survival 1.1.23__cp314-cp314-manylinux_2_39_aarch64.whl
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- survival/__init__.py +5 -0
- survival/__init__.pyi +963 -0
- survival/py.typed +0 -0
- survival/survival.cpython-314-aarch64-linux-gnu.so +0 -0
- survival-1.1.23.dist-info/METADATA +675 -0
- survival-1.1.23.dist-info/RECORD +8 -0
- survival-1.1.23.dist-info/WHEEL +4 -0
- survival-1.1.23.dist-info/licenses/LICENSE +21 -0
survival/__init__.pyi
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from typing import Any
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class AaregOptions:
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def __init__(
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self,
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formula: str,
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data: list[list[float]],
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variable_names: list[str],
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weights: list[float] | None = None,
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subset: list[int] | None = None,
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na_action: str | None = None,
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qrtol: float = 1e-8,
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nmin: int | None = None,
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dfbeta: bool = False,
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taper: float = 0.0,
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test: list[str] = ...,
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cluster: list[int] | None = None,
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model: bool = False,
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x: bool = False,
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y: bool = False,
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) -> None: ...
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class PSpline:
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coefficients: list[float] | None
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fitted: bool
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def __init__(
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self,
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x: list[float],
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df: int,
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theta: float,
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eps: float,
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method: str,
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boundary_knots: tuple[float, float],
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intercept: bool,
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penalty: bool,
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) -> None: ...
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def fit(self) -> list[float]: ...
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def predict(self, new_x: list[float]) -> list[float]: ...
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@property
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def df(self) -> int: ...
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@property
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def eps(self) -> float: ...
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class CoxCountOutput:
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pass
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class LinkFunctionParams:
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def __init__(self, edge: float) -> None: ...
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def blogit(self, input: float) -> float: ...
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def bprobit(self, input: float) -> float: ...
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def bcloglog(self, input: float) -> float: ...
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def blog(self, input: float) -> float: ...
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class Subject:
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id: int
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covariates: list[float]
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is_case: bool
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is_subcohort: bool
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stratum: int
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def __init__(
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self,
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id: int,
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covariates: list[float],
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is_case: bool,
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is_subcohort: bool,
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stratum: int,
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) -> None: ...
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class CoxPHModel:
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baseline_hazard: list[float]
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risk_scores: list[float]
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event_times: list[float]
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censoring: list[int]
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def __init__(self) -> None: ...
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@staticmethod
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def new_with_data(
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covariates: list[list[float]],
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event_times: list[float],
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censoring: list[int],
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) -> "CoxPHModel": ...
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def fit(self, n_iters: int = 20) -> None: ...
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def predict(self, covariates: list[list[float]]) -> list[float]: ...
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def get_coefficients(self) -> list[list[float]]: ...
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def brier_score(self) -> float: ...
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def survival_curve(
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self,
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covariates: list[list[float]],
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time_points: list[float] | None = None,
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) -> tuple[list[float], list[list[float]]]: ...
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def add_subject(self, subject: Subject) -> None: ...
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def hazard_ratios(self) -> list[float]: ...
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def hazard_ratios_with_ci(
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self, confidence_level: float = 0.95
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) -> tuple[list[float], list[float], list[float]]: ...
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def log_likelihood(self) -> float: ...
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def aic(self) -> float: ...
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def bic(self) -> float: ...
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def cumulative_hazard(
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self, covariates: list[list[float]]
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) -> tuple[list[float], list[list[float]]]: ...
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def predicted_survival_time(
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self, covariates: list[list[float]], percentile: float = 0.5
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) -> list[float | None]: ...
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def restricted_mean_survival_time(
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self, covariates: list[list[float]], tau: float
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) -> list[float]: ...
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def martingale_residuals(self) -> list[float]: ...
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def deviance_residuals(self) -> list[float]: ...
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def dfbeta(self) -> list[list[float]]: ...
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def n_events(self) -> int: ...
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def n_observations(self) -> int: ...
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def summary(self) -> str: ...
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class SurvFitKMOutput:
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time: list[float]
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n_risk: list[float]
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n_event: list[float]
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n_censor: list[float]
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estimate: list[float]
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std_err: list[float]
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conf_lower: list[float]
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conf_upper: list[float]
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class FineGrayOutput:
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row: list[int]
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start: list[float]
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end: list[float]
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wt: list[float]
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add: list[int]
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class SurvivalFit:
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coefficients: list[float]
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iterations: int
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variance_matrix: list[list[float]]
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log_likelihood: float
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convergence_flag: int
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score_vector: list[float]
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class DistributionType:
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pass
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class SurvDiffResult:
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observed: list[float]
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expected: list[float]
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variance: list[list[float]]
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chi_squared: float
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degrees_of_freedom: int
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class CchMethod:
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Prentice: "CchMethod"
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SelfPrentice: "CchMethod"
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LinYing: "CchMethod"
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IBorgan: "CchMethod"
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IIBorgan: "CchMethod"
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class CohortData:
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@staticmethod
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def new() -> "CohortData": ...
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def add_subject(self, subject: Subject) -> None: ...
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def get_subject(self, id: int) -> Subject: ...
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def fit(self, method: "CchMethod") -> CoxPHModel: ...
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class SurvFitAJ:
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n_risk: list[list[float]]
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n_event: list[list[float]]
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n_censor: list[list[float]]
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pstate: list[list[float]]
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cumhaz: list[list[float]]
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std_err: list[list[float]] | None
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std_chaz: list[list[float]] | None
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std_auc: list[list[float]] | None
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influence: list[list[float]] | None
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n_enter: list[list[float]] | None
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n_transition: list[list[float]]
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class SplitResult:
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row: list[int]
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interval: list[int]
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start: list[float]
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end: list[float]
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censor: list[bool]
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class ClogitDataSet:
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def __init__(self) -> None: ...
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def add_observation(
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self,
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case_control_status: int,
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stratum: int,
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covariates: list[float],
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) -> None: ...
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def get_num_observations(self) -> int: ...
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def get_num_covariates(self) -> int: ...
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class ConditionalLogisticRegression:
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coefficients: list[float]
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max_iter: int
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tol: float
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iterations: int
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converged: bool
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def __init__(
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self,
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data: ClogitDataSet,
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max_iter: int = 100,
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tol: float = 1e-6,
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) -> None: ...
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def fit(self) -> None: ...
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def predict(self, covariates: list[float]) -> float: ...
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def odds_ratios(self) -> list[float]: ...
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class BootstrapResult:
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coefficients: list[float]
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ci_lower: list[float]
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ci_upper: list[float]
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se: list[float]
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n_bootstrap: int
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class CVResult:
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scores: list[float]
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mean_score: float
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se_score: float
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n_folds: int
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class TestResult:
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statistic: float
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p_value: float
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df: int
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test_type: str
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class ProportionalityTest:
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variable_names: list[str]
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chi_squared: list[float]
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p_values: list[float]
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global_chi_squared: float
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global_p_value: float
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global_df: int
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class NelsonAalenResult:
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time: list[float]
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cumulative_hazard: list[float]
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variance: list[float]
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ci_lower: list[float]
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ci_upper: list[float]
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n_risk: list[int]
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n_events: list[int]
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def survival(self) -> list[float]: ...
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class StratifiedKMResult:
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strata: list[int]
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times: list[list[float]]
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survival: list[list[float]]
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ci_lower: list[list[float]]
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ci_upper: list[list[float]]
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n_risk: list[list[int]]
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n_events: list[list[int]]
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class LogRankResult:
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statistic: float
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p_value: float
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df: int
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observed: list[float]
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expected: list[float]
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variance: float
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weight_type: str
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class TrendTestResult:
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statistic: float
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p_value: float
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trend_direction: str
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class SampleSizeResult:
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n_total: int
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n_events: int
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n_per_group: list[int]
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power: float
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alpha: float
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hazard_ratio: float
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method: str
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class AccrualResult:
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n_total: int
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accrual_time: float
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followup_time: float
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study_duration: float
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expected_events: float
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class CalibrationResult:
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risk_groups: list[float]
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predicted: list[float]
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observed: list[float]
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n_per_group: list[int]
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hosmer_lemeshow_stat: float
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hosmer_lemeshow_pvalue: float
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calibration_slope: float
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calibration_intercept: float
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class PredictionResult:
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linear_predictor: list[float]
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risk_score: list[float]
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survival_prob: list[list[float]]
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times: list[float]
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class RiskStratificationResult:
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risk_groups: list[int]
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cutpoints: list[float]
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group_sizes: list[int]
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group_event_rates: list[float]
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group_median_risk: list[float]
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class TdAUCResult:
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times: list[float]
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auc: list[float]
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integrated_auc: float
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class RMSTResult:
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rmst: float
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variance: float
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se: float
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ci_lower: float
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ci_upper: float
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tau: float
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class RMSTComparisonResult:
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rmst_diff: float
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rmst_ratio: float
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diff_se: float
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diff_ci_lower: float
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diff_ci_upper: float
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ratio_ci_lower: float
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ratio_ci_upper: float
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p_value: float
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rmst_group1: RMSTResult
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rmst_group2: RMSTResult
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class MedianSurvivalResult:
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median: float | None
|
|
336
|
+
ci_lower: float | None
|
|
337
|
+
ci_upper: float | None
|
|
338
|
+
quantile: float
|
|
339
|
+
|
|
340
|
+
class CumulativeIncidenceResult:
|
|
341
|
+
time: list[float]
|
|
342
|
+
cif: list[list[float]]
|
|
343
|
+
variance: list[list[float]]
|
|
344
|
+
event_types: list[int]
|
|
345
|
+
n_risk: list[int]
|
|
346
|
+
|
|
347
|
+
class NNTResult:
|
|
348
|
+
nnt: float
|
|
349
|
+
nnt_ci_lower: float
|
|
350
|
+
nnt_ci_upper: float
|
|
351
|
+
absolute_risk_reduction: float
|
|
352
|
+
arr_ci_lower: float
|
|
353
|
+
arr_ci_upper: float
|
|
354
|
+
time_horizon: float
|
|
355
|
+
|
|
356
|
+
class LandmarkResult:
|
|
357
|
+
landmark_time: float
|
|
358
|
+
n_at_risk: int
|
|
359
|
+
n_excluded: int
|
|
360
|
+
time: list[float]
|
|
361
|
+
status: list[int]
|
|
362
|
+
original_indices: list[int]
|
|
363
|
+
|
|
364
|
+
class ConditionalSurvivalResult:
|
|
365
|
+
given_time: float
|
|
366
|
+
target_time: float
|
|
367
|
+
conditional_survival: float
|
|
368
|
+
ci_lower: float
|
|
369
|
+
ci_upper: float
|
|
370
|
+
n_at_risk: int
|
|
371
|
+
|
|
372
|
+
class HazardRatioResult:
|
|
373
|
+
hazard_ratio: float
|
|
374
|
+
ci_lower: float
|
|
375
|
+
ci_upper: float
|
|
376
|
+
se_log_hr: float
|
|
377
|
+
z_statistic: float
|
|
378
|
+
p_value: float
|
|
379
|
+
|
|
380
|
+
class SurvivalAtTimeResult:
|
|
381
|
+
time: float
|
|
382
|
+
survival: float
|
|
383
|
+
ci_lower: float
|
|
384
|
+
ci_upper: float
|
|
385
|
+
n_at_risk: int
|
|
386
|
+
n_events: int
|
|
387
|
+
|
|
388
|
+
class LifeTableResult:
|
|
389
|
+
interval_start: list[float]
|
|
390
|
+
interval_end: list[float]
|
|
391
|
+
n_at_risk: list[float]
|
|
392
|
+
n_deaths: list[float]
|
|
393
|
+
n_censored: list[float]
|
|
394
|
+
n_effective: list[float]
|
|
395
|
+
hazard: list[float]
|
|
396
|
+
survival: list[float]
|
|
397
|
+
se_survival: list[float]
|
|
398
|
+
|
|
399
|
+
def aareg(options: AaregOptions) -> dict[str, Any]: ...
|
|
400
|
+
|
|
401
|
+
def survfitkm(
|
|
402
|
+
time: list[float],
|
|
403
|
+
status: list[float],
|
|
404
|
+
weights: list[float] | None = None,
|
|
405
|
+
entry_times: list[float] | None = None,
|
|
406
|
+
position: list[int] | None = None,
|
|
407
|
+
reverse: bool | None = None,
|
|
408
|
+
computation_type: int | None = None,
|
|
409
|
+
) -> SurvFitKMOutput: ...
|
|
410
|
+
|
|
411
|
+
def survreg(
|
|
412
|
+
time: list[float],
|
|
413
|
+
status: list[float],
|
|
414
|
+
covariates: list[list[float]],
|
|
415
|
+
weights: list[float] | None = None,
|
|
416
|
+
offsets: list[float] | None = None,
|
|
417
|
+
initial_beta: list[float] | None = None,
|
|
418
|
+
strata: list[int] | None = None,
|
|
419
|
+
distribution: str | None = None,
|
|
420
|
+
max_iter: int | None = None,
|
|
421
|
+
eps: float | None = None,
|
|
422
|
+
tol_chol: float | None = None,
|
|
423
|
+
) -> SurvivalFit: ...
|
|
424
|
+
|
|
425
|
+
def survdiff2(
|
|
426
|
+
time: list[float],
|
|
427
|
+
status: list[int],
|
|
428
|
+
group: list[int],
|
|
429
|
+
strata: list[int] | None = None,
|
|
430
|
+
rho: float | None = None,
|
|
431
|
+
) -> SurvDiffResult: ...
|
|
432
|
+
|
|
433
|
+
def coxmart(
|
|
434
|
+
time: list[float],
|
|
435
|
+
status: list[int],
|
|
436
|
+
score: list[float],
|
|
437
|
+
weights: list[float] | None = None,
|
|
438
|
+
strata: list[int] | None = None,
|
|
439
|
+
method: int | None = None,
|
|
440
|
+
) -> list[float]: ...
|
|
441
|
+
|
|
442
|
+
def finegray(
|
|
443
|
+
tstart: list[float],
|
|
444
|
+
tstop: list[float],
|
|
445
|
+
ctime: list[float],
|
|
446
|
+
cprob: list[float],
|
|
447
|
+
extend: list[bool],
|
|
448
|
+
keep: list[bool],
|
|
449
|
+
) -> FineGrayOutput: ...
|
|
450
|
+
|
|
451
|
+
def perform_cox_regression_frailty(
|
|
452
|
+
time: list[float],
|
|
453
|
+
event: list[int],
|
|
454
|
+
covariates: list[list[float]],
|
|
455
|
+
offset: list[float] | None = None,
|
|
456
|
+
weights: list[float] | None = None,
|
|
457
|
+
strata: list[int] | None = None,
|
|
458
|
+
frail: list[int] | None = None,
|
|
459
|
+
max_iter: int | None = None,
|
|
460
|
+
eps: float | None = None,
|
|
461
|
+
) -> dict[str, Any]: ...
|
|
462
|
+
|
|
463
|
+
def perform_pyears_calculation(
|
|
464
|
+
n: int,
|
|
465
|
+
ny: int,
|
|
466
|
+
doevent: bool,
|
|
467
|
+
doexpect: bool,
|
|
468
|
+
edim: int,
|
|
469
|
+
efac: list[int],
|
|
470
|
+
edims: list[int],
|
|
471
|
+
ecut: list[float],
|
|
472
|
+
expect: list[float],
|
|
473
|
+
y: list[float],
|
|
474
|
+
wt: list[float],
|
|
475
|
+
data: list[float],
|
|
476
|
+
odim: int,
|
|
477
|
+
ofac: list[int],
|
|
478
|
+
odims: list[int],
|
|
479
|
+
ocut: list[float],
|
|
480
|
+
) -> dict[str, Any]: ...
|
|
481
|
+
|
|
482
|
+
def perform_concordance1_calculation(
|
|
483
|
+
y: list[float],
|
|
484
|
+
wt: list[float],
|
|
485
|
+
indx: list[int],
|
|
486
|
+
ntree: int,
|
|
487
|
+
sortstop: list[int],
|
|
488
|
+
sortstart: list[int],
|
|
489
|
+
) -> dict[str, Any]: ...
|
|
490
|
+
|
|
491
|
+
def perform_concordance3_calculation(
|
|
492
|
+
y: list[float],
|
|
493
|
+
wt: list[float],
|
|
494
|
+
indx: list[int],
|
|
495
|
+
ntree: int,
|
|
496
|
+
sortstop: list[int],
|
|
497
|
+
sortstart: list[int],
|
|
498
|
+
nvar: int,
|
|
499
|
+
covar: list[float],
|
|
500
|
+
need_residuals: bool,
|
|
501
|
+
) -> dict[str, Any]: ...
|
|
502
|
+
|
|
503
|
+
def perform_concordance_calculation(
|
|
504
|
+
y: list[float],
|
|
505
|
+
wt: list[float],
|
|
506
|
+
indx: list[int],
|
|
507
|
+
ntree: int,
|
|
508
|
+
sortstop: list[int],
|
|
509
|
+
sortstart: list[int] | None = None,
|
|
510
|
+
nvar: int | None = None,
|
|
511
|
+
covar: list[float] | None = None,
|
|
512
|
+
need_residuals: bool = False,
|
|
513
|
+
) -> dict[str, Any]: ...
|
|
514
|
+
|
|
515
|
+
def perform_score_calculation(
|
|
516
|
+
time_data: list[float],
|
|
517
|
+
covariates: list[float],
|
|
518
|
+
strata: list[int],
|
|
519
|
+
score: list[float],
|
|
520
|
+
weights: list[float],
|
|
521
|
+
method: int,
|
|
522
|
+
) -> dict[str, Any]: ...
|
|
523
|
+
|
|
524
|
+
def perform_agscore3_calculation(
|
|
525
|
+
time_data: list[float],
|
|
526
|
+
covariates: list[float],
|
|
527
|
+
strata: list[int],
|
|
528
|
+
score: list[float],
|
|
529
|
+
weights: list[float],
|
|
530
|
+
method: int,
|
|
531
|
+
sort1: list[int],
|
|
532
|
+
) -> dict[str, Any]: ...
|
|
533
|
+
|
|
534
|
+
def perform_pystep_calculation(
|
|
535
|
+
edim: int,
|
|
536
|
+
data: list[float],
|
|
537
|
+
efac: list[int],
|
|
538
|
+
edims: list[int],
|
|
539
|
+
ecut: list[list[float]],
|
|
540
|
+
tmax: float,
|
|
541
|
+
) -> dict[str, Any]: ...
|
|
542
|
+
|
|
543
|
+
def perform_pystep_simple_calculation(
|
|
544
|
+
odim: int,
|
|
545
|
+
data: list[float],
|
|
546
|
+
ofac: list[int],
|
|
547
|
+
odims: list[int],
|
|
548
|
+
ocut: list[list[float]],
|
|
549
|
+
timeleft: float,
|
|
550
|
+
) -> dict[str, Any]: ...
|
|
551
|
+
|
|
552
|
+
def collapse(
|
|
553
|
+
y: list[float],
|
|
554
|
+
x: list[int],
|
|
555
|
+
istate: list[int],
|
|
556
|
+
id: list[int],
|
|
557
|
+
wt: list[float],
|
|
558
|
+
order: list[int],
|
|
559
|
+
) -> dict[str, Any]: ...
|
|
560
|
+
|
|
561
|
+
def cox_callback(
|
|
562
|
+
time1: list[float],
|
|
563
|
+
time2: list[float],
|
|
564
|
+
status: list[int],
|
|
565
|
+
covar: list[float],
|
|
566
|
+
offset: list[float],
|
|
567
|
+
weights: list[float],
|
|
568
|
+
strata: list[int],
|
|
569
|
+
sort1: list[int],
|
|
570
|
+
sort2: list[int],
|
|
571
|
+
method: int,
|
|
572
|
+
eps: float,
|
|
573
|
+
tol_chol: float,
|
|
574
|
+
beta: list[float],
|
|
575
|
+
) -> dict[str, Any]: ...
|
|
576
|
+
|
|
577
|
+
def coxcount1(
|
|
578
|
+
time1: list[float],
|
|
579
|
+
time2: list[float],
|
|
580
|
+
status: list[int],
|
|
581
|
+
strata: list[int],
|
|
582
|
+
sort1: list[int],
|
|
583
|
+
sort2: list[int],
|
|
584
|
+
) -> dict[str, Any]: ...
|
|
585
|
+
|
|
586
|
+
def coxcount2(
|
|
587
|
+
time1: list[float],
|
|
588
|
+
time2: list[float],
|
|
589
|
+
status: list[int],
|
|
590
|
+
strata: list[int],
|
|
591
|
+
sort1: list[int],
|
|
592
|
+
sort2: list[int],
|
|
593
|
+
) -> dict[str, Any]: ...
|
|
594
|
+
|
|
595
|
+
def norisk(
|
|
596
|
+
time1: list[float],
|
|
597
|
+
time2: list[float],
|
|
598
|
+
status: list[int],
|
|
599
|
+
sort1: list[int],
|
|
600
|
+
sort2: list[int],
|
|
601
|
+
strata: list[int],
|
|
602
|
+
) -> list[int]: ...
|
|
603
|
+
|
|
604
|
+
def cipoisson(k: int, time: float, p: float, method: str) -> tuple[float, float]: ...
|
|
605
|
+
def cipoisson_exact(k: int, time: float, p: float) -> tuple[float, float]: ...
|
|
606
|
+
def cipoisson_anscombe(k: int, time: float, p: float) -> tuple[float, float]: ...
|
|
607
|
+
|
|
608
|
+
def concordance(
|
|
609
|
+
y: list[float],
|
|
610
|
+
wt: list[float],
|
|
611
|
+
indx: list[int],
|
|
612
|
+
ntree: int,
|
|
613
|
+
sortstop: list[int],
|
|
614
|
+
sortstart: list[int],
|
|
615
|
+
strata: list[int],
|
|
616
|
+
) -> dict[str, Any]: ...
|
|
617
|
+
|
|
618
|
+
def agexact(
|
|
619
|
+
maxiter: int,
|
|
620
|
+
nused: int,
|
|
621
|
+
nvar: int,
|
|
622
|
+
start: list[float],
|
|
623
|
+
stop: list[float],
|
|
624
|
+
event: list[int],
|
|
625
|
+
covar: list[float],
|
|
626
|
+
offset: list[float],
|
|
627
|
+
strata: list[int],
|
|
628
|
+
sort: list[int],
|
|
629
|
+
beta: list[float],
|
|
630
|
+
eps: float,
|
|
631
|
+
tol_chol: float,
|
|
632
|
+
) -> dict[str, Any]: ...
|
|
633
|
+
|
|
634
|
+
def agsurv4(
|
|
635
|
+
y: list[float],
|
|
636
|
+
wt: list[float],
|
|
637
|
+
surv: list[float],
|
|
638
|
+
varh: list[float],
|
|
639
|
+
nrisk: list[float],
|
|
640
|
+
nevent: list[float],
|
|
641
|
+
ncensor: list[float],
|
|
642
|
+
strata: list[int],
|
|
643
|
+
) -> dict[str, Any]: ...
|
|
644
|
+
|
|
645
|
+
def agsurv5(
|
|
646
|
+
y: list[float],
|
|
647
|
+
wt: list[float],
|
|
648
|
+
id: list[int],
|
|
649
|
+
cluster: list[int],
|
|
650
|
+
risk: list[float],
|
|
651
|
+
position: list[int],
|
|
652
|
+
strata: list[int],
|
|
653
|
+
se_type: int,
|
|
654
|
+
) -> dict[str, Any]: ...
|
|
655
|
+
|
|
656
|
+
def agmart(
|
|
657
|
+
time: list[float],
|
|
658
|
+
status: list[int],
|
|
659
|
+
score: list[float],
|
|
660
|
+
weights: list[float],
|
|
661
|
+
strata: list[int],
|
|
662
|
+
method: int,
|
|
663
|
+
) -> list[float]: ...
|
|
664
|
+
|
|
665
|
+
def brier(
|
|
666
|
+
predictions: list[float],
|
|
667
|
+
outcomes: list[int],
|
|
668
|
+
weights: list[float] | None = None,
|
|
669
|
+
) -> float: ...
|
|
670
|
+
|
|
671
|
+
def integrated_brier(
|
|
672
|
+
predictions: list[list[float]],
|
|
673
|
+
outcomes: list[int],
|
|
674
|
+
times: list[float],
|
|
675
|
+
weights: list[float] | None = None,
|
|
676
|
+
) -> float: ...
|
|
677
|
+
|
|
678
|
+
def tmerge(
|
|
679
|
+
id: list[int],
|
|
680
|
+
time1: list[float],
|
|
681
|
+
newx: list[float],
|
|
682
|
+
nid: list[int],
|
|
683
|
+
ntime: list[float],
|
|
684
|
+
x: list[float],
|
|
685
|
+
) -> list[float]: ...
|
|
686
|
+
|
|
687
|
+
def tmerge2(
|
|
688
|
+
id: list[int],
|
|
689
|
+
time1: list[float],
|
|
690
|
+
nid: list[int],
|
|
691
|
+
ntime: list[float],
|
|
692
|
+
) -> list[int]: ...
|
|
693
|
+
|
|
694
|
+
def tmerge3(
|
|
695
|
+
id: list[int],
|
|
696
|
+
miss: list[bool],
|
|
697
|
+
) -> list[int]: ...
|
|
698
|
+
|
|
699
|
+
def survsplit(
|
|
700
|
+
tstart: list[float],
|
|
701
|
+
tstop: list[float],
|
|
702
|
+
cut: list[float],
|
|
703
|
+
) -> SplitResult: ...
|
|
704
|
+
|
|
705
|
+
def schoenfeld_residuals(
|
|
706
|
+
y: list[float],
|
|
707
|
+
score: list[float],
|
|
708
|
+
strata: list[int],
|
|
709
|
+
covar: list[float],
|
|
710
|
+
nvar: int,
|
|
711
|
+
method: int = 0,
|
|
712
|
+
) -> list[float]: ...
|
|
713
|
+
|
|
714
|
+
def cox_score_residuals(
|
|
715
|
+
y: list[float],
|
|
716
|
+
strata: list[int],
|
|
717
|
+
covar: list[float],
|
|
718
|
+
score: list[float],
|
|
719
|
+
weights: list[float],
|
|
720
|
+
nvar: int,
|
|
721
|
+
method: int = 0,
|
|
722
|
+
) -> list[float]: ...
|
|
723
|
+
|
|
724
|
+
def survfitaj(
|
|
725
|
+
y: list[float],
|
|
726
|
+
sort1: list[int],
|
|
727
|
+
sort2: list[int],
|
|
728
|
+
utime: list[float],
|
|
729
|
+
cstate: list[int],
|
|
730
|
+
wt: list[float],
|
|
731
|
+
grp: list[int],
|
|
732
|
+
ngrp: int,
|
|
733
|
+
p0: list[float],
|
|
734
|
+
i0: list[float],
|
|
735
|
+
sefit: int,
|
|
736
|
+
entry: bool,
|
|
737
|
+
position: list[int],
|
|
738
|
+
hindx: list[list[int]],
|
|
739
|
+
trmat: list[list[int]],
|
|
740
|
+
t0: float,
|
|
741
|
+
) -> SurvFitAJ: ...
|
|
742
|
+
|
|
743
|
+
def bootstrap_cox_ci(
|
|
744
|
+
time: list[float],
|
|
745
|
+
status: list[int],
|
|
746
|
+
covariates: list[list[float]],
|
|
747
|
+
n_bootstrap: int = 1000,
|
|
748
|
+
confidence_level: float = 0.95,
|
|
749
|
+
) -> BootstrapResult: ...
|
|
750
|
+
|
|
751
|
+
def bootstrap_survreg_ci(
|
|
752
|
+
time: list[float],
|
|
753
|
+
status: list[int],
|
|
754
|
+
covariates: list[list[float]],
|
|
755
|
+
distribution: str = "weibull",
|
|
756
|
+
n_bootstrap: int = 1000,
|
|
757
|
+
confidence_level: float = 0.95,
|
|
758
|
+
) -> BootstrapResult: ...
|
|
759
|
+
|
|
760
|
+
def cv_cox_concordance(
|
|
761
|
+
time: list[float],
|
|
762
|
+
status: list[int],
|
|
763
|
+
covariates: list[list[float]],
|
|
764
|
+
n_folds: int = 5,
|
|
765
|
+
) -> CVResult: ...
|
|
766
|
+
|
|
767
|
+
def cv_survreg_loglik(
|
|
768
|
+
time: list[float],
|
|
769
|
+
status: list[int],
|
|
770
|
+
covariates: list[list[float]],
|
|
771
|
+
distribution: str = "weibull",
|
|
772
|
+
n_folds: int = 5,
|
|
773
|
+
) -> CVResult: ...
|
|
774
|
+
|
|
775
|
+
def lrt_test(
|
|
776
|
+
log_likelihood_null: float,
|
|
777
|
+
log_likelihood_full: float,
|
|
778
|
+
df: int,
|
|
779
|
+
) -> TestResult: ...
|
|
780
|
+
|
|
781
|
+
def wald_test_py(
|
|
782
|
+
coefficients: list[float],
|
|
783
|
+
variance_matrix: list[list[float]],
|
|
784
|
+
) -> TestResult: ...
|
|
785
|
+
|
|
786
|
+
def score_test_py(
|
|
787
|
+
score: list[float],
|
|
788
|
+
information_matrix: list[list[float]],
|
|
789
|
+
) -> TestResult: ...
|
|
790
|
+
|
|
791
|
+
def ph_test(
|
|
792
|
+
time: list[float],
|
|
793
|
+
status: list[int],
|
|
794
|
+
schoenfeld_residuals: list[list[float]],
|
|
795
|
+
variable_names: list[str],
|
|
796
|
+
) -> ProportionalityTest: ...
|
|
797
|
+
|
|
798
|
+
def nelson_aalen_estimator(
|
|
799
|
+
time: list[float],
|
|
800
|
+
status: list[int],
|
|
801
|
+
weights: list[float] | None = None,
|
|
802
|
+
confidence_level: float | None = None,
|
|
803
|
+
) -> NelsonAalenResult: ...
|
|
804
|
+
|
|
805
|
+
def stratified_kaplan_meier(
|
|
806
|
+
time: list[float],
|
|
807
|
+
status: list[int],
|
|
808
|
+
strata: list[int],
|
|
809
|
+
confidence_level: float | None = None,
|
|
810
|
+
) -> StratifiedKMResult: ...
|
|
811
|
+
|
|
812
|
+
def logrank_test(
|
|
813
|
+
time: list[float],
|
|
814
|
+
status: list[int],
|
|
815
|
+
group: list[int],
|
|
816
|
+
weight_type: str | None = None,
|
|
817
|
+
) -> LogRankResult: ...
|
|
818
|
+
|
|
819
|
+
def fleming_harrington_test(
|
|
820
|
+
time: list[float],
|
|
821
|
+
status: list[int],
|
|
822
|
+
group: list[int],
|
|
823
|
+
p: float,
|
|
824
|
+
q: float,
|
|
825
|
+
) -> LogRankResult: ...
|
|
826
|
+
|
|
827
|
+
def logrank_trend(
|
|
828
|
+
time: list[float],
|
|
829
|
+
status: list[int],
|
|
830
|
+
group: list[int],
|
|
831
|
+
scores: list[float] | None = None,
|
|
832
|
+
) -> TrendTestResult: ...
|
|
833
|
+
|
|
834
|
+
def sample_size_survival(
|
|
835
|
+
hazard_ratio: float,
|
|
836
|
+
power: float | None = None,
|
|
837
|
+
alpha: float | None = None,
|
|
838
|
+
allocation_ratio: float | None = None,
|
|
839
|
+
sided: int | None = None,
|
|
840
|
+
) -> SampleSizeResult: ...
|
|
841
|
+
|
|
842
|
+
def sample_size_survival_freedman(
|
|
843
|
+
hazard_ratio: float,
|
|
844
|
+
prob_event: float,
|
|
845
|
+
power: float | None = None,
|
|
846
|
+
alpha: float | None = None,
|
|
847
|
+
allocation_ratio: float | None = None,
|
|
848
|
+
sided: int | None = None,
|
|
849
|
+
) -> SampleSizeResult: ...
|
|
850
|
+
|
|
851
|
+
def power_survival(
|
|
852
|
+
n_events: int,
|
|
853
|
+
hazard_ratio: float,
|
|
854
|
+
alpha: float | None = None,
|
|
855
|
+
allocation_ratio: float | None = None,
|
|
856
|
+
sided: int | None = None,
|
|
857
|
+
) -> float: ...
|
|
858
|
+
|
|
859
|
+
def expected_events(
|
|
860
|
+
n_total: int,
|
|
861
|
+
hazard_control: float,
|
|
862
|
+
hazard_ratio: float,
|
|
863
|
+
accrual_time: float,
|
|
864
|
+
followup_time: float,
|
|
865
|
+
allocation_ratio: float | None = None,
|
|
866
|
+
dropout_rate: float | None = None,
|
|
867
|
+
) -> AccrualResult: ...
|
|
868
|
+
|
|
869
|
+
def calibration(
|
|
870
|
+
predicted_risk: list[float],
|
|
871
|
+
observed_event: list[int],
|
|
872
|
+
n_groups: int | None = None,
|
|
873
|
+
) -> CalibrationResult: ...
|
|
874
|
+
|
|
875
|
+
def predict_cox(
|
|
876
|
+
coef: list[float],
|
|
877
|
+
x: list[list[float]],
|
|
878
|
+
baseline_hazard: list[float],
|
|
879
|
+
baseline_times: list[float],
|
|
880
|
+
pred_times: list[float],
|
|
881
|
+
) -> PredictionResult: ...
|
|
882
|
+
|
|
883
|
+
def risk_stratification(
|
|
884
|
+
risk_scores: list[float],
|
|
885
|
+
events: list[int],
|
|
886
|
+
n_groups: int | None = None,
|
|
887
|
+
) -> RiskStratificationResult: ...
|
|
888
|
+
|
|
889
|
+
def td_auc(
|
|
890
|
+
time: list[float],
|
|
891
|
+
status: list[int],
|
|
892
|
+
risk_score: list[float],
|
|
893
|
+
eval_times: list[float],
|
|
894
|
+
) -> TdAUCResult: ...
|
|
895
|
+
|
|
896
|
+
def rmst(
|
|
897
|
+
time: list[float],
|
|
898
|
+
status: list[int],
|
|
899
|
+
tau: float,
|
|
900
|
+
confidence_level: float | None = None,
|
|
901
|
+
) -> RMSTResult: ...
|
|
902
|
+
|
|
903
|
+
def rmst_comparison(
|
|
904
|
+
time: list[float],
|
|
905
|
+
status: list[int],
|
|
906
|
+
group: list[int],
|
|
907
|
+
tau: float,
|
|
908
|
+
confidence_level: float | None = None,
|
|
909
|
+
) -> RMSTComparisonResult: ...
|
|
910
|
+
|
|
911
|
+
def survival_quantile(
|
|
912
|
+
time: list[float],
|
|
913
|
+
status: list[int],
|
|
914
|
+
quantile: float | None = None,
|
|
915
|
+
confidence_level: float | None = None,
|
|
916
|
+
) -> MedianSurvivalResult: ...
|
|
917
|
+
|
|
918
|
+
def cumulative_incidence(
|
|
919
|
+
time: list[float],
|
|
920
|
+
status: list[int],
|
|
921
|
+
) -> CumulativeIncidenceResult: ...
|
|
922
|
+
|
|
923
|
+
def number_needed_to_treat(
|
|
924
|
+
time: list[float],
|
|
925
|
+
status: list[int],
|
|
926
|
+
group: list[int],
|
|
927
|
+
time_horizon: float,
|
|
928
|
+
confidence_level: float | None = None,
|
|
929
|
+
) -> NNTResult: ...
|
|
930
|
+
|
|
931
|
+
def landmark_analysis(
|
|
932
|
+
time: list[float],
|
|
933
|
+
status: list[int],
|
|
934
|
+
landmark_time: float,
|
|
935
|
+
) -> LandmarkResult: ...
|
|
936
|
+
|
|
937
|
+
def conditional_survival(
|
|
938
|
+
time: list[float],
|
|
939
|
+
status: list[int],
|
|
940
|
+
given_time: float,
|
|
941
|
+
target_time: float,
|
|
942
|
+
confidence_level: float | None = None,
|
|
943
|
+
) -> ConditionalSurvivalResult: ...
|
|
944
|
+
|
|
945
|
+
def hazard_ratio(
|
|
946
|
+
time: list[float],
|
|
947
|
+
status: list[int],
|
|
948
|
+
group: list[int],
|
|
949
|
+
confidence_level: float | None = None,
|
|
950
|
+
) -> HazardRatioResult: ...
|
|
951
|
+
|
|
952
|
+
def survival_at_times(
|
|
953
|
+
time: list[float],
|
|
954
|
+
status: list[int],
|
|
955
|
+
eval_times: list[float],
|
|
956
|
+
confidence_level: float | None = None,
|
|
957
|
+
) -> list[SurvivalAtTimeResult]: ...
|
|
958
|
+
|
|
959
|
+
def life_table(
|
|
960
|
+
time: list[float],
|
|
961
|
+
status: list[int],
|
|
962
|
+
breaks: list[float],
|
|
963
|
+
) -> LifeTableResult: ...
|