def _add_prior(self, prior, name):
alpha_prior = xml.prior(prior,
id="covarion_alpha_prior.s:%s" % name,
name="distribution",
x="@covarion_alpha.s:%s" % name)
xml.Uniform(alpha_prior,
id="CovAlphaUniform:%s" % name,
name="distr",
upper="Infinity")
switch_prior = xml.prior(prior,
id="covarion_s_prior.s:%s" % name,
name="distribution",
x="@covarion_s.s:%s" % name)
gamma = xml.Gamma(switch_prior, id="Gamma.0:%s" % name, name="distr")
xml.parameter(gamma,
text="0.05",
id="covarion_switch_gamma_param1:%s" % name,
name="alpha",
lower="0.0",
upper="0.0")
xml.parameter(gamma,
text="10.0",
id="covarion_switch_gamma_param2:%s" % name,
name="beta",
lower="0.0",
upper="0.0")
def add_prior(self, prior):
# Uniform prior on mean clock rate
sub_prior = xml.prior(prior,
id="clockPrior:%s" % self.name,
name="distribution",
x="@clockRate.c:%s" % self.name)
xml.Uniform(sub_prior,
id="UniformClockPrior:%s" % self.name,
name="distr",
upper="Infinity")
def add_prior(self, beastxml):
"""Add a (calibrated) birth-death tree prior."""
# Tree prior
attribs = {}
attribs["id"] = "BirthDeathModel.t:beastlingTree"
attribs["tree"] = "@Tree.t:beastlingTree"
attribs[
"spec"] = "beast.evolution.speciation.BirthDeathGernhard08Model"
attribs["birthDiffRate"] = "@birthRate.t:beastlingTree"
attribs["relativeDeathRate"] = "@deathRate.t:beastlingTree"
attribs["sampleProbability"] = "@sampling.t:beastlingTree"
attribs[
"type"] = "unscaled" #TODO: Someone dropped the "restricted" type here, which does not exist.
xml.distribution(beastxml.prior, attrib=attribs)
# Birth rate prior
attribs = {}
attribs["id"] = "BirthRatePrior.t:beastlingTree"
attribs["name"] = "distribution"
attribs["x"] = "@birthRate.t:beastlingTree"
sub_prior = xml.prior(beastxml.prior, attrib=attribs)
xml.Uniform(sub_prior, id="Uniform.0", name="distr", upper="Infinity")
# Relative death rate prior
attribs = {}
attribs["id"] = "relativeDeathRatePrior.t:beastlingTree"
attribs["name"] = "distribution"
attribs["x"] = "@deathRate.t:beastlingTree"
sub_prior = xml.prior(beastxml.prior, attrib=attribs)
xml.Uniform(sub_prior, id="Uniform.1", name="distr", upper="Infinity")
# Sample probability prior
attribs = {}
attribs["id"] = "samplingPrior.t:beastlingTree"
attribs["name"] = "distribution"
attribs["x"] = "@sampling.t:beastlingTree"
sub_prior = xml.prior(beastxml.prior, attrib=attribs)
xml.Uniform(sub_prior,
id="Uniform.3",
name="distr",
lower="0",
upper="1")
def add_prior(self, prior):
"""
Add prior distributions for Gamma-distributed rate heterogenetiy, if
configured.
"""
if self.scale_precision:
precision_prior = xml.prior(prior,
id="sphericalPrecisionPrior",
x="@sphericalPrecision",
name="distribution")
xml.Uniform(precision_prior,
id="sphericalPrecisionPriorUniform",
name="distr",
lower="0",
upper="1e10")
def _add_prior(self, prior, name):
switch_prior = xml.prior(
prior,
id="%s:pdcovarion_s_prior.s" % name,
name="distribution",
x="@%s:pdcovarion_s.s" % name)
gamma = xml.Gamma(switch_prior, id="%s: Gamma.0" % name, name="distr")
xml.parameter(
gamma,
text="0.05",
id="%s:pdcovarion_switch_gamma_param1" % name,
name="alpha",
lower="0.0",
upper="0.0")
xml.parameter(
gamma,
text="10.0",
id="%s:pdcovarion_switch_gamma_param2" % name,
name="beta",
lower="0.0",
upper="0.0")
origin_prior = xml.prior(
prior,
id="%s:pdcovarion_origin_prior.s" % name,
name="distribution",
x="@%s:pdcovarion_origin.s" % name)
xml.Uniform(
origin_prior,
id="%s:PDCovOriginUniform" % name,
name="distr",
upper="Infinity")
death_prior = xml.prior(
prior,
id="%s:pdcovarion_death_prior.s" % name,
name="distribution",
x="@{:}:pdcovarion_death.s".format(name))
xml.Exponential(
death_prior,
id="%s:PDCovDeathExp" % name,
name="distr",
mean="1.0")
def add_prior(self, beastxml):
"""
Add Yule birth-process tree prior.
"""
# Tree prior
## Decide whether to use the standard Yule or the fancy calibrated one
if len(beastxml.config.calibrations) == 1:
yule = "calibrated"
elif len(beastxml.config.calibrations) == 2:
# Two calibrations can be handled by the calibrated Yule if they
# are nested
langs1, langs2 = [
c.langs for c in beastxml.config.calibrations.values()
]
if len(set(langs1) & set(langs2)) in (len(langs1), len(langs2)):
yule = "calibrated"
else:
yule = "standard"
else:
yule = "standard"
attribs = {}
attribs["id"] = "YuleModel.t:beastlingTree"
attribs["tree"] = "@Tree.t:beastlingTree"
if yule == "standard":
attribs["spec"] = "beast.evolution.speciation.YuleModel"
attribs["birthDiffRate"] = "@birthRate.t:beastlingTree"
if "root" in beastxml.config.calibrations:
attribs["conditionalOnRoot"] = "true"
elif yule == "calibrated":
attribs["spec"] = "beast.evolution.speciation.CalibratedYuleModel"
attribs["birthRate"] = "@birthRate.t:beastlingTree"
xml.distribution(beastxml.prior, attrib=attribs)
# Birth rate prior
sub_prior = xml.prior(beastxml.prior,
id="YuleBirthRatePrior.t:beastlingTree",
name="distribution",
x="@birthRate.t:beastlingTree")
xml.Uniform(sub_prior, id="Uniform.0", name="distr", upper="Infinity")