NetAnalyzer 0.1.1

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.2.2
+before_install: gem install bundler -v 1.11.2

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in NetAnalyzer.gemspec
+gemspec

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2017 elenarojano
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/NetAnalyzer.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'NetAnalyzer/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "NetAnalyzer"
+  spec.version       = NetAnalyzer::VERSION
+  spec.authors       = ["Elena Rojano, Pedro Seoane"]
+  spec.email         = ["elenarojano@uma.es, seoanezonjic@uma.es"]
+
+  spec.summary       = %q{Network analysis tool that calculate and validate different association indices.}
+  spec.description   = %q{NetAnalyzer is a useful network analysis tool developed in Ruby that can 1) analyse any type of unweighted network, regardless of the number of layers, 2) calculate the relationship between different layers, using various association indices (Jaccard, Simpson, PCC, geometric, cosine and hypergeometric) and 3) validate the results}
+  spec.homepage      = "https://github.com/ElenaRojano/NetAnalyzer"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.11"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_dependency "nmatrix"
+  spec.add_dependency "bigdecimal"
+end

data/README.md

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+# NetAnalyzer
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/NetAnalyzer`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'NetAnalyzer'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install NetAnalyzer
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/ElenaRojano/NetAnalyzer.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/NetAnalyzer.rb

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+#! /usr/bin/env ruby
+
+ROOT_PATH = File.dirname(__FILE__)
+$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'NetAnalyzer'))
+$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'NetAnalyzer', 'methods'))
+
+require 'network'
+require 'optparse'
+
+##############################
+# MAIN METHODS
+##############################
+
+def set_layer(layer_definitions, node_name)
+	layer = nil
+	if layer_definitions.length > 1
+		layer_definitions.each do |layer_name, regexp|
+			if node_name =~ regexp
+				layer = layer_name
+				break
+			end
+		end
+	else
+		layer = layer_definitions.first.first
+	end
+	return layer
+end
+
+##############################
+#OPTPARSE
+##############################
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: #{__FILE__} [options]"
+
+  options[:input_file] = nil
+  opts.on("-i", "--input_file PATH", "Input file to create bipartite networks for further analysis") do |input_file|
+    options[:input_file] = input_file
+  end
+
+  options[:split_char] = "\t"
+  opts.on("-s", "--split_char STRING", "Character for splitting input file. Default: tab") do |split_char|
+    options[:split_char] = split_char
+  end
+
+  options[:output_file] = "network2plot"
+  opts.on("-o", "--output_file PATH", "Output file name") do |output_file|
+    options[:output_file] = output_file
+  end
+
+  options[:assoc_file] = "assoc_values.txt"
+  opts.on("-a", "--assoc_file PATH", "Output file name for association values") do |output_file|
+    options[:assoc_file] = output_file
+  end
+
+  options[:performance_file] = "perf_values.txt"
+  opts.on("-p", "--performance_file PATH", "Output file name for performance values") do |output_file|
+    options[:performance_file] = output_file
+  end
+
+  options[:layers] = [:layer, '-']
+  opts.on("-l", "--layers STRING", "Layer definition on network: layer1name,regexp1;layer2name,regexp2...") do |layers|
+	layers_definition = layers.split(";").map{|layer_attr| layer_attr.split(',')}
+	layers_definition.map!{|layer_attr| [layer_attr.first.to_sym, /#{layer_attr.last}/]}
+    options[:layers] = layers_definition
+  end
+
+  options[:use_layers] = []
+  opts.on("-u", "--use_layers STRING", "Set which layers must be used on association methods: layer1,layer2;layerA,layerB") do |string|
+    options[:use_layers] = string.split(";").map{|layer_attr| layer_attr.split(',').map{|layer| layer.to_sym}}
+  end
+
+  options[:control_file] = nil
+  opts.on("-c", "--control_file PATH", "Control file name") do |file|
+    options[:control_file] = file
+  end
+
+  options[:output_style] = "neato"
+  opts.on("-t", "--output_style STRING", "Style to plot output file") do |output_style|
+    options[:output_style] = output_style
+  end
+
+  options[:meth] = nil
+  opts.on("-m", "--association_method STRING", "Association method to use on network") do |meth|
+    options[:meth] = meth.to_sym
+  end
+
+  options[:no_autorelations] = FALSE
+  opts.on("-N", "--no_autorelations", "Remove association values between nodes os same type") do
+    options[:no_autorelations] = TRUE
+  end
+
+end.parse!
+
+##########################
+#MAIN
+##########################
+
+fullNet = Network.new(options[:layers].map{|layer| layer.first})
+puts "Loading network data"
+File.open(options[:input_file]).each("\n") do |line|
+	line.chomp!
+	pair = line.split(options[:splitChar])
+	node1 = pair[0]
+	node2 = pair[1]
+	fullNet.add_node(node1, set_layer(options[:layers], node1))
+	fullNet.add_node(node2, set_layer(options[:layers], node2))
+	fullNet.add_edge(node1, node2)	
+end
+#fullNet.plot(options[:output_file], options[:output_style])
+
+
+if !options[:meth].nil?
+	puts "Performing association method #{options[:meth]} on network"
+	if options[:meth] == :transference
+		fullNet.generate_adjacency_matrix(options[:use_layers][0][0], options[:use_layers][0][1])
+		fullNet.generate_adjacency_matrix(options[:use_layers][1][0], options[:use_layers][1][1])
+		fullNet.get_association_values(
+			[options[:use_layers][0][0], options[:use_layers][0][1]], 
+			[options[:use_layers][1][0], options[:use_layers][1][1]],
+			:transference)
+	else
+		fullNet.get_association_values(
+			options[:use_layers][0], 
+			options[:use_layers][1].first, 
+			options[:meth])
+	end
+	puts 'Clean autorelations'  if options[:no_autorelations]
+	fullNet.clean_autorelations_on_association_values if options[:no_autorelations]
+	File.open(options[:assoc_file], 'w') do |f|
+		fullNet.association_values[options[:meth]].each do |val|
+			f.puts val.join("\t")
+		end
+	end
+end
+
+if !options[:meth].nil? && !options[:control_file].nil?
+	puts "Doing validation on association values obtained from method #{options[:meth]}"
+	control = []
+	File.open(options[:control_file]).each("\n") do |line|
+		line.chomp!
+		control << line.split("\t")
+	end
+	fullNet.load_control(control)
+	performance = fullNet.get_pred_rec(options[:meth])
+	File.open(options[:performance_file], 'w') do |f|
+		f.puts %w[cut prec rec meth].join("\t")
+		performance.each do |item|
+			item << options[:meth].to_s
+			f.puts item.join("\t")
+		end
+	end
+end
+
+puts "End of analysis: #{options[:meth]}"

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "NetAnalyzer"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/NetAnalyzer.rb

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+require "NetAnalyzer/version"
+
+module NetAnalyzer
+  # Your code goes here...
+end

data/lib/NetAnalyzer/network.rb

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+require 'nodes'
+require 'nmatrix'
+require 'pp'
+require 'bigdecimal'
+
+class Network
+	attr_reader :association_values
+
+	## BASIC METHODS
+	############################################################
+	def initialize(layers)
+		@nodes = {} 
+		@edges = {}
+		@adjacency_matrices = {}
+		@layers = layers
+		@association_values = {}
+		@control_connections = {}
+	end
+	
+	def add_node(nodeID, nodeType = 0)
+		@nodes[nodeID] = Node.new(nodeID, nodeType)
+	end
+
+	def add_edge(nodeID1, nodeID2)
+		query_edge(nodeID1, nodeID2)
+		query_edge(nodeID2, nodeID1)
+	end
+
+	def query_edge(nodeA, nodeB)
+		query = @edges[nodeA]
+		if query.nil?
+			@edges[nodeA] = [nodeB]
+		else
+			query << nodeB
+		end
+	end
+
+	def plot(output_filename, layout="dot")		
+		roboWrite = File.open(output_filename, 'w')
+		roboWrite.puts "digraph g {"
+		@edges.each do |nodeID, associatedIDs|
+			associatedIDs.each do |associatedID|
+				roboWrite.puts "\"#{nodeID}\"->\"#{associatedID}\";"
+			end
+		end
+		roboWrite.puts "}"
+		roboWrite.close
+		cmd = "#{layout} -Tpng #{output_filename} -o #{output_filename}.png"
+		system(cmd)
+	end
+
+	def get_all_intersections
+		intersection_lengths = []
+		get_all_pairs do |node1, node2|
+			intersection_lengths << intersection(node1, node2).length
+		end
+		return intersection_lengths
+	end
+
+	def get_all_pairs(args = {})
+		default = {:meth => :all, :layers => :all}
+		args = default.merge(args)
+		if args[:layers] == :all
+			nodeIDs = @nodes.keys
+		else
+			nodeIDs = []
+			args[:layers].each do |layer|
+				nodeIDs.concat(@nodes.select{|id, node| node.type == layer}.keys)
+			end
+		end
+
+		if args[:meth] == :all
+			while !nodeIDs.empty?
+				node1 = nodeIDs.shift
+				nodeIDs.each do |node2|
+					yield(node1, node2)
+				end
+			end
+		#elsif args[:meth] == :conn
+			
+		end
+	end
+
+	def get_nodes_layer(layers)
+		#for creating ny value in hypergeometric and pcc index
+		nodes = []
+		layers.each do |layer|
+			nodes.concat(@nodes.select{|nodeId, node| node.type == layer}.values)
+		end
+		return nodes
+	end
+
+	def intersection(node1, node2)
+		shared_nodes = []
+		associatedIDs_node1 = @edges[node1]
+		associatedIDs_node2 = @edges[node2]
+		intersectedIDs = associatedIDs_node1 & associatedIDs_node2
+		intersectedIDs.each do |id|
+			shared_nodes << @nodes[id]
+		end
+		return shared_nodes
+	end
+
+	def generate_adjacency_matrix(layerA, layerB)
+		layerAidNodes = @nodes.select{|id, node| node.type == layerA}.keys
+		layerBidNodes = @nodes.select{|id, node| node.type == layerB}.keys
+		adjacency_matrix = []
+		layerAidNodes.each do |nodeA|
+			layerBidNodes.each do |nodeB|
+				if @edges[nodeB].include?(nodeA)
+					adjacency_matrix << 1
+				else
+					adjacency_matrix << 0
+				end
+			end
+		end
+		matrix = NMatrix.new([layerAidNodes.length, layerBidNodes.length], adjacency_matrix)
+		all_info_matrix = [matrix, layerAidNodes, layerBidNodes]
+		@adjacency_matrices[[layerA, layerB]] = all_info_matrix
+		return all_info_matrix
+	end
+
+	def clean_autorelations_on_association_values
+		@association_values.each do |meth, values|
+			values.select!{|relation| @nodes[relation[0]].type != @nodes[relation[1]].type}
+		end
+	end
+
+	## ASSOCIATION METHODS
+	############################################################
+	def get_association_values(layers, base_layer, meth)
+		relations = [] #node A, node B, val
+		if meth == :jaccard #all networks
+			relations = get_jaccard_association(layers, base_layer)
+		elsif meth == :simpson #all networks
+			relations = get_simpson_association(layers, base_layer)
+		elsif meth == :geometric #all networks
+			relations = get_geometric_associations(layers, base_layer)
+		elsif meth == :cosine #all networks
+			relations = get_cosine_associations(layers, base_layer)
+		elsif meth == :pcc #all networks
+			relations = get_pcc_associations(layers, base_layer)
+		elsif meth == :hypergeometric #all networks
+			relations = get_hypergeometric_associations(layers, base_layer)
+		elsif meth == :csi #all networks
+			relations = get_csi_associations(layers, base_layer)
+		elsif meth == :transference #tripartite networks
+			relations = get_association_by_transference_resources(layers, base_layer)
+		end
+		return relations
+	end
+
+	## association methods adjacency matrix based
+	#---------------------------------------------------------
+	# Alaimo 2014, doi: 10.3389/fbioe.2014.00071
+	def get_association_by_transference_resources(firstPairLayers, secondPairLayers, lambda_value1 = 0.5, lambda_value2 = 0.5)
+		matrix1 = @adjacency_matrices[firstPairLayers].first
+		rowIds = @adjacency_matrices[firstPairLayers][1]
+		matrix2 = @adjacency_matrices[secondPairLayers].first
+		colIds =  @adjacency_matrices[secondPairLayers][2]
+		m1rowNumber = matrix1.rows
+		m1colNumber = matrix1.cols
+		m2rowNumber = matrix2.rows
+		m2colNumber = matrix2.cols
+		#puts m1rowNumber, m1colNumber, m2rowNumber, m2colNumber
+		matrix1Weight = graphWeights(m1colNumber, m1rowNumber, matrix1.transpose, lambda_value1)
+		matrix2Weight = graphWeights(m2colNumber, m2rowNumber, matrix2.transpose, lambda_value2)
+		matrixWeightProduct = matrix1Weight.dot(matrix2.dot(matrix2Weight))
+		finalMatrix = matrix1.dot(matrixWeightProduct)
+		relations = nmatrix2relations(finalMatrix, rowIds, colIds)
+		@association_values[:transference] = relations
+		return relations
+	end
+
+	## association methods node pairs based
+	#---------------------------------------------------------
+	# Bass 2013, doi:10.1038/nmeth.2728
+	def get_associations(layers, base_layer) # BASE METHOD
+		relations = []
+		get_all_pairs(layers: layers) do |node1, node2|
+			associatedIDs_node1 = @edges[node1].map{|id| @nodes[id]}.select{|node| node.type == base_layer}.map{|node| node.id}
+			associatedIDs_node2 = @edges[node2].map{|id| @nodes[id]}.select{|node| node.type == base_layer}.map{|node| node.id}
+			intersectedIDs = associatedIDs_node1 & associatedIDs_node2
+			associationValue = yield(associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2)
+			relations << [node1, node2, associationValue]  
+		end
+		return relations
+	end
+
+	def get_jaccard_association(layers, base_layer)
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			unionIDS = associatedIDs_node1 | associatedIDs_node2
+			jaccValue = intersectedIDs.length.to_f/unionIDS.length		
+		end
+		@association_values[:jaccard] = relations
+		return relations
+	end
+
+	def get_simpson_association(layers, base_layer)
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			minLength = [associatedIDs_node1.length, associatedIDs_node2.length].min
+			simpsonValue = intersectedIDs.length.to_f/minLength
+		end
+		@association_values[:simpson] = relations
+		return relations
+	end
+
+	def get_geometric_associations(layers, base_layer)
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|	
+			intersectedIDs = intersectedIDs.length**2
+			productLength = associatedIDs_node1.length * associatedIDs_node2.length
+			geometricValue = intersectedIDs.to_f/productLength
+		end
+		@association_values[:geometric] = relations
+		return relations
+	end
+
+	def get_cosine_associations(layers, base_layer)
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			productLength = Math.sqrt(associatedIDs_node1.length * associatedIDs_node2.length)
+			cosineValue = intersectedIDs.length/productLength
+		end
+		@association_values[:cosine] = relations
+		return relations
+	end
+
+	def get_pcc_associations(layers, base_layer)
+		#for Ny calcule use get_nodes_layer
+		ny = get_nodes_layer(layers).length
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			intersProd = intersectedIDs.length * ny
+			nodesProd = associatedIDs_node1.length * associatedIDs_node2.length
+			nodesSubs = intersProd - nodesProd
+			nodesAInNetwork = ny - associatedIDs_node1.length
+			nodesBInNetwork = ny - associatedIDs_node2.length
+			pccValue = nodesSubs.to_f / Math.sqrt(nodesProd * nodesAInNetwork * nodesBInNetwork)
+		end
+		@association_values[:pcc] = relations
+		return relations
+	end
+
+	def get_hypergeometric_associations(layers, base_layer)
+		ny = get_nodes_layer(layers).length
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			minLength = [associatedIDs_node1.length, associatedIDs_node2.length].min
+			intersection_lengths = intersectedIDs.length
+			sum = 0
+			nA = associatedIDs_node1.length
+			nB = associatedIDs_node2.length
+			#Using index from A layer proyected to B
+			(intersection_lengths..minLength).each do |i|
+				binom_product = binom(nA, i) * binom(ny - nA, nB - i)
+				binom_product_float = binom_product.to_f
+				to_f = false
+				if binom_product_float.infinite? # Handle bignum coercition to bigdecimal to avoid infinity values on float class. 
+					binom_product_float = BigDecimal.new(binom_product)
+					to_f = true
+				end
+				sum += binom_product_float / binom(ny, nB)
+				sum = sum.to_f if to_f # once the operation has finished, sum is corced from bigdecimal to float
+			end
+			if sum == 0
+				hypergeometricValue = 0
+			else
+				hypergeometricValue = -Math.log10(sum)
+			end
+			hypergeometricValue
+		end
+		@association_values[:hypergeometric] = relations
+		return relations
+	end
+
+	def add_record(hash, key, key2, value)
+		query = hash[key]
+		if query.nil?
+			hash[key]={key2 => value}
+		else
+			query[key2] = value
+		end
+	end
+
+	def get_csi_associations(layers, base_layer)
+		pcc_relations = get_pcc_associations(layers, base_layer)
+		indexed_pcc_relations = {}
+		pcc_relations.each do |node1, node2, assoc_index|
+			if assoc_index > 0
+				add_record(indexed_pcc_relations, node1, node2, assoc_index)
+				add_record(indexed_pcc_relations, node2, node1, assoc_index)
+			end
+		end
+		ny = get_nodes_layer(layers).length
+		relations = get_associations(layers, base_layer) do |associatedIDs_node1, associatedIDs_node2, intersectedIDs, node1, node2|
+			query = indexed_pcc_relations[node1]
+			if query.nil?
+				valid_A_nodes = []
+				pccAB = -0.05
+			else
+				nested_query = query[node2]
+				if nested_query.nil?
+					pccAB = -0.05
+				else
+					pccAB = nested_query - 0.05
+				end
+				valid_A_nodes = query.select{|node_id, pcc| pcc>= pccAB}.keys
+			end
+			query2 = indexed_pcc_relations[node2]
+			if query2.nil?
+				valid_B_nodes = []
+			else
+				valid_B_nodes = query2.select{|node_id, pcc| pcc>= pccAB}.keys
+			end
+			valid_connections = valid_A_nodes | valid_B_nodes
+			csiValue = 1 - valid_connections.length.to_f/ny
+		end
+		@association_values[:csi] = relations
+		return relations
+	end
+
+	## PERFORMANCE METHODS
+	############################################################
+	def load_control(ref_array)
+		control = {}
+		ref_array.each do |node1, node2|
+			if node2 != '-'
+				query = control[node1]
+				if query.nil?
+					control[node1] = [node2]
+				else
+					query << node2
+				end
+			end
+		end
+		@control_connections = control
+		return control
+	end
+
+	def load_prediction(pairs_array)
+		pred = {}
+		min = nil
+		max = nil
+		pairs_array.each do |key, label, score|
+			query = pred[key]
+			if !min.nil? && !max.nil?
+				min = score if score < min
+				max = score if score > max
+			else
+				min = score; max = score
+			end
+			if query.nil?
+				pred[key] = [[label], [score]]
+			else
+				query.first << label
+				query.last << score
+			end
+		end
+		return pred, [min, max]
+	end
+
+
+	# Pandey 2007, Association Analysis-based Transformations for Protein Interaction Networks: A Function Prediction Case Study
+	def get_pred_rec(meth, cut_number = 100, top_number = 10000)
+		performance = [] #cut, pred, rec
+		preds, limits = load_prediction(@association_values[meth])
+		cuts = get_cuts(limits, cut_number)
+		cuts.each do |cut|
+			prec, rec = pred_rec(preds, cut, top_number)
+			performance << [cut, prec, rec]
+		end
+		return performance
+	end
+
+	def pred_rec(preds, cut, top)
+		predicted_labels = 0 #m
+		true_labels = 0 #n
+		common_labels = 0 # k
+		@control_connections.each do |key, c_labels|
+			true_labels += c_labels.length #n
+			pred_info = preds[key]
+			if !pred_info.nil?
+				labels, scores = pred_info
+				reliable_labels = get_reliable_labels(labels, scores, cut, top)
+
+				predicted_labels += reliable_labels.length #m
+				common_labels += (c_labels & reliable_labels).length #k
+			end
+		end
+		prec = common_labels.to_f/predicted_labels
+		rec = common_labels.to_f/true_labels
+		prec = 0.0 if prec.nan?
+		rec = 0.0 if rec.nan?
+		return prec, rec
+	end
+
+
+
+	## AUXILIAR METHODS
+	#######################################################################################
+	private
+
+	def get_cuts(limits, n_cuts)
+		cuts = []
+		range = (limits.last - limits.first).to_f/n_cuts
+		cut = limits.first
+		n_cuts.times do
+			cuts << cut
+			cut += range
+		end
+		return cuts
+	end
+
+	def get_reliable_labels(labels, scores, cut, top)
+		reliable_labels = []
+		scores.each_with_index do |score, i|
+			reliable_labels << [labels[i], score] if score >= cut
+		end
+		reliable_labels = reliable_labels.sort!{|l1,l2| l2.last <=> l1.last}[0..top-1].map{|pred| pred.first}
+		return reliable_labels
+	end
+	
+	def graphWeights (rowsNumber, colsNumber, inputMatrix, lambdaValue = 0.5)
+		invMatrix = inputMatrix.sum(0).map{|e| 1.0/ e}
+	 	diagonalColSums = NMatrix.diag(invMatrix)
+	 	rowsSums = inputMatrix.sum(1).to_flat_a
+	 	ky = NMatrix.new([rowsNumber, rowsNumber], rowsSums).map{|e| e ** lambdaValue } 	
+	 	invertLambdaVal = (1 - lambdaValue)
+	 	kx = NMatrix.new([rowsNumber, rowsNumber], rowsSums).transpose.map{|e| e ** invertLambdaVal } 
+	 	nx = (ky * kx).map{|e| 1.0/ e}
+	 	weigth = (inputMatrix.dot(diagonalColSums)).transpose
+	 	weigth = inputMatrix.dot(weigth)
+	 	weigth = nx * weigth
+	 	return weigth
+	end
+
+	def nmatrix2relations(finalMatrix, rowIds, colIds)
+		relations = []
+		rowIds.each_with_index do |rowId, rowPos|
+			colIds.each_with_index do |colId, colPos|
+				associationValue = finalMatrix[rowPos, colPos]
+				relations << [rowId, colId, associationValue]
+			end
+		end
+		return relations
+	end
+
+	def binom(n,k)
+		if k > 0 && k < n
+  			res = (1+n-k..n).inject(:*)/(1..k).inject(:*)
+  		else
+  			res = 1
+  		end
+	end
+end

data/lib/NetAnalyzer/nodes.rb

@@ -0,0 +1,7 @@
+class Node
+	attr_reader :type, :id
+	def initialize(id, type)
+		@id = id
+		@type = type
+	end
+end

data/lib/NetAnalyzer/version.rb

@@ -0,0 +1,3 @@
+module NetAnalyzer
+  VERSION = "0.1.1"
+end

metadata

@@ -0,0 +1,136 @@
+--- !ruby/object:Gem::Specification
+name: NetAnalyzer
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Elena Rojano, Pedro Seoane
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-01-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.11'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: nmatrix
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bigdecimal
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: NetAnalyzer is a useful network analysis tool developed in Ruby that
+  can 1) analyse any type of unweighted network, regardless of the number of layers,
+  2) calculate the relationship between different layers, using various association
+  indices (Jaccard, Simpson, PCC, geometric, cosine and hypergeometric) and 3) validate
+  the results
+email:
+- elenarojano@uma.es, seoanezonjic@uma.es
+executables:
+- NetAnalyzer.rb
+- console
+- setup
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- NetAnalyzer.gemspec
+- README.md
+- Rakefile
+- bin/NetAnalyzer.rb
+- bin/console
+- bin/setup
+- lib/NetAnalyzer.rb
+- lib/NetAnalyzer/network.rb
+- lib/NetAnalyzer/nodes.rb
+- lib/NetAnalyzer/version.rb
+homepage: https://github.com/ElenaRojano/NetAnalyzer
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: Network analysis tool that calculate and validate different association indices.
+test_files: []