[beast-mcmc] r6756 committed - Update Pybus et al (2012) citation

[beast...@googlecode.com]

Revision: 6756
Author: msuchard
Date: Fri Apr 24 19:39:23 2015 UTC
Log: Update Pybus et al (2012) citation
https://code.google.com/p/beast-mcmc/source/detail?r=6756

Modified:

/trunk/src/dr/evomodel/continuous/IntegratedMultivariateTraitLikelihood.java

=======================================
---
/trunk/src/dr/evomodel/continuous/IntegratedMultivariateTraitLikelihood.java
Mon Jan 26 01:55:24 2015 UTC
+++
/trunk/src/dr/evomodel/continuous/IntegratedMultivariateTraitLikelihood.java
Fri Apr 24 19:39:23 2015 UTC
@@ -1,7 +1,7 @@
/*
* IntegratedMultivariateTraitLikelihood.java
*
- * Copyright (c) 2002-2014 Alexei Drummond, Andrew Rambaut and Marc Suchard
+ * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
@@ -239,12 +239,25 @@
citations.add(
new Citation(
new Author[]{
- new Author("O", "Pybus"),
+ new Author("OG", "Pybus"),
+ new Author("MA", "Suchard"),
new Author("P", "Lemey"),
+ new Author("F", "Bernadin"),
new Author("A", "Rambaut"),
- new Author("MA", "Suchard")
+ new Author("FW", "Crawford"),
+ new Author("RR", "Gray"),
+ new Author("N", "Arinaminpathy"),
+ new Author("S", "Stramer"),
+ new Author("MP", "Busch"),
+ new Author("E", "Delwart")
+
},
- Citation.Status.IN_PREPARATION
+ "Unifying the spatial epidemiology and evolution
of emerging epidemics",
+ 2012,
+ "Proceedings of the National Academy of Sciences",
+ 109,
+ 15066, 15071,
+ Citation.Status.PUBLISHED
)
);
return citations;
@@ -1090,8 +1103,42 @@

}

- ;
+ class StandarizedCacheHelper extends CacheHelper {

+ public StandarizedCacheHelper(int dim, int nodeCount, boolean
cacheBranches) {
+ super(dim * nodeCount, cacheBranches);
+ this.dim = dim;
+ this.nodeCount = nodeCount;
+
+
+ }
+
+ public void setTipMeans(double[] traitValue, int dim, int index,
NodeRef node) {
+ //System.arraycopy(traitValue, 0, meanCache, dim * index, dim);
+ for (int i = 0; i < dim; ++i) {
+ setMeanCache(dim * index + i, traitValue[i]);
+ }
+ }
+
+ public void setTipMeans(double[] traitValue, int dim, int index) {
+// System.arraycopy(traitValue, 0, meanCache, dim * index, dim);
+ for (int i = 0; i < dim; ++i) {
+ setMeanCache(dim * index + i, traitValue[i]);
+ }
+ }
+
+// public void copyToMeanCache(double[] src, int destPos, int
length) {
+// System.arraycopy(src, 0, meanCache, destPos, length);
+// }
+
+ public void setMeanCache(int index, double value) {
+ final int thisDim = index % dim;
+ meanCache[index] = value;
+ }
+
+ private final int dim;
+ private final int nodeCount;
+ }

class DriftCacheHelper extends CacheHelper {

@@ -1191,6 +1238,31 @@

}

+ private CacheHelper createCacheHelper(IntegratedDiffusionType type,
int cacheLength, boolean cacheBranches) {
+ CacheHelper helper = null;
+ switch (type) {
+ case PLAIN:
+ helper = new CacheHelper(cacheLength, cacheBranches);
+ break;
+ case SCALED:
+ helper = new CacheHelper(cacheLength, cacheBranches);
+ break;
+ case DRIFT:
+ helper = new DriftCacheHelper(cacheLength, cacheBranches);
+ break;
+ case OU:
+ helper = new OUCacheHelper(cacheLength, cacheBranches);
+ break;
+ }
+ return helper;
+ }
+
+ public enum IntegratedDiffusionType {
+ PLAIN,
+ SCALED,
+ DRIFT,
+ OU,
+ }

// protected boolean hasDrift;