[beast-mcmc] r6743 committed - Minor change to marginal likelihood estimate when sampling from the pr...

[beast...@googlecode.com]

Revision: 6743
Author: bael...@gmail.com
Date: Thu Apr 23 09:55:14 2015 UTC
Log: Minor change to marginal likelihood estimate when sampling from
the prior.
https://code.google.com/p/beast-mcmc/source/detail?r=6743

Modified:
/trunk/src/dr/inference/trace/MarginalLikelihoodAnalysis.java
/trunk/src/dr/inference/trace/PathSamplingAnalysis.java

=======================================
--- /trunk/src/dr/inference/trace/MarginalLikelihoodAnalysis.java Mon Apr
8 11:54:12 2013 UTC
+++ /trunk/src/dr/inference/trace/MarginalLikelihoodAnalysis.java Thu Apr
23 09:55:14 2015 UTC
@@ -100,12 +100,16 @@
*/
public double logMarginalLikelihoodArithmetic(List<Double> v) {

- final int size = v.size();
+ int size = v.size();

double sum = LogTricks.logZero;

for (int i = 0; i < size; i++) {
- sum = LogTricks.logSum(sum, v.get(i));
+ if (!Double.isNaN(v.get(i)) && !Double.isInfinite(v.get(i))) {
+ sum = LogTricks.logSum(sum, v.get(i));
+ } else {
+ size--;
+ }
}

return sum - StrictMath.log(size);
=======================================
--- /trunk/src/dr/inference/trace/PathSamplingAnalysis.java Mon Oct 1
20:28:17 2012 UTC
+++ /trunk/src/dr/inference/trace/PathSamplingAnalysis.java Thu Apr 23
09:55:14 2015 UTC
@@ -159,7 +159,7 @@

if (burnin < 0 || burnin >= maxState) {
burnin = maxState / 5;
- System.out.println("WARNING: Burn-in larger than
total number of states - using to 20%");
+ System.out.println("WARNING: Burn-in larger than
total number of states - using 20%");
}

burnin = 0;