diff --git a/build.xml b/build.xml
index a5d5f44..1c88ff3 100644
--- a/build.xml
+++ b/build.xml
@@ -17,7 +17,7 @@
-
+
@@ -32,7 +32,7 @@
-
+
diff --git a/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java b/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
index 038868b..d6627f3 100644
--- a/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
+++ b/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
@@ -158,6 +158,21 @@ public void test3intsmitRho() throws Exception {
bdssm.initAndValidate();
assertEquals(-106.06555718977357, bdssm.calculateTreeLogLikelihood(tree), 1e-4);
}
+ case 3:{
+ BirthDeathSkylineModel bdssm = new BirthDeathSkylineModel();
+ bdssm.setInputValue("tree", tree);
+ bdssm.setInputValue("origin", new RealParameter("2"));
+ bdssm.setInputValue("conditionOnSurvival", false);
+
+ bdssm.setInputValue("birthRate", new RealParameter("3. 2. 4. 4."));
+ bdssm.setInputValue("deathRate", new RealParameter("2.5 1. .5 0.5"));
+ bdssm.setInputValue("samplingRate", new RealParameter("2. 0.5 1. 2.0"));
+ bdssm.setInputValue("rho", new RealParameter("0.05 0.01"));
+ bdssm.setInputValue("rhoSamplingTimes","0. 1.");
+ bdssm.setInputValue("intervalTimes", new RealParameter("0. 0.5 1. 1.1"));
+ bdssm.initAndValidate();
+ assertEquals(-109.6105592003162, bdssm.calculateTreeLogLikelihood(tree), 1e-4);
+ }
}
}
}
@@ -700,7 +715,7 @@ public void testLikelihoodCalculation5reverseAll() throws Exception {
public void testTreeParser() throws Exception {
TreeParser tree = new TreeParser();
- String newick = "(((1[&state='1']:1, (2[&state='0']:.5)[&state='1']:1.5)[&state='1']:2)[&state='0']:1, (3[&state='0']:1.5, (4[&state='1']:1.5)[&state='0']:1 )[&state='0']:2)[&state='0']:1;";
+ String newick = "(((1[&state='1']:1, (2[&state='0']:0.5)[&state='1']:1.5)[&state='1']:2)[&state='0']:1, (3[&state='0']:1.5, (4[&state='1']:1.5)[&state='0']:1 )[&state='0']:2)[&state='0']:1;";
tree.initByName("adjustTipHeights",false, "singlechild", true, "newick", newick);
printNodeState(tree.getRoot());
diff --git a/version.xml b/version.xml
index ad10ba1..2e6ca60 100644
--- a/version.xml
+++ b/version.xml
@@ -1,3 +1,3 @@
-
+