def get_userdatatype(self, feature, fname):
if not self.beastxml._binary_userdatatype_created:
self.beastxml._binary_userdatatype_created = True
return xml.userDataType(None,
id="BinaryDatatype",
spec="beast.evolution.datatype.Binary")
return xml.userDataType(None, idref="BinaryDatatype")
def get_userdatatype(self, feature, fname):
if not self.beastxml._covarion_userdatatype_created:
self.beastxml._covarion_userdatatype_created = True
return xml.userDataType(
None,
id="TwoStateCovarionDatatype",
spec="beast.evolution.datatype.TwoStateCovarion")
return xml.userDataType(None, idref="TwoStateCovarionDatatype")
def get_userdatatype(self, feature, fname):
return xml.userDataType(None,
id="featureDataType.%s" % fname,
spec="beast.evolution.datatype.UserDataType",
codeMap=self.codemaps[feature],
codelength="-1",
states=self.valuecounts[feature])
def add_data(self, distribution):
"""
Add <data> element corresponding to the indicated feature, descending
from the indicated likelihood distribution.
"""
data = xml.data(distribution,
id="locationData",
spec="sphericalGeo.AlignmentFromTraitMap")
traitmap = xml.traitMap(data,
id="geographyTraitmap",
spec="sphericalGeo.TreeTraitMap",
initByMean="true",
randomizelower="-90 -180",
randomizeupper="90 180",
traitName="location",
tree="@Tree.t:beastlingTree")
xml.parameter(traitmap,
text="0.0 0.0",
id="locationParameter",
spec="sphericalGeo.LocationParameter",
dimension=2 *
(2 * len(self.config.languages.languages) - 1),
minordimension="2")
loc_data_text_bits = []
for lang in self.config.languages.languages:
lat, lon = self.config.locations.get(lang, ("?", "?"))
if "?" in (lat, lon):
if lang not in self.sampling_points:
self.sampling_points.append(lang)
log.info(
"Location of language %s will be sampled. You may wish to add a prior."
% lang,
model=self)
else:
bit = "%s=%.2f %.2f" % (lang, lat, lon)
loc_data_text_bits.append(bit)
traitmap.text = ",\n".join(loc_data_text_bits)
xml.userDataType(data,
id="LocationDataType",
spec="sphericalGeo.LocationDataType")
def get_userdatatype(self, feature, fname):
if not self.beastxml._covarion_userdatatype_created:
self.beastxml._covarion_userdatatype_created = True
return xml.userDataType(
None,
id="PseudoDolloCovarionDatatype",
spec="beast.evolution.datatype.UserDataType",
states="5",
codelength="1",
codeMap="""
A = 0,
1 = 1 4,
B = 1,
0 = 0 2 3 ,
? = 0 1 2 3 4,
- = 0 1 2 3 4,
C = 2,
D = 3,
E = 4
""")
else:
return xml.userDataType(None, idref="PseudoDolloCovarionDatatype")