dynast.estimation.alpha

Module Contents

Functions

read_alpha(alpha_path: str, group_by: Optional[List[str]] = None) → Union[float, Dict[str, float], Dict[Tuple[str, Ellipsis], float]]	Read alpha CSV as a dictionary, with group_by columns as keys.
estimate_alpha(df_counts: pandas.DataFrame, pi_c: Union[float, Dict[str, float], Dict[Tuple[str, Ellipsis], float]], alpha_path: str, conversions: FrozenSet[str] = frozenset({'TC'}), group_by: Optional[List[str]] = None, pi_c_group_by: Optional[List[str]] = None) → str	Estimate the detection rate alpha.

dynast.estimation.alpha.read_alpha(alpha_path: str, group_by: Optional[List[str]] = None) → Union[float, Dict[str, float], Dict[Tuple[str, Ellipsis], float]]

Read alpha CSV as a dictionary, with group_by columns as keys.

Parameters

alpha_path

Path to CSV containing alpha values

group_by

Columns to group by, defaults to None

Returns

Dictionary with group_by columns as keys (tuple if multiple)

dynast.estimation.alpha.estimate_alpha(df_counts: pandas.DataFrame, pi_c: Union[float, Dict[str, float], Dict[Tuple[str, Ellipsis], float]], alpha_path: str, conversions: FrozenSet[str] = frozenset({'TC'}), group_by: Optional[List[str]] = None, pi_c_group_by: Optional[List[str]] = None) → str

Estimate the detection rate alpha.

Parameters

df_counts

Pandas dataframe containing conversion counts

pi_c

Labeled mutation rate

alpha_path

Path to output CSV containing alpha estimates

conversions

Conversions to consider

group_by

Columns to group by

pi_c_group_by

Columns that were used to group when calculating pi_c

Returns

Path to output CSV containing alpha estimates