fathom 0.3.0 → 0.3.1

data/.autotest

@@ -0,0 +1,10 @@
+# require 'autotest/fsevent'
+# require 'autotest/growl'
+
+Autotest.add_hook :initialize do |autotest|
+  # Keeps me from calling something document_spec.rb
+  # %w{.git .svn .hg .DS_Store ._* vendor tmp log doc}.each do |exception|
+  %w{.git .svn .hg .DS_Store ._* vendor tmp log}.each do |exception|
+    autotest.add_exception(exception)
+  end
+end

data/Gemfile

@@ -1,6 +1,14 @@
 source 'http://rubygems.org'
 
-gem "rspec"
-gem "ruby-debug"
 gem "fastercsv"
 gem 'uuid'
+# gem 'spira'
+# gem 'rdf'
+gem 'sparql-algebra'
+
+group :test do
+  gem "ruby-debug"
+  gem "rspec"
+  gem "ZenTest"
+end
+

data/Gemfile.lock

@@ -1,11 +1,15 @@
 GEM
   remote: http://rubygems.org/
   specs:
+    ZenTest (4.4.0)
+    addressable (2.2.2)
     columnize (0.3.1)
     diff-lcs (1.1.2)
     fastercsv (1.5.3)
     linecache (0.43)
     macaddr (1.0.0)
+    rdf (0.3.0.pre)
+      addressable (>= 2.2)
     rspec (2.0.1)
       rspec-core (~> 2.0.1)
       rspec-expectations (~> 2.0.1)
@@ -21,6 +25,8 @@ GEM
       ruby-debug-base (~> 0.10.3.0)
     ruby-debug-base (0.10.3)
       linecache (>= 0.3)
+    sparql-algebra (0.0.1)
+      rdf (= 0.3.0.pre)
     uuid (2.3.1)
       macaddr (~> 1.0)
 
@@ -28,7 +34,9 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  ZenTest
   fastercsv
   rspec
   ruby-debug
+  sparql-algebra
   uuid

data/TODO.md

@@ -1,30 +1,7 @@
 TODO
 ====
 
-Reorganizing (0.2.5)
-------------
-
-I've just made some big refactoring steps regarding the organization of the system and the distributions.  To make sure we're there:
-
-* Go back and test the 4 distributions I decided on
-* Finish the discrete ideas, adding size to the node and automatically using that for stats
-* Create the idea of a labeled, multinomial node
-* Add SQLite3 for in-memory set operations for a labeled, multinomial node
-* Make sure we are not defining methods on all objects in a class when they should only be set for a single object.
-
-Also, the general organization of the system could be broken down better:
-
-* agent
-* distributions
-* node
-* import
-* causal_graph
-* belief_network
-* knowledge_base
-* apophenia
-* simulation
-
-Belief Networks (0.3)
+Belief Networks (0.3.1)
 ---------------
 
 To get these delivered, I need to revisit the edge logic, to make sure it's easy to extend each edge with an object.
@@ -35,11 +12,21 @@ Then:
 * Network propagation
 * Network testing (polytree)
 
-Agent Based Modeling (0.3.1)
+Reorganizing (0.3.2)
+------------
+
+I've just made some big refactoring steps regarding the organization of the system and the distributions.  To make sure we're there:
+
+* Fix the inheritance structure
+* Go back and test the 4 distributions I decided on
+* Add SQLite3 for in-memory set operations for a labeled, multinomial node
+
+Agent Based Modeling (0.3.3)
 --------------------
 
 * Add parameter-passing standards for callbacks
 * Add EventMachine and async capabilities (Including the cluster idea)
+* Make sure the scope of dynamic methods defined are correct (class, object, singleton) (on properties and simulation)
 
 Knowledge Base (0.4)
 --------------

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/lib/fathom.rb

@@ -21,24 +21,27 @@ module Fathom
   
   # Autoload classes and modules so that we only load as much of the library as we're using.
   # This allows us to have a fairly large library without taking up a lot of memory unless we need it.
-  autoload :Inverter, "inverter"
   autoload :Node, "node"
-  autoload :PlausibleRange, "plausible_range"
+  autoload :BeliefNode, "node/belief_node"
+  autoload :DataCollection, "node/data_collection"
+  autoload :DataNode, "node/data_node"
+  autoload :DiscreteNode, "node/discrete_node"
+  autoload :MCNode, "node/mc_node"
+  autoload :PlausibleRange, "node/plausible_range"
+  autoload :Fact, "node/fact"
+  autoload :Decision, "node/decision"
+  autoload :CPMNode, 'node/cpm_node'
+
   autoload :ValueDescription, "value_description"
-  autoload :ValueAggregator, "value_aggregator"
-  autoload :ValueMultiplier, "value_multiplier"
   autoload :MonteCarloSet, "monte_carlo_set"
-  autoload :MCNode, "mc_node"
-  autoload :CausalGraph, "causal_graph"
-  autoload :DataNode, "data_node"
   autoload :KnowledgeBase, "knowledge_base"
 
   autoload :Import, "import"
   autoload :ImportNode, "import/import_node"
   autoload :YAMLImport, 'import/yaml_import'
   autoload :CSVImport, 'import/csv_import'
-  autoload :RDFImport, 'import/rdf_import'
-  autoload :SQLiteImport, 'import/sqlite_import'
+  # autoload :RDFImport, 'import/rdf_import'
+  # autoload :SQLiteImport, 'import/sqlite_import'
   
   autoload :Simulation, 'simulation'
   autoload :TickMethods, 'simulation/tick_methods'
@@ -48,10 +51,10 @@ module Fathom
   autoload :Properties, 'agent/properties'
   autoload :AgentCluster, 'agent/agent_cluster'
   
-  autoload :NumericMethods, 'numeric_methods'
-  autoload :EnforcedName, 'enforced_name'
+  autoload :EnforcedName, 'node/node_extensions/enforced_name'
+  autoload :NumericMethods, 'node/node_extensions/numeric_methods'
   
-  autoload :Distributions, 'distributions'
+  require 'distributions'
   module Distributions
     autoload :Gaussian, 'distributions/gaussian'
     autoload :Uniform, 'distributions/uniform'
@@ -66,4 +69,4 @@ module Fathom
 end
 
 # Temporary
-include Fathom
+# include Fathom

data/lib/fathom/agent.rb

@@ -4,14 +4,6 @@ class Fathom::Agent
   # =================
   # = Class Methods =
   # =================
-  class << self
-    def define_node_accessor(name, node)
-      method_name = ("node_for_" + name.to_s.downcase.gsub(/\s+/, '_')).to_sym
-      define_method(method_name) do
-        node
-      end
-    end
-  end
   
   include Properties
   
@@ -36,7 +28,14 @@ class Fathom::Agent
       nodes.each do |name, node|
         next unless self.class.properties.include?(name)
         states[name] = node.respond_to?(:rand) ? node.rand : node
-        self.class.define_node_accessor(name, node)
+
+        method_name = ("node_for_" + name.to_s.downcase.gsub(/\s+/, '_')).to_sym
+        (class << self; self; end).module_eval do
+          define_method method_name do
+            node
+          end
+        end
+        
       end
     end
   

data/lib/fathom/archive/conditional_probability_matrix.rb

@@ -113,4 +113,7 @@ class ConditionalProbabilityMatrix
     def get_index(node, label)
       node.labels.index(label)
     end
+end
+
+class CPM < ConditionalProbabilityMatrix
 end

data/lib/fathom/archive/node.rb

@@ -23,7 +23,10 @@ class Node
   end
   
   def inspect
-    "Node: #{self.labels.inspect} #{self.probabilities.inspect}"
+    matched_array = []
+    self.labels.each_with_index {|e, i| matched_array << e; matched_array << self.probabilities[i]}
+    "Node: #{self.name.to_s} #{self.labels.inspect} #{self.probabilities.to_a.inspect}"
+    "Node: #{self.name.to_s} #{matched_array.inspect}"
   end
   
   def belief
@@ -34,7 +37,27 @@ class Node
   alias :l :likelihood
   alias :p :probabilities
   
+  def probability(label)
+    probabilities[index_for(label)]
+  end
+  
+  def inverse_probability(label)
+    1 - probability(label)
+  end
+  
+  def odds(label)
+    probability(label) / inverse_probability(label)
+  end
+  
+  def to_a
+    self.probabilities.to_a
+  end
+  
   protected
+  
+    def index_for(label)
+      labels.index(label)
+    end
 
     def assert_likelihood
       @likelihood = Vector.ary_to_gv(Array.new(@probabilities.size, 1))

data/lib/fathom/distributions/discrete_uniform.rb

@@ -6,40 +6,19 @@ class Fathom::Distributions::DiscreteUniform
       @rng ||= GSL::Rng.alloc(GSL::Rng::MT19937_1999, Kernel.rand(100_000))
     end
     
-    def rand
-      (rng.ugaussian / size).floor + 1
-    end
-    
-    def inverse_cdf(opts={})
-      mean = opts[:mean]
-      sd = opts[:sd]
-      sd ||= opts[:std]
-      sd ||= opts[:standard_deviation]
-      lower = opts.fetch(:lower, true)
-      lower = false if opts[:upper]
-      confidence_interval = opts.fetch(:confidence_interval, 0.05)
-      value = lower ? GSL::Cdf.ugaussian_Pinv(confidence_interval) : GSL::Cdf.ugaussian_Qinv(confidence_interval)
-      value + mean
-    end
-    alias :lower_bound :inverse_cdf
-
-    def upper_bound(opts={})
-      inverse_cdf(opts.merge(:lower => false))
-    end
-
-    def interval_values(opts={})
-      confidence_interval = opts.fetch(:confidence_interval, 0.9)
-      bound = (1 - confidence_interval) / 2.0
-      [lower_bound(opts.merge(:confidence_interval => bound)), upper_bound(opts.merge(:confidence_interval => bound))]
-    end
-    
-    # If only I had the background to explain what this is....
-    # I want to know how many standard deviations are expressed by the confidence interval
-    # I can then divide  the range by this number to get the standard deviation
-    def standard_deviations_under(confidence_interval)
-      GSL::Cdf.ugaussian_Qinv((1 - confidence_interval) / 2) * 2
+    # Bounded from 0 to size - 1
+    def rand(size)
+      value = get_rand(size)
+      while value < 0 or value >= size
+        value = get_rand(size)
+      end
+      value
     end
     
+    protected
+      def get_rand(size)
+        (rng.ugaussian / size).floor + 1
+      end
     
   end
 end

data/lib/fathom/import.rb

@@ -33,50 +33,53 @@ require File.expand_path(File.join(File.dirname(__FILE__), '..', 'fathom'))
   This way data from spreadsheets or YAML files can easily be added to the knowledge base.
   
 =end  
-class Fathom::Import
+
+module Fathom
+  class Import
   
-  class << self
-    def import(opts={})
-      importer = new(opts)
-      importer.import
+    class << self
+      def import(opts={})
+        importer = new(opts)
+        importer.import
+      end
     end
-  end
   
-  attr_reader :content, :options, :import_node
+    attr_reader :content, :options, :import_node
   
-  def initialize(opts={})
-    @options = OptionsHash.new(opts)
-    @content = @options[:content]
-    @import_node = ImportNode.new(opts)
-  end
+    def initialize(opts={})
+      @options = OptionsHash.new(opts)
+      @content = @options[:content]
+      @import_node = ImportNode.new(opts)
+    end
   
-  def import
-    import_methods.each do |method|
-      klass, initialization_data = self.send(method.to_sym)
-      initialization_data.each do |values|
-        extract_nodes(klass, values)
+    def import
+      import_methods.each do |method|
+        klass, initialization_data = self.send(method.to_sym)
+        initialization_data.each do |values|
+          extract_nodes(klass, values)
+        end
       end
+      self.import_node
     end
-    self.import_node
-  end
   
-  protected
+    protected
   
-    # Just blankly try to initiate a node.  If it fails, silently fail for now.
-    def extract_nodes(klass, values)
-      begin
-        node = klass.new(values)
-        if node
-          self.import_node.add_child(node) 
-          Fathom.knowledge_base[node.name] = node
+      # Just blankly try to initiate a node.  If it fails, silently fail for now.
+      def extract_nodes(klass, values)
+        begin
+          node = klass.new(values)
+          if node
+            self.import_node.add_child(node) 
+            Fathom.knowledge_base[node.name] = node
+          end
+        rescue
+          nil
         end
-      rescue
-        nil
       end
-    end
     
-    def import_methods
-      (self.methods - self.class.superclass.instance_methods).map {|m| m if m =~ /import_\w+/}.compact
-    end
-  
+      def import_methods
+        (self.methods - self.class.superclass.instance_methods).map {|m| m if m =~ /import_\w+/}.compact
+      end
+
+  end
 end

data/lib/fathom/import/yaml_import.rb

@@ -2,7 +2,7 @@ require File.expand_path(File.join(File.dirname(__FILE__), '..', '..', 'fathom')
 require 'open-uri'
 require 'yaml'
 
-class Fathom::YAMLImport < Import
+class Fathom::YAMLImport < Fathom::Import
   def import_plausible_ranges
     assert_yaml_content
     plausible_ranges = extract_plausible_ranges
@@ -15,6 +15,12 @@ class Fathom::YAMLImport < Import
     [DataNode, data_nodes]
   end
   
+  def import_facts
+    assert_yaml_content
+    facts = extract_facts
+    [Fact, facts]
+  end
+  
   protected
     def assert_yaml_content
       return @yaml_content if @yaml_content
@@ -27,7 +33,21 @@ class Fathom::YAMLImport < Import
         @yaml_content = YAML.load(file_contents)
     end
     
+    def extract_facts
+      return [] unless @yaml_content
+      output = []
+      @yaml_content.each do |e|
+        next unless e.is_a?(Array)
+        next unless e.first.to_s.match(/fact/i)
+        obj = e[1]
+        next unless obj.is_a?(Hash)
+        output << obj
+      end
+      output
+    end
+    
     def extract_plausible_ranges
+      return [] unless @yaml_content
       @yaml_content.inject([]) do |list, array|
         name, value = array.first, array.last
         if value.is_a?(Hash)
@@ -40,6 +60,7 @@ class Fathom::YAMLImport < Import
     end
     
     def extract_data_nodes
+      return [] unless @yaml_content
       @yaml_content.inject([]) do |list, array|
         name, value = array.first, array.last
         list << {:name => name, :values => value} if value.is_a?(Array)