Correct GMRF Weights

beast-dev · Apr 2, 2024 · 42b92d5 · 42b92d5
1 parent fab5f00
commit 42b92d5
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/ci/TestXML/testGaussianMarkovRandomField.xml b/ci/TestXML/testGaussianMarkovRandomField.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" standalone="yes"?>
 <beast>
 
-	<parameter id="data" value="90 78 34 12"/>
+	<parameter id="data" value="1 2 3 6"/>
 
 	<taxa id="taxa">
 		<taxon id="A"/>
@@ -38,10 +38,10 @@
 		<distribution>
 			<GaussianMarkovRandomField dim="4" matchPseudoDeterminant="false">
 				<precision>
-					<parameter id="precision" value="0.1"/>
+					<parameter id="precision" value="3"/>
 				</precision>
 				<mean>
-					<parameter id="mean" value="0"/>
+					<parameter id="mean" value="3"/>
 				</mean>
 				<weightProvider>
 					<treeModel idref="treeModel"/>

diff --git a/src/dr/inference/distribution/Weights.java b/src/dr/inference/distribution/Weights.java
@@ -46,7 +46,7 @@ public double weight(int index1, int index2) {
                 index1 = temp;
             }
 
-            return (intervals.getInterval(index1) + intervals.getInterval(index2))/2;
+            return 2/(intervals.getInterval(index1) + intervals.getInterval(index2));
         }
 
     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -46,7 +46,7 @@ public double weight(int index1, int index2) { @@
                     index1 = temp;
                 }
-                return (intervals.getInterval(index1) + intervals.getInterval(index2))/2;
+                return 2/(intervals.getInterval(index1) + intervals.getInterval(index2));
             }
         }
@@ Expand Down @@