treeflow.evolution.calibration.calibration module

class treeflow.evolution.calibration.calibration.MRCACalibration(taxa: Iterable[str], range: Iterable[float], name: str | None = None)

Bases: object

get_mrca_index(tree: NumpyRootedTree)

get_normal_sd(interval_mass=0.95)

Get the standard deviation for a Normal distribution which places interval_mass probability mass on the interval between low and high

get_normal_mean()

class treeflow.evolution.calibration.calibration.MRCACalibrationSet(calibration_dicts: Iterable[Dict[str, object]])

Bases: object

get_mrca_index_array(tree: NumpyRootedTree) → ndarray

get_mrca_index_tensor(tree: NumpyRootedTree) → Tensor

get_normal_sd_array(interval_mass=0.95)

get_normal_sd_tensor(interval_mass=0.95, dtype=tf.float64)

get_normal_mean_array()

get_normal_mean_tensor(dtype=tf.float64)