nimbus 0.5 → 0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/lib/nimbus/configuration.rb +0 -6
- data/lib/nimbus/tree.rb +2 -3
- data/spec/fixtures/config.yml +0 -1
- metadata +2 -2
data/lib/nimbus/configuration.rb
CHANGED
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@@ -8,7 +8,6 @@ module Nimbus
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:forest_size,
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:tree_SNP_sample_size,
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:tree_SNP_total_count,
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-
:tree_max_branches,
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:tree_node_min_size,
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:loss_function_discrete,
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:loss_function_continuous,
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@@ -24,7 +23,6 @@ module Nimbus
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:forest_size => 500,
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:tree_SNP_sample_size => 60,
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:tree_SNP_total_count => 200,
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:tree_max_branches => 2000,
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:tree_node_min_size => 5,
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:loss_function_discrete => 'majority_class',
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@@ -48,7 +46,6 @@ module Nimbus
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@forest_size = DEFAULTS[:forest_size]
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@tree_SNP_sample_size = DEFAULTS[:tree_SNP_sample_size]
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@tree_SNP_total_count = DEFAULTS[:tree_SNP_total_count]
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-
@tree_max_branches = DEFAULTS[:tree_max_branches]
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@tree_node_min_size = DEFAULTS[:tree_node_min_size]
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@loss_function_discrete = DEFAULTS[:loss_function_discrete]
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@loss_function_continuous = DEFAULTS[:loss_function_continuous]
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@@ -62,7 +59,6 @@ module Nimbus
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{
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:snp_sample_size => @tree_SNP_sample_size,
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:snp_total_count => @tree_SNP_total_count,
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:tree_max_branches => @tree_max_branches,
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:tree_node_min_size => @tree_node_min_size
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}
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end
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@@ -98,7 +94,6 @@ module Nimbus
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@forest_size = user_config_params['forest']['forest_size'].to_i if user_config_params['forest']['forest_size']
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@tree_SNP_total_count = user_config_params['forest']['SNP_total_count'].to_i if user_config_params['forest']['SNP_total_count']
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@tree_SNP_sample_size = user_config_params['forest']['SNP_sample_size_mtry'].to_i if user_config_params['forest']['SNP_sample_size_mtry']
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-
@tree_max_branches = user_config_params['forest']['max_branches'].to_i if user_config_params['forest']['max_branches']
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@tree_node_min_size = user_config_params['forest']['node_min_size'].to_i if user_config_params['forest']['node_min_size']
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end
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@@ -169,7 +164,6 @@ module Nimbus
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Nimbus.message "* Forest size: #{@forest_size} trees"
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Nimbus.message "* Total SNP count: #{@tree_SNP_total_count}"
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Nimbus.message "* SNPs sample size (mtry): #{@tree_SNP_sample_size}"
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-
Nimbus.message "* Maximum number of branches per tree: #{@tree_max_branches}"
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Nimbus.message "* Minimun node size in tree: #{@tree_node_min_size}"
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Nimbus.message "*" * 50
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data/lib/nimbus/tree.rb
CHANGED
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@@ -1,14 +1,13 @@
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module Nimbus
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class Tree
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attr_accessor :snp_sample_size, :snp_total_count, :node_min_size, :
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+
attr_accessor :snp_sample_size, :snp_total_count, :node_min_size, :structure, :predictions
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attr_accessor :individuals, :id_to_fenotype
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def initialize(options)
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@snp_total_count = options[:snp_total_count]
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@snp_sample_size = options[:snp_sample_size]
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@node_min_size = options[:tree_node_min_size]
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@max_branches = options[:tree_max_branches]
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end
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def seed(all_individuals, individuals_sample, ids_fenotypes)
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@@ -57,7 +56,7 @@ module Nimbus
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def self.traverse(tree_structure, data)
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return tree_structure if tree_structure.is_a? Numeric
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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)
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-
return self.traverse( tree_structure.values.first[ data[tree_structure.keys.first].to_i ], data)
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return self.traverse( tree_structure.values.first[ data[tree_structure.keys.first].to_i - 1 ], data)
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end
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data/spec/fixtures/config.yml
CHANGED
metadata
CHANGED
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@@ -2,7 +2,7 @@
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name: nimbus
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version: !ruby/object:Gem::Version
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prerelease:
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version: "0.
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version: "0.6"
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platform: ruby
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authors:
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- "Juanjo Baz\xC3\xA1n"
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@@ -11,7 +11,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2011-08-
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date: 2011-08-22 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rspec
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