rgraphum 0.0.1.alpha
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- data/.gitignore +26 -0
- data/GLOSSARIES.md +108 -0
- data/GREMLIN.md +1398 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +136 -0
- data/Rakefile +16 -0
- data/bin/.irbrc +41 -0
- data/bin/rgraphum_console +61 -0
- data/bin/rgraphum_runner +57 -0
- data/examples/ba_model/make.rb +19 -0
- data/examples/ba_model/make_dummy_twitter_rt_data.rb +0 -0
- data/examples/basic/check_modularity.rb +27 -0
- data/examples/basic/make_graph.rb +12 -0
- data/examples/parser/dot.rb +28 -0
- data/examples/sis_model/lifegame.rb +161 -0
- data/graph_struct.jpg +0 -0
- data/lib/rgraphum/analyzer/linear_regression.rb +31 -0
- data/lib/rgraphum/analyzer/meme_tracker.rb +296 -0
- data/lib/rgraphum/analyzer/twitter/rt_at_mark.rb +45 -0
- data/lib/rgraphum/analyzer.rb +8 -0
- data/lib/rgraphum/cluster.rb +67 -0
- data/lib/rgraphum/communities.rb +65 -0
- data/lib/rgraphum/community.rb +86 -0
- data/lib/rgraphum/cosine_similarity_matrix.rb +40 -0
- data/lib/rgraphum/edge.rb +194 -0
- data/lib/rgraphum/edges.rb +161 -0
- data/lib/rgraphum/ext/cosine_similarity_matrix.rb +79 -0
- data/lib/rgraphum/ext/linear_regression.rb +22 -0
- data/lib/rgraphum/ext/tf_idf.rb +52 -0
- data/lib/rgraphum/graph/gremlin.rb +193 -0
- data/lib/rgraphum/graph/math/clustering_coefficient.rb +53 -0
- data/lib/rgraphum/graph/math/community_detection.rb +141 -0
- data/lib/rgraphum/graph/math/degree_distribution.rb +50 -0
- data/lib/rgraphum/graph/math/dijkstra.rb +331 -0
- data/lib/rgraphum/graph/math.rb +45 -0
- data/lib/rgraphum/graph.rb +267 -0
- data/lib/rgraphum/importer.rb +97 -0
- data/lib/rgraphum/marshal.rb +26 -0
- data/lib/rgraphum/motifs.rb +8 -0
- data/lib/rgraphum/parsers/flare.rb +42 -0
- data/lib/rgraphum/parsers/gephi.rb +193 -0
- data/lib/rgraphum/parsers/graphviz.rb +78 -0
- data/lib/rgraphum/parsers/miserables.rb +54 -0
- data/lib/rgraphum/parsers.rb +32 -0
- data/lib/rgraphum/path.rb +37 -0
- data/lib/rgraphum/query.rb +130 -0
- data/lib/rgraphum/rgraphum_array.rb +159 -0
- data/lib/rgraphum/rgraphum_array_dividers.rb +43 -0
- data/lib/rgraphum/rgraphum_random.rb +5 -0
- data/lib/rgraphum/simulator/ba_model.rb +140 -0
- data/lib/rgraphum/simulator/sir_model.rb +178 -0
- data/lib/rgraphum/simulator/sis_model.rb +158 -0
- data/lib/rgraphum/simulator.rb +29 -0
- data/lib/rgraphum/statistic/power_law.rb +9 -0
- data/lib/rgraphum/t.rb +12 -0
- data/lib/rgraphum/tf_idf.rb +27 -0
- data/lib/rgraphum/version.rb +3 -0
- data/lib/rgraphum/vertex.rb +354 -0
- data/lib/rgraphum/vertices.rb +97 -0
- data/lib/rgraphum.rb +38 -0
- data/performance/add-vertices-edges.rb +20 -0
- data/performance/add-vertices.rb +12 -0
- data/performance/build-graph.rb +19 -0
- data/performance/delete-graph.rb +24 -0
- data/performance/delete-vertices.rb +25 -0
- data/performance/refer-graph.rb +23 -0
- data/rgraphum.gemspec +30 -0
- data/test/lib/rgraphum/analyzer/linear_regression_test.rb +20 -0
- data/test/lib/rgraphum/analyzer/meme_tracker_test.rb +383 -0
- data/test/lib/rgraphum/analyzer/twitter/rt_at_mark_test.rb +120 -0
- data/test/lib/rgraphum/array_test.rb +95 -0
- data/test/lib/rgraphum/bubble_test.rb +7 -0
- data/test/lib/rgraphum/communities_test.rb +53 -0
- data/test/lib/rgraphum/cosine_similarity_test.rb +18 -0
- data/test/lib/rgraphum/edge_test.rb +89 -0
- data/test/lib/rgraphum/edges_test.rb +178 -0
- data/test/lib/rgraphum/graph_builder_test.rb +64 -0
- data/test/lib/rgraphum/graph_dup_test.rb +199 -0
- data/test/lib/rgraphum/graph_plus_test.rb +80 -0
- data/test/lib/rgraphum/graph_test.rb +512 -0
- data/test/lib/rgraphum/gremlin_test.rb +145 -0
- data/test/lib/rgraphum/importers/idg_json_edges.json +20 -0
- data/test/lib/rgraphum/importers/idg_json_test.rb +207 -0
- data/test/lib/rgraphum/importers/idg_json_vertices.json +46 -0
- data/test/lib/rgraphum/math/average_distance_matrix_test.rb +142 -0
- data/test/lib/rgraphum/math/clustering_coefficient_test.rb +219 -0
- data/test/lib/rgraphum/math/community_test.rb +78 -0
- data/test/lib/rgraphum/math/degree_distribution_test.rb +40 -0
- data/test/lib/rgraphum/math/dijkstra_test.rb +146 -0
- data/test/lib/rgraphum/math/modularity_test.rb +154 -0
- data/test/lib/rgraphum/math/quick_average_distance_matrix_test.rb +84 -0
- data/test/lib/rgraphum/path_test.rb +44 -0
- data/test/lib/rgraphum/query/enumerable_test.rb +42 -0
- data/test/lib/rgraphum/query/where_operators_test.rb +75 -0
- data/test/lib/rgraphum/query/where_test.rb +59 -0
- data/test/lib/rgraphum/simulator/ba_model_test.rb +75 -0
- data/test/lib/rgraphum/simulator/sir_model_test.rb +513 -0
- data/test/lib/rgraphum/simulator/sis_model_test.rb +478 -0
- data/test/lib/rgraphum/simulator_test.rb +22 -0
- data/test/lib/rgraphum/tf_idf_test.rb +30 -0
- data/test/lib/rgraphum/vertex_test.rb +50 -0
- data/test/lib/rgraphum/vertices_test.rb +180 -0
- data/test/test_helper.rb +98 -0
- data/tmp/.gitkeep +0 -0
- metadata +254 -0
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# coding: utf-8
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require 'test_helper'
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require 'rgraphum'
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class BAModelTest < MiniTest::Test
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def setup
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make_graph
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end
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def test_simurate
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end
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def test_edges_per_min
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# 99 * 99 * 20 - 20 = 196_000 sec
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# 196_000 / 60 min
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ba = Rgraphum::Simulator::BAModel.new
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assert_equal 99 / ( 196_000 / 60.0 ) , ba.edges_per_min(@graph)
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end
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def test_vertices_per_min
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# 99 * 99 * 20 = 196_020 sec
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# 196_020 / 60 = 3_267 min
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ba = Rgraphum::Simulator::BAModel.new
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assert_equal 100.0 / 3_267 , ba.vertices_per_min(@graph)
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end
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def test_edges_size_array_per_interval
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ba = Rgraphum::Simulator::BAModel.new
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mini_graph = Rgraphum::Graph.new
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base_time = ( Time.now.to_i / 60 ) * 60
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mini_graph.vertices = [ {id: 1,start: Time.now},{id: 2,start: Time.now},{id: 3,start: Time.now}]
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mini_graph.edges = [ {id: 1,start: base_time + 30, source: 1,target: 2 },
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{id: 2,start: base_time + 90, source: 2,target: 3 },
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{id: 3,start: base_time + 60 * 2, source: 3,target: 1 } ]
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array = ba.edges_size_array_per_interval( mini_graph, 1 )
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assert_equal [1,1,1], array
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mini_graph.edges.delete(3)
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array = ba.edges_size_array_per_interval( mini_graph, 1 )
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assert_equal [1,1], array
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array = ba.edges_size_array_per_interval( @graph, 1 )
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assert_equal 3268, array.size
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assert_equal 99, array.inject(:+)
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end
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private
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def make_graph
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today = Time.at( ( Time.now.to_i/ ( 3600 * 24 ) ) * 3600 * 24 - Time.now.utc_offset )
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@graph = Rgraphum::Graph.new
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vertices = 100.times.map do |t|
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{id: t, label: t.to_s, start: today + 20 * t * t }
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end
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@graph.vertices = vertices
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edges = @graph.vertices.map do |vertex|
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{id: vertex.id,source: @graph.vertices[0], target: vertex, start: vertex.start, weight: 1}
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end
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@graph.edges = edges
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@graph.edges.delete(0)
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@graph
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end
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end
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# coding: utf-8
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require 'test_helper'
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require 'rgraphum'
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class SIRModelTest < MiniTest::Test
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def setup
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# A -- B -- C
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# | | |
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# D -- E -- F
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# | | |
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# G -- H -- I
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v = {}
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@graph = Rgraphum::Graph.new
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v[:a] = @graph.vertices.build(label: "A")
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v[:b] = @graph.vertices.build(label: "B")
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v[:c] = @graph.vertices.build(label: "C")
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v[:d] = @graph.vertices.build(label: "D")
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v[:e] = @graph.vertices.build(label: "E")
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v[:f] = @graph.vertices.build(label: "F")
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v[:g] = @graph.vertices.build(label: "G")
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v[:h] = @graph.vertices.build(label: "H")
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v[:i] = @graph.vertices.build(label: "I")
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@graph.edges.build(source: v[:a], target: v[:b])
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@graph.edges.build(source: v[:b], target: v[:c])
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@graph.edges.build(source: v[:a], target: v[:d])
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@graph.edges.build(source: v[:b], target: v[:e])
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@graph.edges.build(source: v[:c], target: v[:f])
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@graph.edges.build(source: v[:d], target: v[:e])
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@graph.edges.build(source: v[:e], target: v[:f])
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@graph.edges.build(source: v[:d], target: v[:g])
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@graph.edges.build(source: v[:e], target: v[:h])
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@graph.edges.build(source: v[:f], target: v[:i])
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@graph.edges.build(source: v[:g], target: v[:h])
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@graph.edges.build(source: v[:h], target: v[:i])
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end
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def test_initial_sir_map
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sir = Rgraphum::Simulator::SIRModel.new(graph: @graph)
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assert_equal %w(A B C D E F G H I), sir.vertices.map(&:label)
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assert_equal %w(s s s s s s s s s).map(&:to_sym), sir.sir_map
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end
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def test_set_sir_map
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sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
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sir = Rgraphum::Simulator::SIRModel.new(graph: @graph, sir_map: sir_map)
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assert_equal %w(A B C D E F G H I), sir.vertices.map(&:label)
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assert_equal %w(s i s i s i s i s).map(&:to_sym), sir.sir_map
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end
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def test_infection_rate
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sir = Rgraphum::Simulator::SIRModel.new(graph: @graph, infection_rate: 0.5)
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assert_equal 0.5, sir.infection_rate
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assert_raises(ArgumentError) do
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Rgraphum::Simulator::SIRModel.new(graph: @graph, infection_rate: -0.1)
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end
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assert_raises(ArgumentError) do
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Rgraphum::Simulator::SIRModel.new(graph: @graph, infection_rate: 1.1)
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end
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end
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def test_recovery_rate
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sir = Rgraphum::Simulator::SIRModel.new(graph: @graph, recovery_rate: 0.5)
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assert_equal 0.5, sir.recovery_rate
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assert_raises(ArgumentError) do
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Rgraphum::Simulator::SIRModel.new(graph: @graph, recovery_rate: -0.1)
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end
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assert_raises(ArgumentError) do
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Rgraphum::Simulator::SIRModel.new(graph: @graph, recovery_rate: 1.1)
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end
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end
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def test_zero_periods_simulate
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initial_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
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sir = Rgraphum::Simulator::SIRModel.new(graph: @graph, sir_map: initial_sir_map)
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sir.simulate periods: 0
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expected_sir_map = initial_sir_map
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assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
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end
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def test_infected_1?
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# A -- B -- C S -- I -- S
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# | | | | | |
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# D -- E -- F I -- S -- I
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# | | | | | |
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# G -- H -- I S -- I -- S
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options = {
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graph: @graph,
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sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
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infection_rate: 1.0,
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recovery_rate: 0.0,
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}
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sir = Rgraphum::Simulator::SIRModel.new(options)
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v1 = sir.vertices[0]
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assert_equal false, sir.infected?(v1)
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assert_equal false, sir.infected?(v1, 0)
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assert_equal true, sir.infected?(v1, 1)
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v2 = sir.vertices[1]
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assert_equal true, sir.infected?(v2)
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assert_equal true, sir.infected?(v2, 0)
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assert_equal true, sir.infected?(v2, 1)
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end
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def test_infected_2?
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# A -- B -- C S -- I -- S
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# | | | | | |
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# D -- E -- F I -- S -- I
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# | | | | | |
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# G -- H -- I S -- I -- S
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options = {
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graph: @graph,
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sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
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infection_rate: 0.1,
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recovery_rate: 0.0,
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t_per_period: 0.5,
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}
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sir = Rgraphum::Simulator::SIRModel.new(options)
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v1 = sir.vertices[0]
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assert_equal false, sir.infected?(v1, 0)
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assert_equal false, sir.infected?(v1, 1)
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assert_equal false, sir.infected?(v1, 2)
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assert_equal false, sir.infected?(v1, 3)
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assert_equal false, sir.infected?(v1, 9)
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assert_equal true, sir.infected?(v1, 10)
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end
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def test_recovered?
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# A -- B -- C I -- I -- I
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# | | | | | |
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# D -- E -- F I -- I -- I
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# | | | | | |
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# G -- H -- I I -- I -- I
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options = {
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graph: @graph,
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sir_map: [:i, :i, :i, :i, :i, :i, :i, :i, :i],
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infection_rate: 0.0,
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recovery_rate: 1.0,
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}
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sir = Rgraphum::Simulator::SIRModel.new(options)
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v1 = sir.vertices[0]
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assert_equal false, sir.recovered?(v1)
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assert_equal false, sir.recovered?(v1, 0)
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assert_equal true, sir.recovered?(v1, 1)
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end
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# def test_susceptible?
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# # A -- B -- C S -- I -- I
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# # | | | | | |
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# # D -- E -- F I -- I -- I
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# # | | | | | |
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# # G -- H -- I I -- I -- I
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# options = {
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# graph: @graph,
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# sir_map: [:s, :i, :i, :i, :i, :i, :i, :i, :i],
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# infection_rate: 1.0,
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# recovery_rate: 0.0,
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# }
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# sir = Rgraphum::Simulator::SIRModel.new(options)
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# v1 = sir.vertices[0]
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# assert_equal true, sir.susceptible?(v1)
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175
|
+
# assert_equal true, sir.susceptible?(v1, 0)
|
176
|
+
# assert_equal false, sir.susceptible?(v1, 1)
|
177
|
+
|
178
|
+
# v2 = sir.vertices[1]
|
179
|
+
# assert_equal false, sir.susceptible?(v2)
|
180
|
+
# assert_equal false, sir.susceptible?(v2, 0)
|
181
|
+
# assert_equal false, sir.susceptible?(v2, 1)
|
182
|
+
# end
|
183
|
+
|
184
|
+
def test_next_period_only_with_infection_rate
|
185
|
+
# A -- B -- C S -- I -- S
|
186
|
+
# | | | | | |
|
187
|
+
# D -- E -- F I -- S -- I
|
188
|
+
# | | | | | |
|
189
|
+
# G -- H -- I S -- I -- S
|
190
|
+
options = {
|
191
|
+
graph: @graph,
|
192
|
+
sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
|
193
|
+
infection_rate: 0.2,
|
194
|
+
recovery_rate: 0.0,
|
195
|
+
t_per_period: 1,
|
196
|
+
}
|
197
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
198
|
+
|
199
|
+
# initial state
|
200
|
+
# A -- B -- C S -- I -- S 0 I 0
|
201
|
+
# | | | | | |
|
202
|
+
# D -- E -- F I -- S -- I I 0 I
|
203
|
+
# | | | | | |
|
204
|
+
# G -- H -- I S -- I -- S 0 I 0
|
205
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
206
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
207
|
+
|
208
|
+
# 1st period
|
209
|
+
# A -- B -- C S -- I -- S 0.4 I 0.4
|
210
|
+
# | | | | | |
|
211
|
+
# D -- E -- F I -- S -- I I 0.8 I
|
212
|
+
# | | | | | |
|
213
|
+
# G -- H -- I S -- I -- S 0.4 I 0.4
|
214
|
+
sir.next_period
|
215
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
216
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
217
|
+
|
218
|
+
# 2nd period
|
219
|
+
# A -- B -- C S -- I -- S 0.8 I 0.8
|
220
|
+
# | | | | | |
|
221
|
+
# D -- E -- F I -- S -- I I I I
|
222
|
+
# | | | | | |
|
223
|
+
# G -- H -- I S -- I -- S 0.8 I 0.8
|
224
|
+
sir.next_period
|
225
|
+
expected_sir_map = [:s, :i, :s, :i, :i, :i, :s, :i, :s]
|
226
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should change"
|
227
|
+
|
228
|
+
# 3rd period
|
229
|
+
# A -- B -- C S -- I -- S I I I
|
230
|
+
# | | | | | |
|
231
|
+
# D -- E -- F I -- S -- I I I I
|
232
|
+
# | | | | | |
|
233
|
+
# G -- H -- I S -- I -- S I I I
|
234
|
+
sir.next_period
|
235
|
+
expected_sir_map = [:i, :i, :i, :i, :i, :i, :i, :i, :i]
|
236
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should only contain I"
|
237
|
+
|
238
|
+
# 4th period
|
239
|
+
# A -- B -- C S -- I -- S I I I
|
240
|
+
# | | | | | |
|
241
|
+
# D -- E -- F I -- S -- I I I I
|
242
|
+
# | | | | | |
|
243
|
+
# G -- H -- I S -- I -- S I I I
|
244
|
+
sir.next_period
|
245
|
+
expected_sir_map = [:i, :i, :i, :i, :i, :i, :i, :i, :i]
|
246
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should only contain I"
|
247
|
+
end
|
248
|
+
|
249
|
+
def test_next_period_only_with_recovery_rate
|
250
|
+
# A -- B -- C S -- I -- S
|
251
|
+
# | | | | | |
|
252
|
+
# D -- E -- F I -- S -- I
|
253
|
+
# | | | | | |
|
254
|
+
# G -- H -- I S -- I -- S
|
255
|
+
options = {
|
256
|
+
graph: @graph,
|
257
|
+
sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
|
258
|
+
infection_rate: 0,
|
259
|
+
recovery_rate: 0.3,
|
260
|
+
t_per_period: 1,
|
261
|
+
}
|
262
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
263
|
+
|
264
|
+
# initial state
|
265
|
+
# A -- B -- C S -- I -- S S 0 S
|
266
|
+
# | | | | | |
|
267
|
+
# D -- E -- F I -- S -- I 0 S 0
|
268
|
+
# | | | | | |
|
269
|
+
# G -- H -- I S -- I -- S S 0 S
|
270
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
271
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
272
|
+
|
273
|
+
# 1st period
|
274
|
+
# A -- B -- C S -- I -- S S 0.3 S
|
275
|
+
# | | | | | |
|
276
|
+
# D -- E -- F I -- S -- I 0.3 S 0.3
|
277
|
+
# | | | | | |
|
278
|
+
# G -- H -- I S -- I -- S S 0.3 S
|
279
|
+
sir.next_period
|
280
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
281
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
282
|
+
|
283
|
+
# 2nd period
|
284
|
+
# A -- B -- C S -- I -- S S 0.6 S
|
285
|
+
# | | | | | |
|
286
|
+
# D -- E -- F I -- S -- I 0.6 S 0.6
|
287
|
+
# | | | | | |
|
288
|
+
# G -- H -- I S -- I -- S S 0.6 S
|
289
|
+
sir.next_period
|
290
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
291
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
292
|
+
|
293
|
+
# 3rd period
|
294
|
+
# A -- B -- C S -- I -- S S 0.9 S
|
295
|
+
# | | | | | |
|
296
|
+
# D -- E -- F I -- S -- I 0.9 S 0.9
|
297
|
+
# | | | | | |
|
298
|
+
# G -- H -- I S -- I -- S S 0.9 S
|
299
|
+
sir.next_period
|
300
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
301
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
302
|
+
|
303
|
+
# 4th period
|
304
|
+
# A -- B -- C S -- I -- S S R S
|
305
|
+
# | | | | | |
|
306
|
+
# D -- E -- F I -- S -- I R S R
|
307
|
+
# | | | | | |
|
308
|
+
# G -- H -- I S -- I -- S S R S
|
309
|
+
sir.next_period
|
310
|
+
expected_sir_map = [:s, :r, :s, :r, :s, :r, :s, :r, :s]
|
311
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should only contain S"
|
312
|
+
end
|
313
|
+
|
314
|
+
def test_next_period_1
|
315
|
+
# A -- B -- C I -- I -- S
|
316
|
+
# | | | | | |
|
317
|
+
# D -- E -- F I -- S -- I
|
318
|
+
# | | | | | |
|
319
|
+
# G -- H -- I S -- I -- S
|
320
|
+
options = {
|
321
|
+
graph: @graph,
|
322
|
+
sir_map: [:i, :i, :s, :i, :s, :i, :s, :i, :s],
|
323
|
+
infection_rate: 0.2, # S -> I
|
324
|
+
recovery_rate: 0.3, # I -> S
|
325
|
+
t_per_period: 1,
|
326
|
+
}
|
327
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
328
|
+
|
329
|
+
# initial state
|
330
|
+
# A -- B -- C I -- I -- S I0 I0 S0
|
331
|
+
# | | | | | |
|
332
|
+
# D -- E -- F I -- S -- I I0 S0 I0
|
333
|
+
# | | | | | |
|
334
|
+
# G -- H -- I S -- I -- S S0 I0 S0
|
335
|
+
expected_sir_map = [:i, :i, :s, :i, :s, :i, :s, :i, :s]
|
336
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
337
|
+
|
338
|
+
# 1st period
|
339
|
+
# A -- B -- C I -- I -- S I0.3 I0.3 S0.4
|
340
|
+
# | | | | | |
|
341
|
+
# D -- E -- F I -- S -- I I0.3 S0.8 I0.3
|
342
|
+
# | | | | | |
|
343
|
+
# G -- H -- I S -- I -- S S0.4 I0.3 S0.4
|
344
|
+
sir.next_period
|
345
|
+
expected_sir_map = [:i, :i, :s, :i, :s, :i, :s, :i, :s]
|
346
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
347
|
+
|
348
|
+
# 2nd period
|
349
|
+
# A -- B -- C I -- I -- S I0.6 I0.6 S0.8
|
350
|
+
# | | | | | |
|
351
|
+
# D -- E -- F I -- I -- I I0.6 I0 I0.6
|
352
|
+
# | | | | | |
|
353
|
+
# G -- H -- I S -- I -- S S0.8 I0.6 S0.8
|
354
|
+
sir.next_period
|
355
|
+
expected_sir_map = [:i, :i, :s, :i, :i, :i, :s, :i, :s]
|
356
|
+
assert_equal expected_sir_map, sir.sir_map
|
357
|
+
|
358
|
+
# 3rd period
|
359
|
+
# A -- B -- C I -- I -- I I0.9 I0.9 I0
|
360
|
+
# | | | | | |
|
361
|
+
# D -- E -- F I -- I -- I I0.9 I0.3 I0.9
|
362
|
+
# | | | | | |
|
363
|
+
# G -- H -- I I -- I -- I I0 I0.9 I0
|
364
|
+
sir.next_period
|
365
|
+
expected_sir_map = [:i, :i, :i, :i, :i, :i, :i, :i, :i]
|
366
|
+
assert_equal expected_sir_map, sir.sir_map
|
367
|
+
|
368
|
+
# 4th period
|
369
|
+
# A -- B -- C S -- S -- I R R I0.3
|
370
|
+
# | | | | | |
|
371
|
+
# D -- E -- F S -- I -- S R I0.6 R
|
372
|
+
# | | | | | |
|
373
|
+
# G -- H -- I I -- S -- I I0.3 R I0.3
|
374
|
+
sir.next_period
|
375
|
+
expected_sir_map = [:r, :r, :i, :r, :i, :r, :i, :r, :i]
|
376
|
+
assert_equal expected_sir_map, sir.sir_map
|
377
|
+
|
378
|
+
# 5th period
|
379
|
+
# A -- B -- C S -- S -- S R R I0.6
|
380
|
+
# | | | | | |
|
381
|
+
# D -- E -- F S -- I -- S R I0.9 R
|
382
|
+
# | | | | | |
|
383
|
+
# G -- H -- I I -- S -- I I0.6 R I0.6
|
384
|
+
sir.next_period
|
385
|
+
expected_sir_map = [:r, :r, :i, :r, :i, :r, :i, :r, :i]
|
386
|
+
assert_equal expected_sir_map, sir.sir_map
|
387
|
+
|
388
|
+
# 6th period
|
389
|
+
# A -- B -- C S -- S -- I R R I0.9
|
390
|
+
# | | | | | |
|
391
|
+
# D -- E -- F S -- S -- I R R R
|
392
|
+
# | | | | | |
|
393
|
+
# G -- H -- I I -- I -- I I0.9 R I0.9
|
394
|
+
sir.next_period
|
395
|
+
expected_sir_map = [:r, :r, :i, :r, :r, :r, :i, :r, :i]
|
396
|
+
assert_equal expected_sir_map, sir.sir_map
|
397
|
+
|
398
|
+
# 7th period
|
399
|
+
# A -- B -- C S -- S -- I R R R
|
400
|
+
# | | | | | |
|
401
|
+
# D -- E -- F S -- S -- I R R R
|
402
|
+
# | | | | | |
|
403
|
+
# G -- H -- I I -- I -- I R R R
|
404
|
+
sir.next_period
|
405
|
+
expected_sir_map = [:r, :r, :r, :r, :r, :r, :r, :r, :r]
|
406
|
+
assert_equal expected_sir_map, sir.sir_map
|
407
|
+
end
|
408
|
+
|
409
|
+
def test_simulate_only_with_infection_rate
|
410
|
+
# A -- B -- C S -- I -- S
|
411
|
+
# | | | | | |
|
412
|
+
# D -- E -- F I -- S -- I
|
413
|
+
# | | | | | |
|
414
|
+
# G -- H -- I S -- I -- S
|
415
|
+
options = {
|
416
|
+
graph: @graph,
|
417
|
+
sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
|
418
|
+
infection_rate: 0.2,
|
419
|
+
recovery_rate: 0.0,
|
420
|
+
t_per_period: 1,
|
421
|
+
}
|
422
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
423
|
+
|
424
|
+
# initial state
|
425
|
+
# A -- B -- C S -- I -- S 0.4 I 0.4
|
426
|
+
# | | | | | |
|
427
|
+
# D -- E -- F I -- S -- I I 0.8 I
|
428
|
+
# | | | | | |
|
429
|
+
# G -- H -- I S -- I -- S 0.4 I 0.4
|
430
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
431
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
432
|
+
|
433
|
+
# 3rd period
|
434
|
+
# A -- B -- C S -- I -- S I I I
|
435
|
+
# | | | | | |
|
436
|
+
# D -- E -- F I -- S -- I I I I
|
437
|
+
# | | | | | |
|
438
|
+
# G -- H -- I S -- I -- S I I I
|
439
|
+
sir.simulate periods: 3
|
440
|
+
expected_sir_map = [:i, :i, :i, :i, :i, :i, :i, :i, :i]
|
441
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should only contain I"
|
442
|
+
end
|
443
|
+
|
444
|
+
def test_simulate_only_with_recovery_rate
|
445
|
+
# A -- B -- C S -- I -- S
|
446
|
+
# | | | | | |
|
447
|
+
# D -- E -- F I -- S -- I
|
448
|
+
# | | | | | |
|
449
|
+
# G -- H -- I S -- I -- S
|
450
|
+
options = {
|
451
|
+
graph: @graph,
|
452
|
+
sir_map: [:s, :i, :s, :i, :s, :i, :s, :i, :s],
|
453
|
+
infection_rate: 0,
|
454
|
+
recovery_rate: 0.3,
|
455
|
+
t_per_period: 1,
|
456
|
+
}
|
457
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
458
|
+
|
459
|
+
# initial state
|
460
|
+
# A -- B -- C S -- I -- S S I S
|
461
|
+
# | | | | | |
|
462
|
+
# D -- E -- F I -- S -- I I S I
|
463
|
+
# | | | | | |
|
464
|
+
# G -- H -- I S -- I -- S S I S
|
465
|
+
expected_sir_map = [:s, :i, :s, :i, :s, :i, :s, :i, :s]
|
466
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
467
|
+
|
468
|
+
# 4th period
|
469
|
+
# A -- B -- C S -- I -- S S R S
|
470
|
+
# | | | | | |
|
471
|
+
# D -- E -- F I -- S -- I R S R
|
472
|
+
# | | | | | |
|
473
|
+
# G -- H -- I S -- I -- S S R S
|
474
|
+
sir.simulate periods: 4
|
475
|
+
expected_sir_map = [:s, :r, :s, :r, :s, :r, :s, :r, :s]
|
476
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should only contain S"
|
477
|
+
end
|
478
|
+
|
479
|
+
def test_simulate
|
480
|
+
# A -- B -- C I -- I -- S
|
481
|
+
# | | | | | |
|
482
|
+
# D -- E -- F I -- S -- I
|
483
|
+
# | | | | | |
|
484
|
+
# G -- H -- I S -- I -- S
|
485
|
+
options = {
|
486
|
+
graph: @graph,
|
487
|
+
sir_map: [:i, :i, :s, :i, :s, :i, :s, :i, :s],
|
488
|
+
infection_rate: 0.2, # S -> I
|
489
|
+
recovery_rate: 0.3, # I -> S
|
490
|
+
t_per_period: 1,
|
491
|
+
}
|
492
|
+
sir = Rgraphum::Simulator::SIRModel.new(options)
|
493
|
+
|
494
|
+
# initial state
|
495
|
+
# A -- B -- C I -- I -- S I0 I0 S0
|
496
|
+
# | | | | | |
|
497
|
+
# D -- E -- F I -- S -- I I0 S0 I0
|
498
|
+
# | | | | | |
|
499
|
+
# G -- H -- I S -- I -- S S0 I0 S0
|
500
|
+
expected_sir_map = [:i, :i, :s, :i, :s, :i, :s, :i, :s]
|
501
|
+
assert_equal expected_sir_map, sir.sir_map, "sir_map should not change"
|
502
|
+
|
503
|
+
# 6th period
|
504
|
+
# A -- B -- C S -- S -- I R R I
|
505
|
+
# | | | | | |
|
506
|
+
# D -- E -- F S -- S -- I R R R
|
507
|
+
# | | | | | |
|
508
|
+
# G -- H -- I I -- I -- I I R I
|
509
|
+
sir.simulate periods: 6
|
510
|
+
expected_sir_map = [:r, :r, :i, :r, :r, :r, :i, :r, :i]
|
511
|
+
assert_equal expected_sir_map, sir.sir_map
|
512
|
+
end
|
513
|
+
end
|