BUG: incorrect gaussian kernel on Graph (#789)

Author: martinfleis

libpysal/graph/_kernel.py

@@ -34,7 +34,7 @@ def _parabolic(distances, bandwidth):
 
 def _gaussian(distances, bandwidth):
     u = distances / bandwidth
-    return numpy.exp(-((u / 2) ** 2)) / (numpy.sqrt(2) * numpy.pi)
+    return numpy.exp(-((u / 2) ** 2)) / (numpy.sqrt(2 * numpy.pi))
 
 
 def _bisquare(distances, bandwidth):

libpysal/graph/tests/test_builders.py

@@ -237,26 +237,26 @@ def test_kernel_precompute(self):
         g = graph.Graph.build_kernel(distmat, metric="precomputed")
         expected = np.array(
             [
-                0.07131664,
-                0.14998932,
-                0.09804811,
-                0.0402638,
-                0.07131664,
-                0.18556845,
-                0.17529176,
-                0.16394507,
-                0.14998932,
-                0.18556845,
-                0.17495794,
-                0.11561449,
-                0.09804811,
-                0.17529176,
-                0.17495794,
-                0.19116432,
-                0.0402638,
-                0.16394507,
-                0.11561449,
-                0.19116432,
+                0.126,
+                0.266,
+                0.174,
+                0.071,
+                0.126,
+                0.329,
+                0.311,
+                0.291,
+                0.266,
+                0.329,
+                0.31,
+                0.205,
+                0.174,
+                0.311,
+                0.31,
+                0.339,
+                0.071,
+                0.291,
+                0.205,
+                0.339,
             ]
         )
 

libpysal/graph/tests/test_kernel.py

@@ -210,8 +210,8 @@ def test_kernels(kernel, grocs):
         assert weight.mean() == pytest.approx(0.10312196315841769)
         assert weight.max() == pytest.approx(0.749881829575671)
     elif kernel == "gaussian":
-        assert weight.mean() == pytest.approx(0.1124559308071747)
-        assert weight.max() == pytest.approx(0.22507021331712948)
+        assert weight.mean() == pytest.approx(0.19932294761630429)
+        assert weight.max() == pytest.approx(0.3989265663183409)
     elif kernel == "bisquare":
         assert weight.mean() == pytest.approx(0.09084085210598618)
         assert weight.max() == pytest.approx(0.9372045972129259)

libpysal/graph/tests/test_triangulation.py

@@ -259,26 +259,26 @@ def test_kernel():
     _, _, weight = _delaunay(cau_coords, kernel="gaussian")
     expected = np.array(
         [
-            0.1305618,
-            0.17359059,
-            0.22312817,
-            0.1305618,
-            0.1339654,
-            0.03259559,
-            0.17359059,
-            0.1339654,
-            0.06948067,
-            0.180294,
-            0.03259559,
-            0.06948067,
-            0.02004257,
-            0.22312817,
-            0.180294,
-            0.02004257,
+            0.231415,
+            0.307681,
+            0.395484,
+            0.231415,
+            0.237447,
+            0.057774,
+            0.307681,
+            0.237447,
+            0.123151,
+            0.319563,
+            0.057774,
+            0.123151,
+            0.035525,
+            0.395484,
+            0.319563,
+            0.035525,
         ]
     )
 
-    np.testing.assert_array_almost_equal(expected, weight)
+    np.testing.assert_array_almost_equal(weight, expected)
 
 
 @pytest.mark.network