def calcNoderateMultipliers(t, hTarget = None, method = 1) :
nh = nodeHeights(t,allTipsZero=0)
if hTarget is None:
hm = mean([nh[c] for c in t.get_terminals()])
hTarget = nh[t.root] - hm
meth = [nodeRateMultiplier,nodeRateMultiplier1][method]
rt = t.node(t.root)
for c in rt.succ :
meth(t, t.node(c), hTarget, nh)
return hTarget
def _treeBranchAssignmentExprs(tree, hRoot,
withDerivative = False, withInit = False) :
allid = set(tree.all_ids()) # taxa
terms = set(tree.get_terminals())
# internal nodes
allint = allid - terms
# unrooted has dated tips when rooted somewhere
nh = nodeHeights(tree, allTipsZero = False)
# Node before its descendants
nInOrder = getPreOrder(tree, includeTaxa=True)
# Reversed, child before parent
nhInOrder = [(nh[x],x) for x in reversed(nInOrder)]
nInOrder = [x for x in nInOrder if x not in terms]
nParams = len(nInOrder) - 1
if withInit :
htox = []
sr = []
sr.append("h%d = %.15g" % (nInOrder[0], hRoot))
for i,k in enumerate(nInOrder[1:]):
h = tree.node(k).prev
sr.append("h%d = x[%d] * h%d" % (k, i, h))
if withInit:
htox.append("x[%d] = %.15g" % (i, nh[k]/nh[h]))
if withDerivative:
if h == tree.root :
sr.append("d_h%d_x = [%s]" % (k,der(i, nParams, -1)))
else :
sr.append("d_h%d_x = [%s]" % (k,der(i, nParams, h)))
for h,n in nhInOrder[:-1] :
assert n != tree.root
p = tree.node(n).prev
if n in terms:
sr.append("b%d=(h%d) # %d" % (n, p, n))
if withDerivative:
if p == tree.root :
sr.append("d_b%d_x = [0]*%d" % (n,nParams))
else :
sr.append("d_b%d_x = d_h%d_x" % (n,p))
else :
sr.append("b%d=(h%d - h%d) # %d" % (n, p, n, n))
if withDerivative:
if p == tree.root :
sr.append("d_b%d_x = [-v for v in d_h%d_x]" % (n,n))
else :
sr.append("d_b%d_x = [u-v for u,v in zip(d_h%d_x, d_h%d_x)]" % (n,p,n))
if withInit:
return sr, htox
return sr
def treeHeightEstimate(t) : """ Distance between root to mean tip age. """ nh = nodeHeights(t, allTipsZero=False) hm = mean([nh[c] for c in t.get_terminals()]) return nh[t.root] - hm