def optLogLike(self,
verbose=1,
newtAndBrentPowell=1,
allBrentPowell=0,
simplex=0):
"""Calculate the likelihood of the tree, with optimization.
There are 3 optimization methods-- choose one. I've made
'newtAndBrentPowell' the default, as it is fast and seems to be
working. The 'allBrentPowell' optimizer used to be the default,
as it seems to be the most robust, although it is slow. It would
be good for checking important calculations. The simplex
optimizer is the slowest, and will sometimes find better optima
for difficult data, but often fails to optimize (with no
warning)."""
if verbose:
theStartTime = time.clock()
self._commonCStuff()
# We want only one opt method.
if newtAndBrentPowell:
newtAndBrentPowell = 1
if allBrentPowell:
allBrentPowell = 1
if simplex:
simplex = 1
if (newtAndBrentPowell + allBrentPowell + simplex) != 1:
gm = ['Tree.optLogLike()']
gm.append("Choose 1 opt method.")
raise Glitch, gm
# Do the opt.
if allBrentPowell:
pf.p4_allBrentPowellOptimize(self.cTree)
elif simplex:
from Tree import Tree
pf.p4_simplexOptimize(self.cTree, self, Tree.simplexDump)
else:
pf.p4_newtSetup(self.cTree)
pf.p4_newtAndBrentPowellOpt(self.cTree)
self.logLike = pf.p4_treeLogLike(self.cTree,
0) # second arg is getSiteLikes
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for n in self.iterNodesNoRoot():
n.br.len = brLens[n.nodeNum]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
if verbose:
print "optLogLike = %f" % self.logLike
theEndTime = time.clock()
print "cpu time %s seconds." % (theEndTime - theStartTime)
def optLogLike(self, verbose=1, newtAndBrentPowell=1, allBrentPowell=0, simplex=0):
"""Calculate the likelihood of the tree, with optimization.
There are 3 optimization methods-- choose one. I've made
'newtAndBrentPowell' the default, as it is fast and seems to be
working. The 'allBrentPowell' optimizer used to be the default,
as it seems to be the most robust, although it is slow. It would
be good for checking important calculations. The simplex
optimizer is the slowest, and will sometimes find better optima
for difficult data, but often fails to optimize (with no
warning)."""
if verbose:
theStartTime = time.clock()
self._commonCStuff()
# We want only one opt method.
if newtAndBrentPowell:
newtAndBrentPowell = 1
if allBrentPowell:
allBrentPowell = 1
if simplex:
simplex = 1
if (newtAndBrentPowell + allBrentPowell + simplex) != 1:
gm = ['Tree.optLogLike()']
gm.append("Choose 1 opt method.")
raise Glitch(gm)
# Do the opt.
if allBrentPowell:
pf.p4_allBrentPowellOptimize(self.cTree)
elif simplex:
from .Tree import Tree
pf.p4_simplexOptimize(self.cTree, self, Tree.simplexDump)
else:
pf.p4_newtSetup(self.cTree)
pf.p4_newtAndBrentPowellOpt(self.cTree)
self.logLike = pf.p4_treeLogLike(self.cTree, 0) # second arg is getSiteLikes
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for n in self.iterNodesNoRoot():
n.br.len = brLens[n.nodeNum]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
if verbose:
print("optLogLike = %f" % self.logLike)
theEndTime = time.clock()
print("cpu time %s seconds." % (theEndTime - theStartTime))
def optLogLike(self, verbose=1, newtAndBrentPowell=1, allBrentPowell=0):
"""Calculate the likelihood of the tree, with optimization.
There are two optimization methods-- choose one. I've made
'newtAndBrentPowell' the default, as it is fast and seems to be
working. The 'allBrentPowell' optimizer used to be the default,
as it seems to be the most robust, although it is slow. It would
be good for checking important calculations.
"""
if verbose:
theStartTime = time.clock()
self._commonCStuff()
# We want only one opt method.
if newtAndBrentPowell:
newtAndBrentPowell = 1
if allBrentPowell:
allBrentPowell = 1
if (newtAndBrentPowell + allBrentPowell) != 1:
gm = ['Tree.optLogLike()']
gm.append("Choose 1 opt method.")
raise P4Error(gm)
# Do the opt.
if allBrentPowell:
pf.p4_allBrentPowellOptimize(self.cTree)
else:
pf.p4_newtSetup(self.cTree)
pf.p4_newtAndBrentPowellOpt(self.cTree)
# second arg is getSiteLikes
self.logLike = pf.p4_treeLogLike(self.cTree, 0)
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for n in self.iterNodesNoRoot():
n.br.len = brLens[n.nodeNum]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
if verbose:
print "optLogLike = %f" % self.logLike
theEndTime = time.clock()
print "cpu time %s seconds." % (theEndTime - theStartTime)
def optTest(self):
self._commonCStuff()
theStartTime = time.clock()
doXfer = 0
for i in range(1):
if doXfer:
self.model.setCStuff()
self.setCStuff()
pf.p4_setPrams(self.cTree, -1)
self.logLike = pf.p4_treeLogLike(self.cTree, 0)
if doXfer:
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for i in range(len(self.nodes)):
n = self.nodes[i]
if n != self.root:
n.br.len = brLens[i]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
print "time %s seconds." % (time.clock() - theStartTime)
def optTest(self):
self._commonCStuff()
theStartTime = time.clock()
doXfer = 0
for i in range(1):
if doXfer:
self.model.setCStuff()
self.setCStuff()
pf.p4_setPrams(self.cTree, -1)
self.logLike = pf.p4_treeLogLike(self.cTree, 0)
if doXfer:
# get the brLens
brLens = pf.p4_getBrLens(self.cTree)
for i in range(len(self.nodes)):
n = self.nodes[i]
if n != self.root:
n.br.len = brLens[i]
# get the other free prams
prams = pf.p4_getFreePrams(self.cTree)
self.model.restoreFreePrams(prams)
print("time %s seconds." % (time.clock() - theStartTime))
