def add_state(self, state):
BaseClock.add_state(self, state)
# Rate categories
xml.stateNode(state,
text="1",
id="rateCategories.c:%s" % self.name,
spec="parameter.IntegerParameter",
dimension=42)
def add_frequency_state(self, state):
for f in self.features:
fname = "%s:%s" % (self.name, f)
xml.stateNode(
state,
text=1.0 / self.valuecounts[f],
id="feature_freqs_param.s:%s" % fname,
spec="parameter.RealParameter",
dimension=self.valuecounts[f],
lower="0.0",
upper="1.0",
)
def add_state(self, state):
xml.parameter(state,
text="100.0",
id="sphericalPrecision",
lower="0.0",
name="stateNode")
xml.stateNode(state,
id="location.geo",
spec="sphericalGeo.LocationParameter",
minordimension="2",
estimate="true",
value="0.0 0.0",
lower="0.0")
def add_frequency_state(self, state):
attribs = {
"id": "freqs_param.s:%s" % self.name,
"spec": "parameter.RealParameter",
"dimension": "2",
"lower": "0.0",
"upper": "1.0",
}
if self.share_params:
xml.stateNode(state, text="0.5 0.5", attrib=attribs)
else:
for f in self.features:
fname = "%s:%s" % (self.name, f)
attribs["id"] = "freqs_param.s:%s" % fname
xml.stateNode(state, text="0.5 0.5", attrib=attribs)
def add_state(self, state):
BaseClock.add_state(self, state)
xml.stateNode(state,
text=False,
id="Indicators.c:%s" % self.name,
spec="parameter.BooleanParameter",
dimension=42)
xml.stateNode(state,
text="0.1",
id="clockrates.c:%s" % self.name,
spec="parameter.RealParameter",
dimension=42)
self.shape_id = "randomClockGammaShape:%s" % self.name
# Domain and initial values for Gamma params copied from rate heterogeneity
# implementation in BaseModel
xml.parameter(state,
text="5.0",
id=self.shape_id,
name="stateNode",
lower="1.1",
upper="1000.0")
self.scale_id = "randomClockGammaScale:%s" % self.name
xml.parameter(state, text="0.2", id=self.scale_id, name="stateNode")
def add_state(self, state):
BaseModel.add_state(self, state)
for f in self.features:
fname = "%s:%s" % (self.name, f)
N = self.valuecounts[f]
dimension = N*(N-1)
if self.symmetric:
dimension = int(dimension/2)
xml.stateNode(
state,
text="true",
id="rateIndicator.s:%s" % fname,
spec="parameter.BooleanParameter",
dimension=dimension)
xml.parameter(
state,
text="1.0",
id="relativeGeoRates.s:%s" % fname,
name="stateNode",
dimension=dimension)