`lineage.states.stateCommon`¶

Common utilities used between states regardless of distribution.

Module Contents¶

lineage.states.stateCommon.basic_censor(cell)¶: Censors a cell, its daughters, its sister, and it’s sister’s daughters if the cell’s parent is censored.

lineage.states.stateCommon.bern_estimator(bern_obs: np.ndarray, gammas: np.ndarray)¶: A weighted estimator for a Bernoulli distribution.

lineage.states.stateCommon.gamma_LL(logX: npt.NDArray[np.float64], gamma_obs: List[npt.NDArray[np.float64]], time_cen: List[npt.NDArray[np.float64]], gammas: List[npt.NDArray[np.float64]])¶: Log-likelihood for the optionally censored Gamma distribution. The logX is the log transform of the parameters, in case of atonce estimation, it is [shape, scale1, scale2, scale3, scale4].

lineage.states.stateCommon.gamma_estimator(gamma_obs: list[np.ndarray], time_cen: list[np.ndarray], gammas: list[np.ndarray], x0: np.ndarray, phase: str = 'all') → npt.NDArray[np.float64]¶: This is a weighted, closed-form estimator for two parameters of the Gamma distribution for estimating shared shape and separate scale parameters of several drug concentrations at once. In the phase-specific case, we have 3 linear constraints: scale1 > scale2, scale2 > scale3, scale3 > scale 4. In the non-specific case, we have only 1 constraint: scale1 > scale2 ==> A = np.array([1, 3])