def add_tracer_logger(self):
"""
Add file logger, if configured to do so.
"""
if not (self.config.admin.log_probabilities
or self.config.admin.log_params):
return
tracer_logger = xml.logger(self.run,
id="tracelog",
fileName=self.config.admin.path(".log"),
logEvery=self.config.admin.log_every,
sort="smart")
# Log prior, likelihood and posterior
if self.config.admin.log_probabilities:
xml.log(tracer_logger, idref="prior")
xml.log(tracer_logger, idref="likelihood")
xml.log(tracer_logger, idref="posterior")
if self.config.admin.log_params:
# Log tree metadata
self.config.treeprior.add_logging(self, tracer_logger)
for clock in self.config.clocks:
clock.add_param_logs(tracer_logger)
for model in self.config.all_models:
model.add_param_logs(tracer_logger)
# Log calibration clade heights
for clade, cal in sorted(
itertools.chain(self.config.calibrations.items(),
self.config.tip_calibrations.items())):
# Don't log unchanging tip heights
if cal.dist == "point":
continue
xml.log(tracer_logger, idref="%sMRCA" % clade.replace(" ", "_"))
def add_trait_logger(self, suffix=""):
"""Add a logger referencing all AncestralStateLogger likelihoods in the tree."""
trait_logger = xml.logger(self.run,
fileName=self.config.admin.path(suffix +
".log"),
logEvery=self.config.admin.log_every,
id="traitLogger" + suffix)
for model in self.config.models:
for reference in model.metadata:
xml.log(trait_logger, idref=reference)
def add_trait_tree_logger(self, suffix=""):
tree_logger = xml.logger(self.run,
mode="tree",
fileName=self.config.admin.path(suffix +
".nex"),
logEvery=self.config.admin.log_every,
id="treeLogger" + suffix)
log = xml.log(tree_logger,
id="ReconstructedStateTreeLogger",
spec="beast.evolution.tree.TreeWithTraitLogger",
tree="@{:}".format(self.config.treeprior.tree_id))
for model in self.config.models:
for md in model.treedata:
xml.metadata(log, idref=md)
def add_screen_logger(self):
"""
Add the screen logger, if configured to do so.
"""
if self.config.admin.screenlog:
screen_logger = xml.logger(self.run,
id="screenlog",
logEvery=self.config.admin.log_every)
xml.log(screen_logger,
arg="@posterior",
id="ESS.0",
spec="util.ESS")
xml.log(screen_logger, idref="prior")
xml.log(screen_logger, idref="likelihood")
xml.log(screen_logger, idref="posterior")
def add_tree_logger(self,
suffix="",
branchrate_model_id=None,
locations=False):
tree_logger = xml.logger(self.run,
mode="tree",
fileName=self.config.admin.path(suffix +
".nex"),
logEvery=self.config.admin.log_every,
id="treeLogger" + suffix)
log = xml.log(tree_logger,
id="TreeLoggerWithMetaData" + suffix,
spec="beast.evolution.tree.TreeWithMetaDataLogger",
tree="@{:}".format(self.config.treeprior.tree_id),
dp=self.config.admin.log_dp)
if branchrate_model_id:
xml.branchratemodel(log, idref=branchrate_model_id)
if locations:
xml.metadata(log,
text="0.0",
id="location",
spec="sphericalGeo.TraitFunction",
likelihood="@sphericalGeographyLikelihood")