
       Nimbus.message "*" * 50
       

data/lib/nimbus/tree.rb

@@ -1,14 +1,13 @@
 module Nimbus
   
   class Tree
-    attr_accessor :snp_sample_size, :snp_total_count, :node_min_size, :max_branches, :structure, :predictions
+    attr_accessor :snp_sample_size, :snp_total_count, :node_min_size, :structure, :predictions
     attr_accessor :individuals, :id_to_fenotype
     
     def initialize(options)
       @snp_total_count = options[:snp_total_count]
       @snp_sample_size = options[:snp_sample_size]
       @node_min_size = options[:tree_node_min_size]
-      @max_branches = options[:tree_max_branches]
     end
     
     def seed(all_individuals, individuals_sample, ids_fenotypes)
@@ -57,7 +56,7 @@ module Nimbus
     def self.traverse(tree_structure, data)
       return tree_structure if tree_structure.is_a? Numeric
       raise Nimbus::TreeError, "Forest data has invalid structure. Please check your forest data (file)." if !(tree_structure.is_a?(Hash) && tree_structure.keys.size == 1)
-      return self.traverse( tree_structure.values.first[ data[tree_structure.keys.first].to_i ], data)
+      return self.traverse( tree_structure.values.first[ data[tree_structure.keys.first].to_i - 1 ], data)
     end
     
     

data/spec/fixtures/config.yml

@@ -8,5 +8,4 @@ forest:
   forest_size: 10 #how many trees
   SNP_sample_size_mtry: 60 #mtry
   SNP_total_count: 200
-  max_branches: 2000
   node_min_size: 5

metadata

@@ -2,7 +2,7 @@
 name: nimbus
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: "0.5"
+  version: "0.6"
 platform: ruby
 authors: 
 - "Juanjo Baz\xC3\xA1n"
@@ -11,7 +11,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-20 00:00:00 Z
+date: 2011-08-22 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rspec