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));
}
public String asText(int indentlen) {
StringBuilder s = new StringBuilder();
Formatter formatter = new Formatter(s, Locale.US);
if (lft < 0) {
formatter.format("%s ", taxon.getId());
} else {
formatter.format("%s ", "+");
}
while (s.length() < 20 - indentlen) {
formatter.format("%s", " ");
}
formatter.format("%s ", AlloppMisc.nonnegIn8Chars(height));
formatter.format("%20s ", AlloppMisc.FixedBitSetasText(union));
formatter.format("%3d ", nlineages);
for (int c = 0; c < coalheights.size(); c++) {
formatter.format(AlloppMisc.nonnegIn8Chars(coalheights.get(c)) + ",");
}
return s.toString();
}