Merge pull request #5 from facusapienza21/name_bug_fix

Bug regarding name handling

CHANGES.txt

@@ -0,0 +1,4 @@
+optimaladj 0.0.4
+==============
+
+* Fixed a bug reported by Sara Taheri, whereby due to mishandling of node names we could end up including forbidden variables in an adjustment set.

optimaladj/CausalGraph.py

@@ -113,9 +113,9 @@ def forbidden(self, treatment, outcome):
         forbidden = set()
 
         for node in self.causal_vertices(treatment, outcome):
-            forbidden = forbidden.union(nx.descendants(self, node).union(node))
+            forbidden = forbidden.union(nx.descendants(self, node).union({node}))
 
-        return forbidden.union(treatment)
+        return forbidden.union({treatment})
 
     def ignore(self, treatment, outcome, L, N):
         """Returns the set of ignorable vertices with respect to treatment, outcome,

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="optimaladj",
-    version="0.0.3",
+    version="0.0.4",
     author="Facundo Sapienza, Ezequiel Smucler",
     author_email="[email protected]",
     description="A package to compute optimal adjustment sets in causal graphs",

tests/examples.py

@@ -339,6 +339,7 @@ def __init__(self, G, treatment, outcome, L, N):
 G_9.add_nodes_from(costs_9)
 G_9.add_edges_from(
     [
+        ("A", "Y"),
         ("K", "A"),
         ("W1", "K"),
         ("W2", "K"),
@@ -362,3 +363,66 @@ def __init__(self, G, treatment, outcome, L, N):
 OPTIMALS_MINIMAL.append(set(["W7", "W8", "W9"]))
 OPTIMALS_MINIMUM.append(set(["K"]))
 OPTIMALS_MINCOST.append(set(["W7", "W8", "W6"]))
+
+# Regression test for bug on name handling, spotted by Sara Taheri
+
+G_10 = CausalGraph()
+L_10 = []
+N_10 = ["T", "Y", "M1", "M2", "Z1", "Z2", "Z3"]
+costs_10 = [(node, {"cost": 1}) for node in N_10]
+treatment_10 = "T"
+outcome_10 = "Y"
+G_10.add_nodes_from(costs_10)
+G_10.add_edges_from(
+    [
+        ("Z1", "Z2"),
+        ("Z1", "T"),
+        ("Z2", "Z3"),
+        ("Z3", "Y"),
+        ("T", "M1"),
+        ("M1", "M2"),
+        ("M2", "Y"),
+    ]
+)
+
+EXAMPLES.append(CausalGraphExample(G_10, treatment_10, outcome_10, L_10, N_10))
+
+OPTIMALS.append(set(["Z3"]))
+OPTIMALS_MINIMAL.append(set(["Z3"]))
+OPTIMALS_MINIMUM.append(set(["Z3"]))
+OPTIMALS_MINCOST.append(set(["Z3"]))
+
+# Another regression test for bug on name handling, spotted by Sara Taheri
+
+G_11 = CausalGraph()
+L_11 = []
+N_11 = ["T", "Y", "M1", "M2", "M3", "Z1", "Z2", "Z3", "Z4", "Z5"]
+costs_11 = [(node, {"cost": 1}) for node in N_11]
+treatment_11 = "T"
+outcome_11 = "Y"
+G_11.add_nodes_from(costs_11)
+G_11.add_edges_from(
+    [
+        ("Z1", "Z2"),
+        ("Z1", "T"),
+        ("Z2", "Z3"),
+        ("Z3", "Z4"),
+        ("Z4", "Z5"),
+        ("Z5", "Y"),
+        ("T", "M1"),
+        ("M1", "M2"),
+        ("M2", "M3"),
+        ("M3", "Y"),
+        ("U1", "Z1"),
+        ("U1", "T"),
+        ("U2", "Z2"),
+        ("U2", "M1"),
+    ]
+)
+
+EXAMPLES.append(CausalGraphExample(G_11, treatment_11, outcome_11, L_11, N_11))
+
+OPTIMALS.append(set(["Z1", "Z2", "Z5"]))
+OPTIMALS_MINIMAL.append(set(["Z1"]))
+OPTIMALS_MINIMUM.append(set(["Z1"]))
+OPTIMALS_MINCOST.append(set(["Z1"]))

tests/test_CausalGraph.py

@@ -42,7 +42,7 @@ def test_no_adj_minimum_optimal(example=EXAMPLES[0]):
 
 @pytest.mark.parametrize(
     "example, optimal_stored",
-    zip(EXAMPLES[1:4] + [EXAMPLES[8]], OPTIMALS[1:4] + [OPTIMALS[8]]),
+    zip(EXAMPLES[1:4] + EXAMPLES[8:12], OPTIMALS[1:4] + OPTIMALS[8:12]),
 )
 def test_optimal(example, optimal_stored):
     optimal = example.G.optimal_adj_set(
@@ -63,7 +63,7 @@ def test_optimal_failure(example):
 
 
 @pytest.mark.parametrize(
-    "example, optimal_minimal_stored", zip(EXAMPLES[1:8], OPTIMALS_MINIMAL[1:8])
+    "example, optimal_minimal_stored", zip(EXAMPLES[1:12], OPTIMALS_MINIMAL[1:12])
 )
 def test_optimal_minimal(example, optimal_minimal_stored):
     optimal = example.G.optimal_minimal_adj_set(
@@ -73,7 +73,7 @@ def test_optimal_minimal(example, optimal_minimal_stored):
 
 
 @pytest.mark.parametrize(
-    "example, optimal_minimum_stored", zip(EXAMPLES[1:8], OPTIMALS_MINIMUM[1:8])
+    "example, optimal_minimum_stored", zip(EXAMPLES[1:12], OPTIMALS_MINIMUM[1:12])
 )
 def test_optimal_minimum(example, optimal_minimum_stored):
     optimal = example.G.optimal_minimum_adj_set(
@@ -83,7 +83,7 @@ def test_optimal_minimum(example, optimal_minimum_stored):
 
 
 @pytest.mark.parametrize(
-    "example, optimal_mincost_stored", zip(EXAMPLES[1:8], OPTIMALS_MINCOST[1:8])
+    "example, optimal_mincost_stored", zip(EXAMPLES[1:12], OPTIMALS_MINCOST[1:12])
 )
 def test_optimal_mincost(example, optimal_mincost_stored):
     optimal = example.G.optimal_mincost_adj_set(