Update tree prior templates

sebastianduchene · Jun 22, 2017 · 422c2d9 · 422c2d9
1 parent 599fa2e
commit 422c2d9
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Showing 17 changed files with 2,438 additions and 1,376 deletions.
diff --git a/.classpath b/.classpath
@@ -7,5 +7,6 @@
 	<classpathentry combineaccessrules="false" kind="src" path="/TreeStat2"/>
 	<classpathentry kind="lib" path="/beast2/lib/jam.jar"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/bdsky"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/phylodynamics"/>
 	<classpathentry kind="output" path="build"/>
 </classpath>
diff --git a/BD_R2.55_p0.7_n100_rep1.nexus.log b/BD_R2.55_p0.7_n100_rep1.nexus.log
diff --git a/BD_R2.55_p0.7_n100_rep1.nexus.trees b/BD_R2.55_p0.7_n100_rep1.nexus.trees
diff --git a/BD_R2.55_p0.7_n100_rep6.nexus.log b/BD_R2.55_p0.7_n100_rep6.nexus.log
diff --git a/HCV3a_non-param_skyline.log b/HCV3a_non-param_skyline.log
diff --git a/SIR_R2.55_p0.7_n100_rep1.nexus.trees b/SIR_R2.55_p0.7_n100_rep1.nexus.trees
diff --git a/master/BD_hetero_anyN.xml~ b/master/BD_hetero_anyN.xml~
diff --git a/master/CE_hetero_sim.xml~ b/master/CE_hetero_sim.xml~
diff --git a/master/SIR_hetero_anyN.xml b/master/SIR_hetero_anyN.xml
@@ -1,24 +1,24 @@
 <beast version='2.0' namespace='master:master.model:master.conditions:master.outputs:master.postprocessors'>
   <run spec='InheritanceTrajectory'
        samplePopulationSizes="true"
-       verbosity="1" simulationTime=$(origin)>
+       verbosity="1" simulationTime="$(origin)">
     <model spec='Model' id='model'>
       <population spec='Population' id='S' populationName='S'/>
       <population spec='Population' id='I' populationName='I'/>
       <population spec='Population' id='R' populationName='R'/>
       <population spec="Population" id="I_sample" populationName="I_sample"/>
-      <reaction spec='Reaction' reactionName="Infection" rate=$(birth)>
+      <reaction spec='Reaction' reactionName="Infection" rate="$(birth)">
 	S + I -> 2I
       </reaction>
-      <reaction spec='Reaction' reactionName="Recovery" rate=$(death)>
+      <reaction spec='Reaction' reactionName="Recovery" rate="$(death)">
 	I -> R
       </reaction>
-      <reaction spec="Reaction" reactionName="I_sample" rate=$(sampling)>
+      <reaction spec="Reaction" reactionName="I_sample" rate="$(sampling)">
 	I -> I_sample
       </reaction>
     </model>
     <initialState spec='InitState'>
-      <populationSize spec='PopulationSize' population='@S' size=$(S0)/>
+      <populationSize spec='PopulationSize' population='@S' size="$(S0)"/>
       <lineageSeed spec='Individual' population='@I'/>
     </initialState>
 

diff --git a/master/SIR_hetero_anyN.xml~ b/master/SIR_hetero_anyN.xml~
diff --git a/master/SIR_ultra_anyN.xml~ b/master/SIR_ultra_anyN.xml~
diff --git a/src/modeladequacy/util/TreeModelAdequacyAnalyser.java b/src/modeladequacy/util/TreeModelAdequacyAnalyser.java
@@ -111,7 +111,7 @@ private void reportStats(Map<String, Object> origStats, Map<String, Object>[] tr
 				double r95   = stats[(int)(95 * n / 100.0)];
 				double r97_5 = stats[(int)(97.5 * n / 100.0)];
 				int p = 0;
-				while (stats[p] > origStat) {
+				while (p < n && stats[p] > origStat) {
 					p++;
 				}
 				double pValue = (double) p / (double) n;