Reports the number of clades with credibility 1.0

beast-dev · Nov 4, 2024 · d6d2054 · d6d2054
1 parent 6d101cf
commit d6d2054
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/src/dr/app/tools/newtreeannotator/CladeSystem.java b/src/dr/app/tools/newtreeannotator/CladeSystem.java
@@ -263,7 +263,7 @@ public int getTopCladeCredibility(Tree tree, double threshold) {
         traverseTree(tree, new CladeAction() {
             @Override
             public void actOnClade(Clade clade, Tree tree, NodeRef node) {
-                if (clade.getTaxon() == null && clade.getCredibility() > threshold) {
+                if (clade.getTaxon() == null && clade.getCredibility() >= threshold) {
                     minCladeCredibility[0] += 1;
                 }
             }

diff --git a/src/dr/app/tools/newtreeannotator/TreeAnnotator.java b/src/dr/app/tools/newtreeannotator/TreeAnnotator.java
@@ -467,6 +467,7 @@ private Tree getMCCTree(int burnin, CladeSystem cladeSystem, String inputFileNam
         progressStream.println("Best tree's log clade credibility: " + String.format("%.4f", bestScore));
         progressStream.println("Lowest individual clade credibility: " + String.format("%.4f", cladeSystem.getMinimumCladeCredibility(bestTree)));
         progressStream.println("Mean individual clade credibility: " + String.format("%.4f", cladeSystem.getMeanCladeCredibility(bestTree)));
+        progressStream.println("Number of clades with credibility 1.0: " + cladeSystem.getTopCladeCredibility(bestTree, 1.0));
         progressStream.println("Number of clades with credibility > 0.95: " + cladeSystem.getTopCladeCredibility(bestTree, 0.95));
         progressStream.println("Number of clades with credibility > 0.5: " + cladeSystem.getTopCladeCredibility(bestTree, 0.5));
         progressStream.println();