def add_operators(self, beastxml):
if beastxml.config.languages.sample_branch_lengths:
updown = xml.operator(
beastxml.run,
attrib={
"id": "UpDown",
"spec": "UpDownOperator",
"scaleFactor": "0.5",
"weight": "3.0"})
xml.tree(updown, idref="Tree.t:beastlingTree", name="up")
xml.parameter(updown, idref="birthRate.t:beastlingTree", name="down")
### Include clock rates in up/down only if calibrations are given
if beastxml.config.calibrations:
for clock in beastxml.config.clocks:
if clock.estimate_rate:
xml.parameter(updown, idref=clock.mean_rate_id, name="down")
# Birth rate scaler
# Birth rate is *always* scaled.
xml.operator(
beastxml.run,
attrib={"id": "YuleBirthRateScaler.t:beastlingTree",
"spec": "ScaleOperator",
"parameter": "@birthRate.t:beastlingTree",
"scaleFactor": "0.5",
"weight": "3.0"})
def add_likelihood(self, likelihood):
"""
Add likelihood distribution corresponding to all features in the
dataset.
"""
for n, f in enumerate(self.features):
fname = "%s:%s" % (self.name, xml.valid_id(f))
attribs = {
"id": "featureLikelihood:%s" % fname,
"spec": "TreeLikelihood",
"useAmbiguities": "true"
}
if self.pruned:
distribution = xml.distribution(likelihood, attrib=attribs)
# Create pruned tree
tree_id = "Tree.t:prunedBeastlingTree.%s" % fname
tree = xml.tree(distribution,
id=tree_id,
spec="beast.evolution.tree.PrunedTree",
quickshortcut="true",
attrib={'assert': "false"})
xml.tree(tree, idref="Tree.t:beastlingTree")
xml.alignment(tree, idref="pruned_data_%s" % fname)
# Create pruned branchrate
self.clock.add_pruned_branchrate_model(distribution, fname,
tree_id)
else:
attribs[
"branchRateModel"] = "@%s" % self.clock.branchrate_model_id
attribs["tree"] = "@Tree.t:beastlingTree"
distribution = xml.distribution(likelihood, attrib=attribs)
if f in self.reconstruct:
# Use a different likelihood spec (also depending on whether
# the whole tree is reconstructed, or only some nodes)
if self.treewide_reconstruction:
distribution.attrib[
"spec"] = "AncestralStateTreeLikelihood"
self.treedata.append(attribs["id"])
distribution.attrib["tag"] = f
else:
distribution.attrib[
"spec"] = "lucl.beast.statereconstruction.AncestralStatesLogger"
distribution.attrib["value"] = " ".join(
self.pattern_names(f))
for label in self.reconstruct_at:
langs = self.config.language_group(label)
self.beastxml.add_taxon_set(distribution, label, langs)
self.metadata.append(attribs["id"])
distribution.attrib["useAmbiguities"] = "false"
# Sitemodel
self.add_sitemodel(distribution, f, fname)
# Data
self.add_feature_data(distribution, n, f, fname)
def add_state_nodes(self, beastxml):
"""
Add tree-related <state> sub-elements.
"""
state = beastxml.state
self.tree = xml.tree(state, id=self.tree_id, name="stateNode")
xml.taxonset(self.tree, idref="taxa")
if self.type in ["yule", "birthdeath"]:
param = xml.parameter(state,
id="birthRate.t:beastlingTree",
name="stateNode")
if self.birthrate_estimate is not None:
param.text = str(self.birthrate_estimate)
else:
param.text = "1.0"
if self.type in ["birthdeath"]:
xml.parameter(beastxml.state,
text="0.5",
id="deathRate.t:beastlingTree",
name="stateNode")
xml.parameter(beastxml.state,
text="0.2",
id="sampling.t:beastlingTree",
name="stateNode")
elif self.type == "coalescent":
xml.parameter(beastxml.state,
text="1.0",
id="popSize.t:beastlingTree",
name="stateNode")
if beastxml.config.tip_calibrations:
self.add_tip_heights(beastxml.config.tip_calibrations)
def add_state_nodes(self, beastxml):
"""
Add tree-related <state> sub-elements.
"""
state = beastxml.state
self.tree = xml.tree(state, id=self.tree_id, name="stateNode")
xml.taxonset(self.tree, idref="taxa")
if beastxml.config.tip_calibrations:
self.add_tip_heights(beastxml.config.tip_calibrations)
def add_operators(self, beastxml):
"""
Add all <operator>s which act on the tree topology and branch lengths.
"""
"""
Add all <operator>s which act on the tree topology and branch lengths.
"""
# Tree operators
# Operators which affect the tree must respect the sample_topology and
# sample_branch_length options.
if beastxml.config.languages.sample_topology:
## Tree topology operators
xml.operator(beastxml.run,
attrib={
"id": "SubtreeSlide.t:beastlingTree",
"spec": "SubtreeSlide",
"tree": "@Tree.t:beastlingTree",
"markclades": "true",
"weight": "15.0"
})
xml.operator(beastxml.run,
attrib={
"id": "narrow.t:beastlingTree",
"spec": "Exchange",
"tree": "@Tree.t:beastlingTree",
"markclades": "true",
"weight": "15.0"
})
xml.operator(beastxml.run,
attrib={
"id": "wide.t:beastlingTree",
"isNarrow": "false",
"spec": "Exchange",
"tree": "@Tree.t:beastlingTree",
"markclades": "true",
"weight": "3.0"
})
xml.operator(beastxml.run,
attrib={
"id": "WilsonBalding.t:beastlingTree",
"spec": "WilsonBalding",
"tree": "@Tree.t:beastlingTree",
"markclades": "true",
"weight": "3.0"
})
if beastxml.config.languages.sample_branch_lengths:
## Branch length operators
xml.operator(beastxml.run,
attrib={
"id": "UniformOperator.t:beastlingTree",
"spec": "Uniform",
"tree": "@Tree.t:beastlingTree",
"weight": "30.0"
})
xml.operator(beastxml.run,
attrib={
"id": "treeScaler.t:beastlingTree",
"scaleFactor": "0.5",
"spec": "ScaleOperator",
"tree": "@Tree.t:beastlingTree",
"weight": "3.0"
})
xml.operator(beastxml.run,
attrib={
"id": "treeRootScaler.t:beastlingTree",
"scaleFactor": "0.5",
"spec": "ScaleOperator",
"tree": "@Tree.t:beastlingTree",
"rootOnly": "true",
"weight": "3.0"
})
## Up/down operator which scales tree height
if self.type in ["yule", "birthdeath"]:
updown = xml.operator(beastxml.run,
attrib={
"id": "UpDown",
"spec": "UpDownOperator",
"scaleFactor": "0.5",
"weight": "3.0"
})
xml.tree(updown, idref="Tree.t:beastlingTree", name="up")
xml.parameter(updown,
idref="birthRate.t:beastlingTree",
name="down")
### Include clock rates in up/down only if calibrations are given
if beastxml.config.calibrations:
for clock in beastxml.config.clocks:
if clock.estimate_rate:
xml.parameter(updown,
idref=clock.mean_rate_id,
name="down")
if self.type in ["yule", "birthdeath"]:
# Birth rate scaler
# Birth rate is *always* scaled.
xml.operator(beastxml.run,
attrib={
"id": "YuleBirthRateScaler.t:beastlingTree",
"spec": "ScaleOperator",
"parameter": "@birthRate.t:beastlingTree",
"scaleFactor": "0.5",
"weight": "3.0"
})
elif self.type == "coalescent":
xml.operator(beastxml.run,
attrib={
"id": "PopulationSizeScaler.t:beastlingTree",
"spec": "ScaleOperator",
"parameter": "@popSize.t:beastlingTree",
"scaleFactor": "0.5",
"weight": "3.0"
})
if self.type in ["birthdeath"]:
xml.operator(beastxml.run,
attrib={
"id": "SamplingScaler.t:beastlingTree",
"spec": "ScaleOperator",
"parameter": "@sampling.t:beastlingTree",
"scaleFactor": "0.8",
"weight": "1.0"
})
xml.operator(beastxml.run,
attrib={
"id": "DeathRateScaler.t:beastlingTree",
"spec": "ScaleOperator",
"parameter": "@deathRate.t:beastlingTree",
"scaleFactor": "0.5",
"weight": "3.0"
})
# Add a Tip Date scaling operator if required
if beastxml.config.tip_calibrations and beastxml.config.languages.sample_branch_lengths:
# Get a list of taxa with non-point tip cals
tip_taxa = [
next(cal.langs.__iter__())
for cal in beastxml.config.tip_calibrations.values()
if cal.dist != "point"
]
for taxon in tip_taxa:
tiprandomwalker = xml.operator(beastxml.run,
attrib={
"id":
"TipDatesandomWalker:%s" %
taxon,
"spec":
"TipDatesRandomWalker",
"windowSize":
"1",
"tree":
"@Tree.t:beastlingTree",
"weight":
"3.0",
})
beastxml.add_taxon_set(tiprandomwalker, taxon, (taxon, ))