| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/model/ |
| H A D | multispeciescoalescent.py | 42 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION): argument
44 self.ultrametricity_precision = ultrametricity_precision
53 self._species_tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
177 coalescent_tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
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| H A D | coalescent.py | 320 def node_waiting_time_pairs(tree, ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISI… argument
347 tree.calc_node_ages(ultrametricity_precision=ultrametricity_precision)
358 def extract_coalescent_frames(tree, ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECI… argument
385 nwti = node_waiting_time_pairs(tree, ultrametricity_precision=ultrametricity_precision)
418 def log_probability_of_coalescent_tree(tree, haploid_pop_size, ultrametricity_precision=constants.D… argument
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| H A D | reconcile.py | 43 ultrametricity_precision=False, argument
113 self.ultrametricity_precision = ultrametricity_precision
235 self.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
241 contained_tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
441 contained_tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
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| H A D | birthdeath.py | 713 …internal_node_ages = tree.internal_node_ages(ultrametricity_precision=kwargs.get("ultrametricity_p…
755 def fit_pure_birth_model_to_tree(tree, ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PR… argument
792 return fit_pure_birth_model(tree=tree, ultrametricity_precision=ultrametricity_precision)
893 …internal_node_ages = tree.internal_node_ages(ultrametricity_precision=kwargs.get("ultrametricity_p…
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| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/calculate/ |
| H A D | profiledistance.py | 209 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
225 self.ultrametricity_precision = ultrametricity_precision
269 node_ages = tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
284 ultrametricity_precision=self.ultrametricity_precision,)
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| H A D | treemeasure.py | 154 tree.calc_node_ages(ultrametricity_precision=prec)
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| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/legacy/ |
| H A D | coalescent.py | 79 def node_waiting_time_pairs(tree, ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISI… argument
85 ultrametricity_precision=ultrametricity_precision)
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| /dports/science/py-DendroPy/DendroPy-4.4.0/applications/sumtrees/ |
| H A D | sumtrees.py | 174 ultrametricity_precision, argument
195 self.ultrametricity_precision = ultrametricity_precision
207 ultrametricity_precision=self.ultrametricity_precision,
294 ultrametricity_precision, argument
306 self.ultrametricity_precision = ultrametricity_precision
366 ultrametricity_precision=self.ultrametricity_precision,
438 ultrametricity_precision=self.ultrametricity_precision,
455 ultrametricity_precision=self.ultrametricity_precision,
1391 if args.ultrametricity_precision == 0:
1394 args.ultrametricity_precision = -1
[all …]
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| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/datamodel/ |
| H A D | treecollectionmodel.py | 1047 …ultrametricity_precision=kwargs_dict.pop("ultrametricity_precision", constants.DEFAULT_ULTRAMETRIC…
1236 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
1248 self.ultrametricity_precision = ultrametricity_precision
1359 ultrametricity_precision=self.ultrametricity_precision,
2139 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
2151 ultrametricity_precision=ultrametricity_precision,
2169 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
2214 ultrametricity_precision=ultrametricity_precision,
2592 ultrametricity_precision=self._split_distribution.ultrametricity_precision,
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| H A D | treemodel.py | 5548 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
5630 …_age or is_force_min_age or ultrametricity_precision is None or ultrametricity_precision is False …
5638 if d > ultrametricity_precision:
5661 threshold=ultrametricity_precision,
5689 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
5698 … ultrametricity_precision=ultrametricity_precision, is_return_internal_node_ages_only=True,
5707 ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION, argument
5719 ultrametricity_precision=ultrametricity_precision,
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