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Functions1,523 in github.com/derrynknife/SurPyval

↓ 2 callersMethod_op_terms
Per-dimension operator: list of ``(coef, u_value, differentiate)``. Applying the tensor product of the two dimensions' operators to ``C``
surpyval/multivariate/parametric/copula/copula.py:129
↓ 2 callersMethod_phi
(self, Z, *phi_params)
surpyval/univariate/regression/accelerated_failure_time/aft_fitter.py:53
↓ 2 callersMethod_plot_x_bounds
(self, x, params)
surpyval/univariate/parametric/distributions/beta.py:418
↓ 2 callersMethod_postprocess_simulated_model
Hook to adjust the fitted ``NonParametricCounting`` model in place before it is returned. Default is a no-op.
surpyval/recurrent/simulation.py:65
↓ 2 callersFunction_prepare
Group the event times by system and resolve each system's observation window. Returns a list of ``(events_used, T_q)`` per system (with the
surpyval/recurrent/tests.py:159
↓ 2 callersMethod_prepare_Z
Convert ``Z`` to a numeric design matrix, selecting the covariate columns recorded at fit time when a pandas DataFrame is passed.
surpyval/univariate/regression/semi_parametric_regression_model.py:44
↓ 2 callersFunction_regression_data
()
surpyval/tests/recurrent/test_parametric_inference.py:83
↓ 2 callersFunction_round_vals
(x)
surpyval/utils/__init__.py:13
↓ 2 callersMethod_set_simulation_seed
(self, seed)
surpyval/recurrent/simulation.py:33
↓ 2 callersMethod_simulate_count_xicn
Simulate ``items`` count-terminated sequences and return the raw event data as an ``xicn`` dict (``events + 1`` exact events per sequ
surpyval/recurrent/simulation.py:72
↓ 2 callersMethod_simulate_time_xicn
Simulate ``items`` time-terminated sequences and return the raw event data as an ``xicn`` dict. Each sequence ends in a right-censore
surpyval/recurrent/simulation.py:96
↓ 2 callersFunction_to_scipy
(obs, c)
surpyval/tests/univariate/nonparametric/test_logrank.py:9
↓ 2 callersFunction_toy_recurrent_data
()
surpyval/tests/recurrent/test_counting_process.py:56
↓ 2 callersFunction_validate_alternative
(alternative: str)
surpyval/recurrent/tests.py:118
↓ 2 callersMethod_z
Standardise ``x`` onto the unit interval.
surpyval/univariate/parametric/distributions/beta4.py:71
↓ 2 callersFunctionadjust_heuristic
Force the Turnbull heuristic when the data is interval censored or truncated, warning that the requested heuristic was changed.
surpyval/univariate/parametric/probability_plotting.py:20
↓ 2 callersMethodaic_c
r""" The Corrected Aikake Information Criterion (AIC) for the model, if it was fit with the ``fit()`` method. Not available if fit wit
surpyval/univariate/parametric/parametric.py:1075
↓ 2 callersMethodbaseline
(cls, beta, x, c, n, Z, e, event)
surpyval/univariate/competing_risks/regression/competing_risks_proportional_hazard.py:114
↓ 2 callersMethodcdf
Joint CDF ``P(X_1 <= x_1, X_2 <= x_2)``.
surpyval/multivariate/parametric/copula/copula_model.py:40
↓ 2 callersFunctioncensor_at
(x, q, where="right")
surpyval/tests/univariate/parametric/test_fit.py:127
↓ 2 callersFunctioncheck_e_and_x
(e, x)
surpyval/utils/__init__.py:1029
↓ 2 callersMethodclear_simulation
(self)
surpyval/recurrent/simulation.py:47
↓ 2 callersFunctioncoerce_xcnt_x
Coerce the ``x`` variable of xcnt-format data into a numpy array. Accepts a 1D array of event values, or a 2D array / list-of-pairs of `
surpyval/utils/__init__.py:301
↓ 2 callersMethodcovariance
Approximate parameter covariance matrix, ordered to match :attr:`parameter_names`. Computed as the inverse of the numerical H
surpyval/recurrent/inference.py:97
↓ 2 callersFunctiondelta_method_var
(model, func)
surpyval/tests/univariate/parametric/test_confidence_bounds.py:30
↓ 2 callersFunctiondraw_probability_plot
Draw the probability plot described by the ``probability_plot_data`` dictionary ``d`` onto the matplotlib axes ``ax``.
surpyval/univariate/parametric/probability_plotting.py:180
↓ 2 callersMethoddv
``dC/dv``. autograd default; override if known.
surpyval/multivariate/parametric/copula/copula.py:58
↓ 2 callersFunctionfallback_minimize
Minimise ``fun`` trying Newton-CG with the supplied jacobian and hessian first, then falling back to BFGS, then Nelder-Mead, whenever a m
surpyval/univariate/parametric/fitters/__init__.py:6
↓ 2 callersMethodff
r""" The cumulative distribution function, or failure function, for a distribution using the parameters found in the ``.params`` attr
surpyval/univariate/parametric/parametric.py:347
↓ 2 callersMethodff
r""" Failure (CDF or unreliability) function for the LogNormal Distribution: .. math:: F(x) = \Phi \left( \frac{\ln(x) -
surpyval/univariate/parametric/distributions/lognormal.py:120
↓ 2 callersMethodff
r""" Failure (CDF or unreliability) function for the Beta Distribution: .. math:: F(x) = \int_{0}^{x}t^{\alpha-1}\left (
surpyval/univariate/parametric/distributions/beta.py:102
↓ 2 callersMethodff
r""" Failure (CDF or unreliability) function for the four-parameter Beta distribution: .. math:: F(x) = I_{z}\le
surpyval/univariate/parametric/distributions/beta4.py:150
↓ 2 callersMethodfit
Fits Cox Proportional Hazards model to the provided data. Parameters ---------- x: array-like The obser
surpyval/univariate/regression/proportional_hazards/cox_ph.py:412
↓ 2 callersMethodfit
Fit the copula and its margins to multivariate survival data. Parameters ---------- x, c, n, t, xl, xr Multivaria
surpyval/multivariate/parametric/copula/copula.py:217
↓ 2 callersMethodfit_from_ecdf
( cls, x: npt.ArrayLike, R: npt.ArrayLike )
surpyval/univariate/nonparametric/nonparametric.py:1216
↓ 2 callersMethodfit_from_recurrent_data
Fit the ARI model from recurrent data. Parameters ---------- data : RecurrentData Data containing the r
surpyval/recurrent/renewal/ari.py:156
↓ 2 callersFunctionformat_truncation
Build the ``(n_rows, 2)`` truncation array from either a ``t`` matrix or separate ``tl``/``tr`` bounds (scalars broadcast to all rows). The d
surpyval/utils/__init__.py:347
↓ 2 callersFunctionfsl_to_xcnt
(f=None, s=None, l=None)
surpyval/utils/__init__.py:964
↓ 2 callersMethodget_uniform_random_number
(self)
surpyval/recurrent/simulation.py:50
↓ 2 callersFunctiongroup_xcnt
(x, c, n, t)
surpyval/utils/__init__.py:81
↓ 2 callersMethodhf
(self, x, Z, event=None, interp="step")
surpyval/univariate/competing_risks/regression/competing_risks_proportional_hazard.py:36
↓ 2 callersMethodhf
(self, x, Z, *params)
surpyval/univariate/regression/accelerated_failure_time/aft_fitter.py:63
↓ 2 callersMethodhf
(self, x, Z, *params)
surpyval/univariate/regression/accelerated_failure_time/accelerated_failure_time.py:36
↓ 2 callersMethodhf
(self, x, Z, *params)
surpyval/univariate/regression/proportional_hazards/proportional_hazards_fitter.py:63
↓ 2 callersMethodhf
(self, x, Z, *params)
surpyval/univariate/regression/accelerated_life/parameter_substitution.py:88
↓ 2 callersMethodiif
Instantaneous intensity function (IIF) or the failure rate of the HPP model. Parameters ---------- x : array
surpyval/recurrent/parametric/hpp.py:57
↓ 2 callersMethodlikelihood
(self, params)
surpyval/univariate/parametric/mixture_model.py:71
↓ 2 callersMethodll_interval_or_truncated
(self, xl, xr, n, *params)
surpyval/univariate/parametric/parametric_fitter.py:194
↓ 2 callersFunctionload_lung
Data on the survival of patients with advanced lung cancer from [6]_. References ---------- .. [6] Loprinzi CL. Laurie JA. Wieand
surpyval/datasets/__init__.py:145
↓ 2 callersFunctionlog_rank_split
r""" Returns the best feature index and value according to the Log-Rank split criterion. That is, it returns .. math:: (u^*
surpyval/experimental/forest/log_rank_split.py:17
↓ 2 callersMethodmcf_cb
( self, x, bound="two-sided", interp="step", confidence=0.95,
surpyval/recurrent/nonparametric/mcf.py:33
↓ 2 callersMethodmean
r""" Mean of the Uniform distribution .. math:: E = \frac{1}{2} \left ( a + b \right ) Parameters -----
surpyval/univariate/parametric/distributions/uniform.py:271
↓ 2 callersMethodmean
r""" Mean of the Beta distribution .. math:: E = \frac{\alpha}{\alpha + \beta} Parameters ----------
surpyval/univariate/parametric/distributions/beta.py:270
↓ 2 callersMethodmean
r""" Mean of the Rayleigh distribution .. math:: E = \sigma \sqrt{\frac{\pi}{2}} Parameters ----------
surpyval/univariate/parametric/distributions/rayleigh.py:278
↓ 2 callersMethodmean_cb
r""" Two-sided confidence interval of the (restricted) mean survival time, using the normal approximation with the standard variance
surpyval/univariate/nonparametric/nonparametric.py:652
↓ 2 callersMethodmpp_inv_y_transform
(self, y, *params)
surpyval/univariate/parametric/distributions/beta.py:387
↓ 2 callersMethodneg_ll
r""" The the negative log-likelihood for the model, if it was fit with the ``fit()`` method. Not available if fit with the ``from_par
surpyval/univariate/regression/parametric_regression_model.py:402
↓ 2 callersMethodneg_ll
(self, params, dims, weights)
surpyval/multivariate/parametric/copula/copula.py:213
↓ 2 callersMethodparameter_initialiser
(self, x)
surpyval/recurrent/parametric/duane.py:51
↓ 2 callersFunctionparse_leaf_type
(leaf_type: str)
surpyval/experimental/forest/tree.py:138
↓ 2 callersFunctionprepare_Z
Convert a covariate input ``Z`` into a numeric design matrix. If ``Z`` is a pandas DataFrame, the columns are selected using the ``featu
surpyval/univariate/regression/regression_data.py:88
↓ 2 callersFunctionprobability_plot_data
Compute everything needed to draw a probability plot of the data against the fitted CDF ``ff``. ``dist`` provides the plotting configura
surpyval/univariate/parametric/probability_plotting.py:44
↓ 2 callersMethodquantile_cb
r""" Two-sided confidence interval of the quantile at each probability p using the Brookmeyer-Crowley method: the interval is
surpyval/univariate/nonparametric/nonparametric.py:538
↓ 2 callersFunctionreject_unsupported_nonparametric
The nonparametric MCF estimators (``NonParametricCounting`` and ``CauseSpecificMCF``) currently only support exact events (``c=0``) and r
surpyval/utils/recurrent_utils.py:25
↓ 2 callersMethodsf
r""" Survival (or reliability) function for the Weibull Distribution: .. math:: R(x) = e^{-\left ( \frac{x}{\alpha} \rig
surpyval/univariate/parametric/distributions/weibull.py:28
↓ 2 callersMethodsf
r""" Survival (or Reliability) function for the Gumbel Distribution: .. math:: R(x) = 1 - e^{e^{-\left ( x - \mu \right
surpyval/univariate/parametric/distributions/gumbel.py:27
↓ 2 callersMethodspearman_rho
Spearman's rho. Default: empirical estimate from a large sample.
surpyval/multivariate/parametric/copula/copula.py:78
↓ 2 callersMethodtime_terminated_simulation_data
Simulate time-terminated recurrence data and return the raw events. Unlike :meth:`time_terminated_simulation` (which returns the fit
surpyval/recurrent/simulation.py:194
↓ 2 callersFunctiontruncate_at
(x, q, where="right")
surpyval/tests/univariate/parametric/test_fit.py:156
↓ 2 callersFunctionturnbull
(x, c, n, t, estimator="Fleming-Harrington")
surpyval/univariate/nonparametric/turnbull.py:13
↓ 2 callersMethodunpack_rr
(self, params, rr)
surpyval/univariate/parametric/distributions/gumbel.py:348
↓ 2 callersFunctionvalidate_cif_event
(event)
surpyval/utils/__init__.py:1148
↓ 2 callersFunctionwrangle_and_check_form_and_Z_cols
(Z_cols, formula, df)
surpyval/utils/__init__.py:1045
↓ 1 callersMethodHf
r""" Cumulative hazard rate for the Gumbel LEV Distribution: .. math:: H(x) = -\ln \left ( R(x) \right ) Parame
surpyval/univariate/parametric/distributions/gumbel_lev.py:182
↓ 1 callersMethodHf
(self, x, Z, event=None, interp="step")
surpyval/univariate/competing_risks/regression/competing_risks_proportional_hazard.py:39
↓ 1 callersMethodHf
( self, x: int | float | ArrayLike, Z: ArrayLike | NDArray )
surpyval/experimental/forest/forest.py:144
↓ 1 callersMethod__init__
(self)
surpyval/univariate/regression/accelerated_life/power.py:28
↓ 1 callersMethod__init__
(self)
surpyval/univariate/regression/accelerated_life/eyring.py:8
↓ 1 callersMethod__init__
(self)
surpyval/univariate/regression/accelerated_life/exponential.py:8
↓ 1 callersFunction_betaincln_raw
(a, b, x)
surpyval/utils/autograd_gamma_compat.py:171
↓ 1 callersMethod_cb_context
Assemble the parameter vector and covariance used by ``cb``. The variance is computed over the extended parameter vector ``(*params,
surpyval/univariate/parametric/parametric.py:867
↓ 1 callersMethod_cb_rate_bound
Confidence bound on the hazard (``hf``) or density (``df``). Both are non-negative, so the bound is computed on the log scale to keep
surpyval/univariate/parametric/parametric.py:942
↓ 1 callersFunction_counting_model_from_xrd
Build a ``NonParametricCounting`` model from an explicit ``(x, r, d)`` triple so its ``mcf``/``mcf_cb``/``plot`` machinery can be reused for
surpyval/recurrent/competing_risks/nonparametric/cause_specific_mcf.py:23
↓ 1 callersFunction_debye1
First Debye function ``D_1(t) = (1/t) int_0^t s/(e^s-1) ds``.
surpyval/multivariate/parametric/copula/archimedean.py:158
↓ 1 callersMethod_em
(self, tol=1e-10, max_iter=1000)
surpyval/univariate/parametric/mixture_model.py:114
↓ 1 callersMethod_eval
(self, u, v, diff_u, diff_v, params)
surpyval/multivariate/parametric/copula/copula.py:117
↓ 1 callersMethod_fit
(self, x, c, n, t, turnbull_estimator)
surpyval/univariate/nonparametric/turnbull.py:176
↓ 1 callersMethod_fit_joint
(self, margins, margin_models, data)
surpyval/multivariate/parametric/copula/copula.py:324
↓ 1 callersMethod_fit_margins
(self, margins, data)
surpyval/multivariate/parametric/copula/copula.py:279
↓ 1 callersFunction_gammainccln_raw
(a, x)
surpyval/utils/autograd_gamma_compat.py:122
↓ 1 callersFunction_gammaincln_raw
(a, x)
surpyval/utils/autograd_gamma_compat.py:98
↓ 1 callersMethod_init_theta
Initial parameter guess. Override per family for robustness.
surpyval/multivariate/parametric/copula/copula.py:362
↓ 1 callersMethod_initial_baseline_params
Initial parameters for the baseline intensity model: the plain NHPP fit of that baseline if it succeeds, otherwise its own parameter
surpyval/recurrent/renewal/ari.py:218
↓ 1 callersMethod_invert_du
(self, u, w, params, iters=60)
surpyval/multivariate/parametric/copula/copula.py:106
↓ 1 callersFunction_kl_true_vs_fit
Monte-Carlo KL(true || fit) in nats, using the offset log-density.
surpyval/tests/univariate/parametric/test_offset_divergence.py:26
↓ 1 callersMethod_log_likelihood
(self, data, *params)
surpyval/univariate/parametric/parametric_fitter.py:212
↓ 1 callersMethod_parameter_initialiser
(self, x, c=None, n=None, t=None, offset=False)
surpyval/univariate/parametric/distributions/gamma.py:39
↓ 1 callersMethod_parameter_initialiser_dist
(self, x, c=None, n=None, t=None)
surpyval/univariate/regression/accelerated_failure_time/accelerated_failure_time.py:50
↓ 1 callersMethod_parameter_names
Names of the entries of ``_mle``, in order. Subclasses override this to label their parameters (e.g. the renewal models prepend the r
surpyval/recurrent/inference.py:67
↓ 1 callersMethod_phi_bounds
(self, Z)
surpyval/univariate/regression/proportional_odds/proportional_odds_fitter.py:43
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