skills/pkpd-modeling/scripts/_models.py

• Disposition · class · L47-L87 — class Disposition
• n_compartments · method · L63-L64 — def n_compartments(self) -> int
• half_lives · method · L67-L68 — def half_lives(self) -> np.ndarray
• terminal_half_life · method · L71-L72 — def terminal_half_life(self) -> float
• vss · method · L75-L76 — def vss(self) -> float
• auc_unit_dose · method · L79-L81 — def auc_unit_dose(self) -> float
• mrt_iv · method · L84-L87 — def mrt_iv(self) -> float
• disposition · function · L90-L136 — def disposition(cl: float, v1: float, q: Sequence[float] = (), vp: Sequence[float] = ()) -> Disposition
• micro_constants · function · L139-L149 — def micro_constants(d: Disposition) -> dict[str, float]
• _absorption_term · function · L155-L168 — def _absorption_term(lam: np.ndarray, ka: float, t: np.ndarray) -> np.ndarray
• conc_bolus · function · L171-L174 — def conc_bolus(t: np.ndarray, dose: float, d: Disposition) -> np.ndarray
• conc_infusion · function · L177-L187 — def conc_infusion(t: np.ndarray, dose: float, duration: float, d: Disposition) -> np.ndarray
• conc_oral · function · L190-L195 — def conc_oral(t: np.ndarray, dose: float, ka: float, d: Disposition, f: float = 1.0, tlag: float = 0.0) -> np.ndarray
• conc_transit · function · L198-L230 — def conc_transit( t: np.ndarray, dose: float, mtt: float, n: float, d: Disposition, f: float = 1.0, ka: float | None = None ) -> np.ndarray
• Dose · class · L237-L254 — class Dose
• post_init · method · L250-L254 — def post_init(self) -> None
• build_regimen · function · L257-L275 — def build_regimen( amount: float, interval: float | None = None, n_doses: int = 1, start: float = 0.0, duration: float = 0.0, route: str = "iv", loading: float | None = None, ) -> list[Dose]
• simulate_linear · function · L278-L306 — def simulate_linear( times: Sequence[float], regimen: Sequence[Dose], d: Disposition, ka: float | None = None, f: float = 1.0, tlag: float = 0.0, ) -> np.ndarray
• steady_state_metrics · function · L309-L337 — def steady_state_metrics(d: Disposition, dose: float, interval: float, f: float = 1.0) -> dict[str, float]
• _require_scipy · function · L343-L345 — def _require_scipy(what: str) -> None
• _integrate_with_doses · function · L348-L404 — def _integrate_with_doses( rhs: Callable[[float, np.ndarray], np.ndarray], y0: np.ndarray, times: np.ndarray, regimen: Sequence[Dose], dose_compartment: int, rtol: float = 1e-8, atol: float = 1e-10, ) -> np.ndarray
• rhs_with_infusions · function · L368-L373 — def rhs_with_infusions(t: float, y: np.ndarray) -> np.ndarray
• simulate_michaelis_menten · function · L407-L449 — def simulate_michaelis_menten( times: Sequence[float], regimen: Sequence[Dose], vmax: float, km: float, v1: float, q: Sequence[float] = (), vp: Sequence[float] = (), ka: float | None = None, f: float = 1.0, ) -> np.ndarray
• rhs · function · L431-L445 — def rhs(_t: float, y: np.ndarray) -> np.ndarray
• simulate_tmdd · function · L452-L544 — def simulate_tmdd( times: Sequence[float], regimen: Sequence[Dose], cl: float, v1: float, kon: float, koff: float, kint: float, ksyn: float, kdeg: float, q: float | None = None, vp: float | None = None, approximation: str = "full", ) -> dict[str, np.ndarray]
• rhs · function · L489-L501 — def rhs(_t: float, y: np.ndarray) -> np.ndarray
• rhs_qss · function · L514-L528 — def rhs_qss(_t: float, y: np.ndarray) -> np.ndarray
• emax · function · L550-L556 — def emax(conc: np.ndarray, e0: float, emax_value: float, ec50: float, hill: float = 1.0) -> np.ndarray
• imax · function · L559-L563 — def imax(conc: np.ndarray, e0: float, imax_value: float, ic50: float, hill: float = 1.0) -> np.ndarray
• effect_compartment · function · L566-L591 — def effect_compartment(times: Sequence[float], conc: Sequence[float], ke0: float) -> np.ndarray
• indirect_response · function · L602-L651 — def indirect_response( times: Sequence[float], conc_fn: Callable[[float], float], kin: float, kout: float, idr_type: int, max_effect: float, c50: float, hill: float = 1.0, ) -> np.ndarray
• drive · function · L629-L632 — def drive(t: float) -> float
• rhs · function · L634-L642 — def rhs(t: float, y: np.ndarray) -> np.ndarray