Added median clade credibility reporting

beast-dev · Nov 6, 2024 · b65c694 · b65c694
1 parent ab851ec
commit b65c694
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Showing 2 changed files with 24 additions and 1 deletion.
diff --git a/src/dr/app/tools/newtreeannotator/CladeSystem.java b/src/dr/app/tools/newtreeannotator/CladeSystem.java
@@ -31,10 +31,10 @@
 import dr.evolution.tree.Tree;
 import dr.evolution.util.Taxon;
 import dr.evolution.util.TaxonList;
+import dr.stats.DiscreteStatistics;
 
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
 
 /**
  * @author Andrew Rambaut
@@ -258,6 +258,28 @@ public boolean expectAllClades() {
         return minCladeCredibility[0] / tree.getInternalNodeCount();
     }
 
+    public double getMedianCladeCredibility(Tree tree) {
+        final double[] cladeCredibility = new double[tree.getInternalNodeCount()];
+        final int[] i = { 0 };
+        traverseTree(tree, new CladeAction() {
+            @Override
+            public void actOnClade(Clade clade, Tree tree, NodeRef node) {
+                if (clade.getTaxon() == null) {
+                    cladeCredibility[i[0]] = clade.getCredibility();
+                    i[0] += 1;
+                }
+            }
+
+            @Override
+            public boolean expectAllClades() {
+                return true;
+            }
+        });
+
+
+        return DiscreteStatistics.median(cladeCredibility);
+    }
+
     /**
      * Returns the number of clades in the tree with threshold credibility or higher
      * @param tree

diff --git a/src/dr/app/tools/newtreeannotator/TreeAnnotator.java b/src/dr/app/tools/newtreeannotator/TreeAnnotator.java
@@ -492,6 +492,7 @@ private MutableTree getHIPSTRTree(CladeSystem cladeSystem) {
     private static void reportStatistics(CladeSystem cladeSystem, Tree tree) {
         progressStream.println("Lowest individual clade credibility: " + String.format("%.4f", cladeSystem.getMinimumCladeCredibility(tree)));
         progressStream.println("Mean individual clade credibility: " + String.format("%.4f", cladeSystem.getMeanCladeCredibility(tree)));
+        progressStream.println("Median individual clade credibility: " + String.format("%.4f", cladeSystem.getMedianCladeCredibility(tree)));
         progressStream.println("Number of clades with credibility 1.0: " + cladeSystem.getTopCladeCredibility(tree, 1.0));
         progressStream.println("Number of clades with credibility > 0.99: " + cladeSystem.getTopCladeCredibility(tree, 0.99) +
                 " (out of " + cladeSystem.getTopCladeCredibility(0.99) + " in all trees)");