Merge pull request #85 from mwien/adjustmentdocs

Write documentation for new adjustment functions

docs/src/library.md

@@ -5,6 +5,7 @@
 ```@docs
 dsep
 cpdag
+alt_cpdag
 vskel
 has_recanting_witness
 backdoor_criterion
@@ -72,3 +73,24 @@ CausalInference.ordered_edges
 CausalInference.insorted
 CausalInference.removesorted!
 ```
+
+## Adjustment
+```@docs
+ancestors
+descendants
+alt_test_dsep
+test_covariate_adjustment
+alt_test_backdoor
+find_dsep
+find_min_dsep
+find_covariate_adjustment
+find_backdoor_adjustment
+find_frontdoor_adjustment
+find_min_covariate_adjustment
+find_min_backdoor_adjustment
+find_min_frontdoor_adjustment
+list_dseps
+list_covariate_adjustment
+list_backdoor_adjustment
+list_frontdoor_adjustment
+```

src/CausalInference.jl

@@ -4,7 +4,7 @@ using Graphs.SimpleGraphs
 using Combinatorics
 using Base.Iterators
 
-export ancestors, descendants, alt_test_dsep, test_covariate_adjustment, alt_test_backdoor, find_dsep, find_min_dsep, find_covariate_adjustment, find_backdoor_adjustment, find_min_covariate_adjustment, find_min_backdoor_adjustment, find_frontdoor_adjustment, list_dseps, list_covariate_adjustment, list_backdoor_adjustment, list_frontdoor_adjustment
+export ancestors, descendants, alt_test_dsep, test_covariate_adjustment, alt_test_backdoor, find_dsep, find_min_dsep, find_covariate_adjustment, find_backdoor_adjustment, find_frontdoor_adjustment, find_min_covariate_adjustment, find_min_backdoor_adjustment, find_min_frontdoor_adjustment, list_dseps, list_covariate_adjustment, list_backdoor_adjustment, list_frontdoor_adjustment
 export dsep, skeleton, gausscitest, dseporacle, partialcor
 export unshielded, pcalg, vskel
 export cpdag, alt_cpdag

src/gensearch.jl

@@ -164,7 +164,7 @@ end
 """
     find_covariate_adjustment(g, X, Y, I = Set{eltype(g)}(), R = setdiff(Set(vertices(g)), X, Y))
 
-Find a covariate adjustment set `Z` with ``I ⊆ Z subseteq ⊆ R`` for sets of vertices `X` and `Y` in `g`, else return `false`. 
+Find a covariate adjustment set `Z` with ``I ⊆ Z ⊆ R`` for sets of vertices `X` and `Y` in `g`, else return `false`. 
 
 Based on the algorithmic approach proposed in https://arxiv.org/abs/1803.00116. 
 """

test/gensearch.jl

@@ -34,9 +34,10 @@ Yvec = [4]
     @test find_min_dsep(g1, X, Y) == Set([2,5])
     @test find_covariate_adjustment(g1, Xint, Yint) == Set([5,6])
     @test find_backdoor_adjustment(g1, X, Y) == Set([5,6])
+    @test find_frontdoor_adjustment(g1, X, Y) == Set([2,3,7])
     @test find_min_covariate_adjustment(g1, Xvec, Yvec) ==  Set(5)
     @test find_min_backdoor_adjustment(g1, Xint, Yvec) == Set(5)
-    @test find_frontdoor_adjustment(g1, X, Y) == Set([2,3,7])
+    @test find_min_frontdoor_adjustment(g1, X, Y) == Set(3)
     @test Set(list_dseps(g1, Xvec, Y)) == Set([Set([3,6]), Set([2,6]), Set([2,3,6]), Set([3,6,7]), Set([2,6,7]), Set([2,3,6,7]), Set([3,5]), Set([2,5]), Set([2,3,5]), Set([3,5,7]), Set([2,5,7]), Set([2,3,5,7]), Set([3,5,6]), Set([2,5,6]), Set([2,3,5,6]), Set([3,5,6,7]), Set([2,5,6,7]), Set([2,3,5,6,7])])
     @test Set(list_covariate_adjustment(g1, X, Yint)) == Set([Set([5,7]), Set([5]), Set([6]), Set([6,7]), Set([5,6]), Set([5,6,7])])
     @test Set(list_backdoor_adjustment(g1, Xvec, Yint)) == Set([Set([5]), Set([6]), Set([5,6])])
@@ -67,8 +68,10 @@ Y = Set(8)
     @test find_covariate_adjustment(g2, X, Y, Set(7), Set([1,2,3,4,5])) == false
     @test find_covariate_adjustment(g2, X, Y, Set{Int64}(), Set([3,4,5,7])) == Set([3,4,5]) 
     @test find_backdoor_adjustment(g2, X, Y) == Set([1,2,3,4,5])
+    @test find_frontdoor_adjustment(g2, X, Y) == Set(7)
     @test find_min_covariate_adjustment(g2, X, Y) ==  Set([3,4])
     @test find_min_backdoor_adjustment(g2, X, Y) == Set([3,4])
+    @test find_min_frontdoor_adjustment(g2, X, Y) == Set(7)
     @test Set(list_dseps(g2, X, Y, Set{Int64}(), Set{Int64}([3,4,5,7]))) == Set([Set([4, 7, 3]), Set([5, 4, 7]), Set([5, 4, 7, 3])])
     @test Set(list_covariate_adjustment(g2, Set([6]), Set([8]), Set(Int[]), setdiff(Set(1:8), [1,2]))) == Set([Set([3,4]), Set([4,5]), Set([3,4,5])])
     @test Set(list_backdoor_adjustment(g2, Set([6]), Set([8]), Set(Int[]), setdiff(Set(1:8), [1,2]))) == Set([Set([3,4]), Set([4,5]), Set([3,4,5])])