public String toString() {
int ngt = piosb.numberOfGeneTrees();
String nl = System.getProperty("line.separator");
String s = nl + pioTreeAsText() + nl;
for (int g = 0; g < ngt; g++) {
s += "Gene tree " + g + nl;
s += piosb.genetreeAsText(g) + nl;
}
s += nl;
return s;
}
private void recordSubtreeLineageCounts(PopsIONode node) {
if (node.lft < 0) {
int spIndex = piosb.speciesId2index(node.getTaxon().getId());
node.nlineages = piosb.nLineages(spIndex);
} else {
node.nlineages = 0;
recordSubtreeLineageCounts(pionodes[node.lft]);
node.nlineages += pionodes[node.lft].nlineages - pionodes[node.lft].coalheights.size();
recordSubtreeLineageCounts(pionodes[node.rgt]);
node.nlineages += pionodes[node.rgt].nlineages - pionodes[node.rgt].coalheights.size();
}
}
public PopsIOSpeciesTreeModel(
PopsIOSpeciesBindings piosb, Parameter popPriorScale, PriorComponent[] priorComponents) {
super(PopsIOSpeciesTreeModelParser.PIO_SPECIES_TREE);
this.piosb = piosb;
this.popPriorScale = popPriorScale;
addVariable(popPriorScale);
popPriorScale.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.priorComponents = priorComponents;
PopsIOSpeciesBindings.SpInfo[] species = piosb.getSpecies();
int nTaxa = species.length;
int nNodes = 2 * nTaxa - 1;
pionodes = new PopsIONode[nNodes];
for (int n = 0; n < nNodes; n++) {
pionodes[n] = new PopsIONode(n);
}
ArrayList<Integer> tojoin = new ArrayList<Integer>(nTaxa);
for (int n = 0; n < nTaxa; n++) {
pionodes[n].setTaxon(species[n].name);
pionodes[n].setHeight(0.0);
pionodes[n].setUnion(piosb.tipUnionFromTaxon(pionodes[n].getTaxon()));
tojoin.add(n);
}
double rate = 1.0;
double treeheight = 0.0;
for (int i = 0; i < nTaxa - 1; i++) {
int numtojoin = tojoin.size();
int j = MathUtils.nextInt(numtojoin);
Integer child0 = tojoin.get(j);
tojoin.remove(j);
int k = MathUtils.nextInt(numtojoin - 1);
Integer child1 = tojoin.get(k);
tojoin.remove(k);
pionodes[nTaxa + i].addChildren(pionodes[child0], pionodes[child1]);
pionodes[nTaxa + i].setHeight(treeheight + randomnodeheight(numtojoin * rate));
treeheight = pionodes[nTaxa + i].getHeight();
tojoin.add(nTaxa + i);
}
rootn = pionodes.length - 1;
double scale = 0.99 * piosb.initialMinGeneNodeHeight() / pionodes[rootn].height;
scaleAllHeights(scale);
pionodes[rootn].fillinUnionsInSubtree(piosb.getSpecies().length);
stree = makeSimpleTree();
Logger.getLogger("dr.evomodel.speciation.popsio")
.info(
"\tConstructing a PopsIO Species Tree Model, please cite:\n"
+ Citable.Utils.getCitationString(this));
}
private void accumSubtreeCoalCountsIntensities(PopsIONode node) {
if (node.lft >= 0) {
accumSubtreeCoalCountsIntensities(pionodes[node.lft]);
accumSubtreeCoalCountsIntensities(pionodes[node.rgt]);
}
int k = node.coalheights.size();
node.coalcount += k;
double[] t = new double[k + 2];
t[0] = node.height;
for (int i = 0; i < k; i++) {
t[i + 1] = node.coalheights.get(i);
}
t[k + 1] = (node.anc < 0) ? piosb.maxGeneTreeHeight() : pionodes[node.anc].height;
int n = node.nlineages;
for (int i = 0; i <= k; i++) {
node.coalintensity += (t[i + 1] - t[i]) * 0.5 * (n - i) * (n - i - 1);
}
}
public void fixupAfterNodeSlide() {
pionodes[rootn].fillinUnionsInSubtree(piosb.getSpecies().length);
stree = makeSimpleTree();
}