BasisSet updates

Author: goedman

src/StructuralCausalModels.jl

@@ -37,6 +37,7 @@ ModelDefinition = Union{OrderedDict, AbstractString, NamedArray}
 include("types/DAG.jl")
 include("types/Path.jl")
 include("types/ConditionalIndependence.jl")
+include("types/BasisSet.jl")
 
 include("methods/dag_methods.jl")
 include("methods/basis_set.jl")
@@ -50,7 +51,6 @@ include("methods/open_paths.jl")
 include("methods/backdoor_paths.jl")
 include("methods/adjustment_sets.jl")
 include("methods/ancestral_graph.jl")
-#include("methods/implied_conditional_independencies.jl")
 
 include("utils/show_dag_path.jl")
 include("utils/ggm_conversions.jl")

src/types/BasisSet.jl

@@ -0,0 +1,30 @@
+import Base: show, getindex, iterate, HasLength, HasEltype, length
+
+struct BasisSet
+  bs::Vector{Vector{Symbol}}
+  BasisSet(bs) = new(sort(bs; by = x -> x[1]))
+end
+
+iterate(b::BasisSet, state=1) =
+  state > length(b.bs) ? nothing : (b.bs[state], state+1)
+
+getindex(b::BasisSet, i::Int) = b.bs[i]
+
+HasLength(b::BasisSet) = length(b.bs)
+
+HasEltype(b::BasisSet) = eltype(b.bs)
+
+length(b::BasisSet) = length(b.bs)
+
+function bs_show(io::IO, bs::BasisSet)
+  println("BasisSet[")
+  for ci in bs.bs
+      show(ConditionalIndependency(ci))
+  end
+  println("]")
+end
+
+show(io::IO, bs::BasisSet) = bs_show(io, bs)
+
+export
+  BasisSet

src/types/ConditionalIndependence.jl

@@ -19,49 +19,13 @@ end
 
 function ci_show(io::IO, ci::ConditionalIndependency)
   if isnothing(ci.c)
-    println("  $(ci.f) \u2210 $(ci.s)")
+    println("  :$(ci.f) \u2210 :$(ci.s)")
   else
-    println("  $(ci.f) \u2210 $(ci.s) | $(ci.c)")
+    println("  :$(ci.f) \u2210 :$(ci.s) | $(ci.c)")
    end 
 end
 
 show(io::IO, ci::ConditionalIndependency) = ci_show(io, ci)
 
-function append(c::ConditionalIndependency)
-  v = [c.f, c.s]
-  !isnothing(c.c) && length(c.c) > 0 && push!(v, c.c...)
-  v
-end
-
-struct BasisSet
-  bs::Vector{ConditionalIndependency}
-end
-
-function BasisSet(b::Array{Array{Symbol,1},1})
-  BasisSet(ConditionalIndependency.(b))
-end
-
-iterate(b::BasisSet, state=1) =
-  state > length(b.bs) ? nothing : (b.bs[state], state+1)
-
-getindex(b::BasisSet, i::Int) = b.bs[i]
-
-HasLength(b::BasisSet) = length(b.bs)
-
-HasEltype(b::BasisSet) = eltype(b.bs)
-
-length(b::BasisSet) = length(b.bs)
-
-function bs_show(io::IO, bs::BasisSet)
-  println("BasisSet[")
-  for ci in bs.bs
-      show(ci)
-  end
-  println("]")
-end
-
-show(io::IO, bs::BasisSet) = bs_show(io, bs)
-
 export
-  BasisSet,
   ConditionalIndependency

test/test_bases_set_01.jl

@@ -0,0 +1,19 @@
+using StructuralCausalModels, Test
+
+ProjDir = @__DIR__
+
+d_str = "dag{k1 -> k2;k2 -> y;v -> x2;w -> k1;x1 -> v;x1 -> w;x2 -> y;x3 -> w;x3 -> y}"
+
+dag = DAG("test_desc", d_str)
+
+to_dagitty(dag) |> display
+
+fname = joinpath(ProjDir, "test_descendents_03.dot")
+to_graphviz(dag, fname)
+Sys.isapple() && run(`open -a GraphViz.app $(fname)`)
+
+display(dag)
+
+bs = basis_set(dag)
+bs |> display
+

test/test_open_paths_02.jl

@@ -9,15 +9,15 @@ dag = DAG("test_open_paths_02", d_string);
 @test to_dagitty(dag.d) == "dag { D <- E; D <- Z; E <- Z; D <- B; Z <- B; E <- A; Z <- A }"
 
 bs = basis_set(dag)
-@test bs[1].f == :B
-@test bs[1].s == :A
-@test bs[1].c == nothing
-@test bs[2].f == :B
-@test bs[2].s == :E
-@test bs[2].c == [:A, :Z]
-@test bs[3].f == :A
-@test bs[3].s == :D
-@test bs[3].c == [:B, :Z, :E]
+@test bs[1][1] == :A
+@test bs[1][2] == :D
+@test bs[1][3:end] == [:B, :Z, :E]
+@test bs[2][1] == :B
+@test bs[2][2] == :A
+@test length(bs[2]) == 2
+@test bs[3][1] == :B
+@test bs[3][2] == :E
+@test bs[3][3:end] == [:A, :Z]
 
 fname = joinpath(ProjDir, "test_open_paths_02.dot")
 to_graphviz(dag, fname)

test/test_open_paths_03.jl

@@ -19,9 +19,9 @@ adjs = adjustment_sets(dag, :X, :Y)
 
 @testset "Open_path_03" begin
 
-  @test bs[1].f == :Z
-  @test bs[1].s == :Y
-  @test bs[1].c == [:X, :I]
+  @test bs[1][1] == :Z
+  @test bs[1][2] == :Y
+  @test bs[1][3:end] == [:X, :I]
   @test bp[1] == [:X, :Z, :I, :Y]
   @test adjs == [[:Z], [:I]]
 

test/test_open_paths_04.jl

@@ -24,9 +24,9 @@ to_graphviz(dag, fname)
   :q => :r, :p => :q, :o => :p, :n => :o, :m => :n, :k => :l, 
   :l => :m, :i => :k)
 @test length(bs) == 117
-@test bs[116].f == :b
-@test bs[116].s == :D
-@test bs[116].c == [:c, :r, :k, :E]
+@test bs[3][1] == :b
+@test bs[3][2] == :D
+@test bs[3][3:end] == [:c, :r, :k, :E]
 @test adjs == [[:i], [:k]]
 
 end

test/test_sr6_4_2.jl

@@ -44,12 +44,12 @@ adjustmentsets = adjustment_sets(dag, :x, :y)
 @testset "sr6_4_2" begin
 
   @test length(basisset) == 8
-  @test basisset[6].f == :u
-  @test basisset[6].s == :y
-  @test basisset[6].c == [:a, :c, :x]
-  @test basisset[8].f == :y
-  @test basisset[8].s == :b
-  @test basisset[8].c == [:c, :x, :u]
+  @test basisset[6][1] == :u
+  @test basisset[6][2] == :y
+  @test basisset[6][3:end] == [:a, :c, :x]
+  @test basisset[8][1] == :y
+  @test basisset[8][2] == :b
+  @test basisset[8][3:end] == [:c, :x, :u]
 
   @test allpaths[1] == [:x, :u, :b, :c, :y]
   @test allpaths[2] == [:x, :u, :a, :c, :y]