augur.traits moduleο
Infer ancestral traits based on a tree.
- augur.traits.mugration_inference(tree=None, seq_meta=None, field='country', confidence=True, missing='?', sampling_bias_correction=None, weights=None)ο
Infer likely ancestral states of a discrete character assuming a time reversible model.
- Parameters:
tree (str) β name of tree file
seq_meta (pandas.DataFrame) β meta data associated with sequences
field (str, optional) β meta data field to use
confidence (bool, optional) β calculate confidence values for inferences
missing (str, optional) β character that is to be interpreted as missing data, default=β?β
sampling_bias_correction (None, optional) β factor by which the transition rate is scaled up to counter sampling bias
weights (None, optional) β vector of equilibrium frequencies that one expects the far ancestor to be sampled from
- Returns:
T (Bio.Phylo.BaseTree.Tree) β Biophyton tree
gtr (treetime.GTR) β GTR model
alphabet (dict) β mapping of character states to
- augur.traits.register_parser(parent_subparsers)ο
- augur.traits.run(args)ο
run mugration inference
- Parameters:
args (argparse.Namespace) β command line arguments are parsed by argparse