How to use the lifelines.utils._to_1d_array function in lifelines

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github CamDavidsonPilon / lifelines / lifelines / fitters / __init__.py View on Github external
def cumulative_hazard_at_times(self, times, label=None) -> pd.Series:
        """
        Return a Pandas series of the predicted cumulative hazard value at specific times.

        Parameters
        -----------
        times: iterable or float
          values to return the cumulative hazard at.
        label: string, optional
          Rename the series returned. Useful for plotting.
        """
        label = utils.coalesce(label, self._label)
        return pd.Series(
            self._cumulative_hazard(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label
        )
github CamDavidsonPilon / lifelines / lifelines / fitters / coxph_fitter.py View on Github external
conditional_after: iterable, optional
            Must be equal is size to X.shape[0] (denoted `n` above).  An iterable (array, list, series) of possibly non-zero values that represent how long the
            subject has already lived for. Ex: if :math:`T` is the unknown event time, then this represents
            :math:`T | T > s`. This is useful for knowing the *remaining* hazard/survival of censored subjects.
            The new timeline is the remaining duration of the subject, i.e. reset back to starting at 0.

        """
        if isinstance(X, pd.Series):
            return self.predict_cumulative_hazard(X.to_frame().T, times=times, conditional_after=conditional_after)

        n = X.shape[0]

        if times is not None:
            times = np.atleast_1d(times).astype(float)
        if conditional_after is not None:
            conditional_after = _to_1d_array(conditional_after).reshape(n, 1)

        if self.strata:
            X = X.copy()
            cumulative_hazard_ = pd.DataFrame()
            if conditional_after is not None:
                X["_conditional_after"] = conditional_after

            for stratum, stratified_X in X.groupby(self.strata):
                try:
                    strata_c_0 = self.baseline_cumulative_hazard_[[stratum]]
                except KeyError:
                    raise StatError(
                        dedent(
                            """The stratum %s was not found in the original training data. For example, try
                            the following on the original dataset, df: `df.groupby(%s).size()`. Expected is that %s is not present in the output."""
                            % (stratum, self.strata, stratum)
github CamDavidsonPilon / lifelines / lifelines / fitters / kaplan_meier_fitter.py View on Github external
def cumulative_density_at_times(self, times, label=None) -> pd.Series:
        """
        Return a Pandas series of the predicted cumulative density at specific times

        Parameters
        -----------
        times: iterable or float

        Returns
        --------
        pd.Series

        """
        label = coalesce(label, self._label)
        return pd.Series(1 - self.predict(times), index=_to_1d_array(times), name=label)
github CamDavidsonPilon / lifelines / lifelines / fitters / kaplan_meier_fitter.py View on Github external
def survival_function_at_times(self, times, label=None) -> pd.Series:
        """
        Return a Pandas series of the predicted survival value at specific times

        Parameters
        -----------
        times: iterable or float

        Returns
        --------
        pd.Series

        """
        label = coalesce(label, self._label)
        return pd.Series(self.predict(times), index=_to_1d_array(times), name=label)
github CamDavidsonPilon / lifelines / lifelines / fitters / __init__.py View on Github external
def hazard_at_times(self, times, label=None) -> pd.Series:
        """
        Return a Pandas series of the predicted hazard at specific times.

        Parameters
        -----------
        times: iterable or float
          values to return the hazard at.
        label: string, optional
          Rename the series returned. Useful for plotting.

        """
        label = utils.coalesce(label, self._label)
        return pd.Series(self._hazard(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
github CamDavidsonPilon / lifelines / lifelines / fitters / __init__.py View on Github external
"""
        Predict the {0} at certain point in time. Uses a linear interpolation if
        points in time are not in the index.

        Parameters
        ----------
        times: scalar, or array
            a scalar or an array of times to predict the value of {0} at.
        interpolate: boolean, optional (default=False)
            for methods that produce a stepwise solution (Kaplan-Meier, Nelson-Aalen, etc), turning this to
            True will use an linear interpolation method to provide a more "smooth" answer.

        """
        if callable(self._estimation_method):
            return (
                pd.DataFrame(self._estimation_method(utils._to_1d_array(times)), index=utils._to_1d_array(times))
                .loc[times]
                .squeeze()
            )

        estimate = getattr(self, self._estimation_method)
        if not interpolate:
            return estimate.asof(times).squeeze()
        return utils.interpolate_at_times_and_return_pandas(estimate, times)