How to use the lifelines.utils.CensoringType.is_interval_censoring function in lifelines

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github CamDavidsonPilon / lifelines / lifelines / fitters / log_normal_fitter.py View on Github external
def _create_initial_point(self, Ts, E, *args):
        if CensoringType.is_right_censoring(self):
            log_T = np.log(Ts[0])
        elif CensoringType.is_left_censoring(self):
            log_T = np.log(Ts[1])
        elif CensoringType.is_interval_censoring(self):
            log_T = np.log(Ts[1])
        return np.array([np.median(log_T), 1.0])
github CamDavidsonPilon / lifelines / lifelines / fitters / generalized_gamma_regression_fitter.py View on Github external
def _create_initial_point(self, Ts, E, entries, weights, Xs):
        # detect constant columns
        constant_col = (Xs.df.var(0) < 1e-8).idxmax()

        import lifelines

        uni_model = lifelines.GeneralizedGammaFitter()

        with warnings.catch_warnings():
            warnings.simplefilter("ignore")

            if utils.CensoringType.is_right_censoring(self):
                uni_model.fit_right_censoring(Ts[0], event_observed=E, entry=entries, weights=weights)
            elif utils.CensoringType.is_interval_censoring(self):
                uni_model.fit_interval_censoring(Ts[0], Ts[1], event_observed=E, entry=entries, weights=weights)
            elif utils.CensoringType.is_left_censoring(self):
                uni_model.fit_left_censoring(Ts[1], event_observed=E, entry=entries, weights=weights)

            # we may use this later in print_summary
            self._ll_null_ = uni_model.log_likelihood_

            d = {}

            d["mu_"] = np.array([0.0] * (len(Xs.mappings["mu_"])))
            if constant_col in Xs.mappings["mu_"]:
                d["mu_"][Xs.mappings["mu_"].index(constant_col)] = uni_model.mu_

            d["sigma_"] = np.array([0.0] * (len(Xs.mappings["sigma_"])))
            if constant_col in Xs.mappings["mu_"]:
                d["sigma_"][Xs.mappings["sigma_"].index(constant_col)] = uni_model.ln_sigma_
github CamDavidsonPilon / lifelines / lifelines / fitters / __init__.py View on Github external
def _fit_model(self, Ts, E, entry, weights, show_progress=True):

        if utils.CensoringType.is_left_censoring(self):
            negative_log_likelihood = self._negative_log_likelihood_left_censoring
        elif utils.CensoringType.is_interval_censoring(self):
            negative_log_likelihood = self._negative_log_likelihood_interval_censoring
        elif utils.CensoringType.is_right_censoring(self):
            negative_log_likelihood = self._negative_log_likelihood_right_censoring

        with warnings.catch_warnings():
            warnings.simplefilter("ignore")

            results = minimize(
                value_and_grad(negative_log_likelihood),  # pylint: disable=no-value-for-parameter
                self._initial_values,
                jac=True,
                method=self._scipy_fit_method,
                args=(Ts, E, entry, weights),
                bounds=self._bounds,
                options={**{"disp": show_progress}, **self._scipy_fit_options},
            )
github CamDavidsonPilon / lifelines / lifelines / plotting.py View on Github external
ax = plt.gca()

    if timeline is None:
        timeline = model.timeline

    COL_EMP = "empirical CDF"

    if CensoringType.is_left_censoring(model):
        empirical_kmf = KaplanMeierFitter().fit_left_censoring(
            model.durations, model.event_observed, label=COL_EMP, timeline=timeline
        )
    elif CensoringType.is_right_censoring(model):
        empirical_kmf = KaplanMeierFitter().fit_right_censoring(
            model.durations, model.event_observed, label=COL_EMP, timeline=timeline
        )
    elif CensoringType.is_interval_censoring(model):
        raise NotImplementedError("lifelines does not have a non-parametric interval model yet.")

    empirical_kmf.plot_cumulative_density(ax=ax, **plot_kwargs)

    dist = get_distribution_name_of_lifelines_model(model)
    dist_object = create_scipy_stats_model_from_lifelines_model(model)
    ax.plot(timeline, dist_object.cdf(timeline), label="fitted %s" % dist, **plot_kwargs)
    ax.legend()
    return ax
github CamDavidsonPilon / lifelines / lifelines / fitters / piecewise_exponential_regression_fitter.py View on Github external
def _ll_null(self):
        if hasattr(self, "_ll_null_"):
            return self._ll_null_

        initial_point = np.zeros(len(self._fitted_parameter_names))

        model = self.__class__(breakpoints=self.breakpoints[:-1], penalizer=self.penalizer)
        regressors = {param_name: ["_intercept"] for param_name in self._fitted_parameter_names}
        if CensoringType.is_right_censoring(self):
            df = pd.DataFrame({"T": self.durations, "E": self.event_observed, "entry": self.entry, "_intercept": 1.0})
            model.fit_right_censoring(
                df, "T", "E", initial_point=initial_point, entry_col="entry", regressors=regressors
            )
        elif CensoringType.is_interval_censoring(self):
            df = pd.DataFrame(
                {
                    "lb": self.lower_bound,
                    "ub": self.upper_bound,
                    "E": self.event_observed,
                    "entry": self.entry,
                    "_intercept": 1.0,
                }
            )
            model.fit_interval_censoring(
                df, "lb", "ub", "E", initial_point=initial_point, entry_col="entry", regressors=regressors
            )
        if CensoringType.is_left_censoring(self):
            raise NotImplementedError()

        self._ll_null_ = model.log_likelihood_