Module: OrderedList
- Defined in:
- lib/rbbt/statistics/random_walk.rb
Instance Attribute Summary collapse
-
#total_weights ⇒ Object
Returns the value of attribute total_weights.
-
#weights ⇒ Object
Returns the value of attribute weights.
Class Method Summary collapse
- .draw_hits(list, set, filename = nil, options = {}) ⇒ Object
- .hits(list, set) ⇒ Object
- .setup(list, weights = nil, total_weights = nil) ⇒ Object
Instance Method Summary collapse
- #draw_hits(set, filename = nil, options = {}) ⇒ Object
- #hits(set) ⇒ Object
- #pvalue(set, cutoff = 0.1, options = {}) ⇒ Object
- #pvalue_up_down(up_set, down_set, cutoff = 0.1, options = {}) ⇒ Object
- #pvalue_weights(set, cutoff = 0.1, options = {}) ⇒ Object
- #score(set) ⇒ Object
- #score_weights(set) ⇒ Object
Instance Attribute Details
#total_weights ⇒ Object
Returns the value of attribute total_weights.
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# File 'lib/rbbt/statistics/random_walk.rb', line 381 def total_weights @total_weights end |
#weights ⇒ Object
Returns the value of attribute weights.
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# File 'lib/rbbt/statistics/random_walk.rb', line 381 def weights @weights end |
Class Method Details
.draw_hits(list, set, filename = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 403 def self.draw_hits(list, set, filename = nil, = {}) hits = OrderedList.hits(list, set) RandomWalk.draw_hits(hits, list.length, filename, ) end |
.hits(list, set) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 394 def self.hits(list, set) set = Set.new(set) unless Set === set hits = [] list.each_with_index do |e,i| hits << i + 1 if set.include? e # count from 1 end hits end |
.setup(list, weights = nil, total_weights = nil) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 383 def self.setup(list, weights = nil, total_weights = nil) list.extend OrderedList list.weights = weights if weights and total_weights.nil? list.total_weights = Misc.sum(weights) else list.total_weights = total_weights end list end |
Instance Method Details
#draw_hits(set, filename = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 425 def draw_hits(set, filename = nil, = {}) OrderedList.draw_hits(self, set, filename, ) end |
#hits(set) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 408 def hits(set) OrderedList.hits(self, set) end |
#pvalue(set, cutoff = 0.1, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 429 def pvalue(set, cutoff = 0.1, = {}) set = Set.new(set.compact) unless Set === set = Misc.add_defaults , :permutations => 10000, :missing => 0 permutations, missing, persist_permutations = Misc. , :permutations, :missing, :persist_permutations hits = hits(set) return 1.0 if hits.length < 3 target_score = RandomWalk.score(hits.sort, self.length, missing) total = self.length if persist_permutations permutations = RandomWalk.persisted_permutations(hits.length, self.length, missing, permutations) RandomWalk.pvalue(permutations, target_score) else # P-value computation target_score_abs = target_score.abs max = (permutations.to_f * cutoff).ceil size = hits.length total = self.length better_permutation_score_count = 1 (1..permutations).each do p= [] RandomWalk.sample_without_replacement(total, size, p) permutation_score = RandomWalk.score(p.sort, total, missing).abs if permutation_score.abs > target_score_abs better_permutation_score_count += 1 end return 1.0 if better_permutation_score_count > max end p = (better_permutation_score_count.to_f + 1) / permutations p = -p if target_score < 0 p end end |
#pvalue_up_down(up_set, down_set, cutoff = 0.1, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 470 def pvalue_up_down(up_set, down_set, cutoff = 0.1, = {}) up_set = Set.new(up_set.compact) unless Set === up_set down_set = Set.new(down_set.compact) unless Set === down_set = Misc.add_defaults , :permutations => 10000, :missing => 0 permutations, missing, persist_permutations = Misc. , :permutations, :missing, :persist_permutations up_hits = hits(up_set) down_hits = hits(down_set) return 1.0 if up_hits.length + down_hits.length < 3 target_score = RandomWalk.score_up_down(up_hits.sort, down_hits.sort, self.length, missing) if persist_permutations permutations = RandomWalk.persisted_permutations_up_down(up_hits.length, down_hits.length, self.length, missing, permutations) RandomWalk.pvalue(permutations, target_score) else # P-value computation target_score_abs = target_score.abs max = (permutations.to_f * cutoff).ceil up_size = up_set.length down_size = down_set.length total = self.length better_permutation_score_count = 1 if size == 0 1.0 else (1..permutations).each do up_p= [] RandomWalk.sample_without_replacement(total, up_size, up_p) down_p= [] RandomWalk.sample_without_replacement(total, down_size, down_p) permutation_score = RandomWalk.score_up_down(up_p.sort, down_p.sort, total, missing).abs if permutation_score.abs > target_score_abs better_permutation_score_count += 1 end return 1.0 if better_permutation_score_count > max end p = (better_permutation_score_count.to_f + 1) / permutations p = -p if target_score < 0 p end end end |
#pvalue_weights(set, cutoff = 0.1, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 523 def pvalue_weights(set, cutoff = 0.1, = {}) raise "No weight defined" if @weights.nil? @total_weights ||= Misc.sum(@weights) set = Set.new(set.compact) unless Set === set = Misc.add_defaults , :permutations => 10000, :missing => 0 permutations, missing = Misc. , :permutations, :missing hits = hits(set) return 1.0 if hits.length < 3 target_score = RandomWalk.score_weights(hits.sort, @weights, @total_weights, self.length, 0) target_score_abs = target_score.abs max = (permutations.to_f * cutoff).ceil size = set.length total = self.length better_permutation_score_count = 1 if size == 0 1.0 else (1..permutations).each do p= [] RandomWalk.sample_without_replacement(total, size, p) permutation_score = RandomWalk.score_weights(p.sort, @weights, @total_weights, total, missing).abs if permutation_score.abs >= target_score_abs better_permutation_score_count += 1 end return 1.0 if better_permutation_score_count > max end p = (better_permutation_score_count.to_f + 1) / permutations p = -p if target_score < 0 p end end |
#score(set) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 412 def score(set) hits = hits(set) RandomWalk.score(hits.sort, self.length, 0) end |
#score_weights(set) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 417 def score_weights(set) raise "No weight defined" if @weights.nil? @total_weights ||= Misc.sum(@weights) hits = hits(set) RandomWalk.score_weights(hits.sort, @weights, @total_weights, self.length, 0) end |