def add_param_logs(self, logger):
"""
Add entires to the logfile corresponding to individual feature
substition rates if rate variation is configured.
"""
if self.config.admin.log_fine_probs:
xml.log(logger, idref="sphericalGeographyLikelihood")
def add_logging(self, beastxml, tracer_logger):
super().add_logging(beastxml, tracer_logger)
# Fine-grained logging
if beastxml.config.admin.log_fine_probs:
xml.log(tracer_logger, idref="YuleModel.t:beastlingTree")
xml.log(tracer_logger, idref="YuleBirthRatePrior.t:beastlingTree")
def add_param_logs(self, logger):
BaseClock.add_param_logs(self, logger)
xml.log(logger,
id="rate.c:%s" % self.name,
spec="beast.evolution.branchratemodel.RateStatistic",
branchratemodel="@%s" % self.branchrate_model_id,
tree="@Tree.t:beastlingTree")
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_logging(self, beastxml, tracer_logger):
# Log tree height
if not beastxml.config.tree_logging_pointless:
xml.log(tracer_logger,
id="treeStats",
spec="beast.evolution.tree.TreeStatLogger",
tree="@Tree.t:beastlingTree")
# Fine-grained logging
if beastxml.config.admin.log_params:
self.add_fine_logging(tracer_logger)
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_param_logs(self, logger):
BinaryModel.add_param_logs(self, logger)
for fname in self.parameter_identifiers():
xml.log(logger, idref="covarion_alpha.s:%s" % fname)
xml.log(logger, idref="covarion_s.s:%s" % fname)
if self.config.admin.log_fine_probs:
xml.log(logger, idref="covarion_alpha_prior.s:%s" % fname)
xml.log(logger, idref="covarion_s_prior.s:%s" % fname)
def add_logging(self, beastxml, tracer_logger):
# Log tree model parameters
if self.type in ["yule", "birthdeath"]:
xml.log(tracer_logger, idref="birthRate.t:beastlingTree")
if self.type in ["birthdeath"]:
xml.log(tracer_logger, idref="deathRate.t:beastlingTree")
xml.log(tracer_logger, idref="sampling.t:beastlingTree")
elif self.type == "coalescent":
xml.log(tracer_logger, idref="popSize.t:beastlingTree")
# Log tree height
if not beastxml.config.tree_logging_pointless:
xml.log(tracer_logger,
id="treeStats",
spec="beast.evolution.tree.TreeStatLogger",
tree="@Tree.t:beastlingTree")
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_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_param_logs(self, logger):
"""
Add entires to the logfile corresponding to individual feature
substition rates if rate variation is configured.
"""
if self.config.admin.log_fine_probs:
if not self.single_sitemodel:
plate = xml.plate(logger, var="feature", range=self.features)
xml.log(plate,
idref="featureLikelihood:%s:$(feature)" % self.name)
if self.rate_variation:
xml.log(logger, idref="featureClockRatePrior.s:%s" % self.name)
xml.log(logger,
idref="featureClockRateGammaScalePrior.s:%s" %
self.name)
if self.frequencies == "estimate":
self.add_frequency_logs(logger)
if self.rate_variation:
plate = xml.plate(logger, var="rate", range=self.all_rates)
xml.log(plate, idref="featureClockRate:%s:$(rate)" % self.name)
# Log the scale, but not the shape, as it is always 1 / scale
# We prefer the scale because it is positively correlated with extent of variation
xml.log(logger, idref="featureClockRateGammaShape:%s" % self.name)
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")
def add_param_logs(self, logger):
RelaxedClock.add_param_logs(self, logger)
# Log lognormal stddev
xml.log(logger, idref="ucldSdev.c:%s" % self.name)
def add_fine_logging(self, tracer_logger):
# Log tree model parameters
xml.log(tracer_logger, idref="birthRate.t:beastlingTree")
xml.log(tracer_logger, idref="YuleModel.t:beastlingTree")
xml.log(tracer_logger, idref="YuleBirthRatePrior.t:beastlingTree")
def add_logging(self, beastxml, tracer_logger):
super().add_logging(beastxml, tracer_logger)
xml.log(
tracer_logger,
idref="birthRate.t:beastlingTree")
def add_fine_logging(self, tracer_logger):
# Log tree model parameters
xml.log(tracer_logger, idref="birthRate.t:beastlingTree")
xml.log(tracer_logger, idref="deathRate.t:beastlingTree")
xml.log(tracer_logger, idref="sampling.t:beastlingTree")
def add_param_logs(self, logger):
BaseModel.add_param_logs(self, logger)
if self.gamma_categories > 0:
xml.log(logger, idref="gammaShape.s:%s" % self.name)
def add_frequency_logs(self, logger):
for fname in self.parameter_identifiers():
xml.log(logger, idref="%s:visiblefrequencies.s" % fname)
def add_frequency_logs(self, logger):
for f in self.features:
fname = "%s:%s" % (self.name, f)
xml.log(logger, idref="feature_freqs_param.s:%s" % fname)
def add_param_logs(self, logger):
# Log mean clock rate
xml.log(logger, idref="clockRate.c:%s" % self.name)
def add_param_logs(self, logger):
BinaryModel.add_param_logs(self, logger)
for fname in self.parameter_identifiers():
xml.log(logger, idref="%s:pdcovarion_s.s" % fname)
xml.log(logger, idref="%s:pdcovarion_origin.s" % fname)
xml.log(logger, idref="%s:pdcovarion_death.s" % fname)
if self.config.admin.log_fine_probs:
xml.log(logger, idref="%s:pdcovarion_s_prior.s" % fname)
xml.log(logger, idref="%s:pdcovarion_origin_prior.s" % fname)
xml.log(logger, idref="%s:pdcovarion_death_prior.s" % fname)
def add_param_logs(self, logger):
RelaxedClock.add_param_logs(self, logger)
xml.log(logger, idref="clockRateGammaShape:%s" % self.name)
def add_fine_logging(self, tracer_logger):
xml.log(tracer_logger, idref="popSize.t:beastlingTree")
def add_param_logs(self, logger):
BaseClock.add_param_logs(self, logger)
xml.log(logger, idref="Indicators.c:%s" % self.name)
xml.log(logger, idref="clockrates.c:%s" % self.name)
xml.log(logger, idref="RandomRateChangesCount:%s" % self.name)
xml.log(logger, idref=self.shape_id)
def add_frequency_logs(self, logger):
for name in self.parameter_identifiers():
xml.log(logger, idref="freqs_param.s:%s" % name)
def add_param_logs(self, logger):
BaseModel.add_param_logs(self, logger)
for f in self.features:
fname = "%s:%s" % (self.name, f)
xml.log(logger, idref="rateIndicator.s:%s" % fname)
xml.log(logger, idref="relativeGeoRates.s:%s" % fname)
