Source code for statsmodels.discrete.count_model

__all__ = ["ZeroInflatedPoisson", "ZeroInflatedGeneralizedPoisson",
           "ZeroInflatedNegativeBinomialP"]

import warnings
import numpy as np
import statsmodels.base.model as base
import statsmodels.base.wrapper as wrap
import statsmodels.regression.linear_model as lm
from statsmodels.discrete.discrete_model import (DiscreteModel, CountModel,
                                                 Poisson, Logit, CountResults,
                                                 L1CountResults, Probit,
                                                 _discrete_results_docs,
                                                 _validate_l1_method,
                                                 GeneralizedPoisson,
                                                 NegativeBinomialP)
from statsmodels.distributions import zipoisson, zigenpoisson, zinegbin
from statsmodels.tools.numdiff import approx_fprime, approx_hess
from statsmodels.tools.decorators import cache_readonly
from statsmodels.tools.sm_exceptions import ConvergenceWarning
from statsmodels.compat.pandas import Appender


_doc_zi_params = """
    exog_infl : array_like or None
        Explanatory variables for the binary inflation model, i.e. for
        mixing probability model. If None, then a constant is used.
    offset : array_like
        Offset is added to the linear prediction with coefficient equal to 1.
    exposure : array_like
        Log(exposure) is added to the linear prediction with coefficient
        equal to 1.
    inflation : {'logit', 'probit'}
        The model for the zero inflation, either Logit (default) or Probit
    """


[docs]class GenericZeroInflated(CountModel): __doc__ = """ Generic Zero Inflated Model %(params)s %(extra_params)s Attributes ---------- endog : ndarray A reference to the endogenous response variable exog : ndarray A reference to the exogenous design. exog_infl : ndarray A reference to the zero-inflated exogenous design. """ % {'params' : base._model_params_doc, 'extra_params' : _doc_zi_params + base._missing_param_doc} def __init__(self, endog, exog, exog_infl=None, offset=None, inflation='logit', exposure=None, missing='none', **kwargs): super(GenericZeroInflated, self).__init__(endog, exog, offset=offset, exposure=exposure, missing=missing, **kwargs) if exog_infl is None: self.k_inflate = 1 self._no_exog_infl = True self.exog_infl = np.ones((endog.size, self.k_inflate), dtype=np.float64) else: self.exog_infl = exog_infl self.k_inflate = exog_infl.shape[1] self._no_exog_infl = False if len(exog.shape) == 1: self.k_exog = 1 else: self.k_exog = exog.shape[1] self.infl = inflation if inflation == 'logit': self.model_infl = Logit(np.zeros(self.exog_infl.shape[0]), self.exog_infl) self._hessian_inflate = self._hessian_logit elif inflation == 'probit': self.model_infl = Probit(np.zeros(self.exog_infl.shape[0]), self.exog_infl) self._hessian_inflate = self._hessian_probit else: raise ValueError("inflation == %s, which is not handled" % inflation) self.inflation = inflation self.k_extra = self.k_inflate if len(self.exog) != len(self.exog_infl): raise ValueError('exog and exog_infl have different number of' 'observation. `missing` handling is not supported') infl_names = ['inflate_%s' % i for i in self.model_infl.data.param_names] self.exog_names[:] = infl_names + list(self.exog_names) self.exog_infl = np.asarray(self.exog_infl, dtype=np.float64) self._init_keys.extend(['exog_infl', 'inflation']) self._null_drop_keys = ['exog_infl'] def _get_exogs(self): """list of exogs, for internal use in post-estimation """ return (self.exog, self.exog_infl)
[docs] def loglike(self, params): """ Loglikelihood of Generic Zero Inflated model. Parameters ---------- params : array_like The parameters of the model. Returns ------- loglike : float The log-likelihood function of the model evaluated at `params`. See notes. Notes ----- .. math:: \\ln L=\\sum_{y_{i}=0}\\ln(w_{i}+(1-w_{i})*P_{main\\_model})+ \\sum_{y_{i}>0}(\\ln(1-w_{i})+L_{main\\_model}) where P - pdf of main model, L - loglike function of main model. """ return np.sum(self.loglikeobs(params))
[docs] def loglikeobs(self, params): """ Loglikelihood for observations of Generic Zero Inflated model. Parameters ---------- params : array_like The parameters of the model. Returns ------- loglike : ndarray The log likelihood for each observation of the model evaluated at `params`. See Notes for definition. Notes ----- .. math:: \\ln L=\\ln(w_{i}+(1-w_{i})*P_{main\\_model})+ \\ln(1-w_{i})+L_{main\\_model} where P - pdf of main model, L - loglike function of main model. for observations :math:`i=1,...,n` """ params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] y = self.endog w = self.model_infl.predict(params_infl) w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) llf_main = self.model_main.loglikeobs(params_main) zero_idx = np.nonzero(y == 0)[0] nonzero_idx = np.nonzero(y)[0] llf = np.zeros_like(y, dtype=np.float64) llf[zero_idx] = (np.log(w[zero_idx] + (1 - w[zero_idx]) * np.exp(llf_main[zero_idx]))) llf[nonzero_idx] = np.log(1 - w[nonzero_idx]) + llf_main[nonzero_idx] return llf
[docs] @Appender(DiscreteModel.fit.__doc__) def fit(self, start_params=None, method='bfgs', maxiter=35, full_output=1, disp=1, callback=None, cov_type='nonrobust', cov_kwds=None, use_t=None, **kwargs): if start_params is None: offset = getattr(self, "offset", 0) + getattr(self, "exposure", 0) if np.size(offset) == 1 and offset == 0: offset = None start_params = self._get_start_params() if callback is None: # work around perfect separation callback #3895 callback = lambda *x: x mlefit = super(GenericZeroInflated, self).fit(start_params=start_params, maxiter=maxiter, disp=disp, method=method, full_output=full_output, callback=callback, **kwargs) zipfit = self.result_class(self, mlefit._results) result = self.result_class_wrapper(zipfit) if cov_kwds is None: cov_kwds = {} result._get_robustcov_results(cov_type=cov_type, use_self=True, use_t=use_t, **cov_kwds) return result
[docs] @Appender(DiscreteModel.fit_regularized.__doc__) def fit_regularized(self, start_params=None, method='l1', maxiter='defined_by_method', full_output=1, disp=1, callback=None, alpha=0, trim_mode='auto', auto_trim_tol=0.01, size_trim_tol=1e-4, qc_tol=0.03, **kwargs): _validate_l1_method(method) if np.size(alpha) == 1 and alpha != 0: k_params = self.k_exog + self.k_inflate alpha = alpha * np.ones(k_params) extra = self.k_extra - self.k_inflate alpha_p = alpha[:-(self.k_extra - extra)] if (self.k_extra and np.size(alpha) > 1) else alpha if start_params is None: offset = getattr(self, "offset", 0) + getattr(self, "exposure", 0) if np.size(offset) == 1 and offset == 0: offset = None start_params = self.model_main.fit_regularized( start_params=start_params, method=method, maxiter=maxiter, full_output=full_output, disp=0, callback=callback, alpha=alpha_p, trim_mode=trim_mode, auto_trim_tol=auto_trim_tol, size_trim_tol=size_trim_tol, qc_tol=qc_tol, **kwargs).params start_params = np.append(np.ones(self.k_inflate), start_params) cntfit = super(CountModel, self).fit_regularized( start_params=start_params, method=method, maxiter=maxiter, full_output=full_output, disp=disp, callback=callback, alpha=alpha, trim_mode=trim_mode, auto_trim_tol=auto_trim_tol, size_trim_tol=size_trim_tol, qc_tol=qc_tol, **kwargs) discretefit = self.result_class_reg(self, cntfit) return self.result_class_reg_wrapper(discretefit)
[docs] def score_obs(self, params): """ Generic Zero Inflated model score (gradient) vector of the log-likelihood Parameters ---------- params : array_like The parameters of the model Returns ------- score : ndarray, 1-D The score vector of the model, i.e. the first derivative of the loglikelihood function, evaluated at `params` """ params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] y = self.endog w = self.model_infl.predict(params_infl) w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) score_main = self.model_main.score_obs(params_main) llf_main = self.model_main.loglikeobs(params_main) llf = self.loglikeobs(params) zero_idx = np.nonzero(y == 0)[0] nonzero_idx = np.nonzero(y)[0] mu = self.model_main.predict(params_main) # TODO: need to allow for complex to use CS numerical derivatives dldp = np.zeros((self.exog.shape[0], self.k_exog), dtype=np.float64) dldw = np.zeros_like(self.exog_infl, dtype=np.float64) dldp[zero_idx,:] = (score_main[zero_idx].T * (1 - (w[zero_idx]) / np.exp(llf[zero_idx]))).T dldp[nonzero_idx,:] = score_main[nonzero_idx] if self.inflation == 'logit': dldw[zero_idx,:] = (self.exog_infl[zero_idx].T * w[zero_idx] * (1 - w[zero_idx]) * (1 - np.exp(llf_main[zero_idx])) / np.exp(llf[zero_idx])).T dldw[nonzero_idx,:] = -(self.exog_infl[nonzero_idx].T * w[nonzero_idx]).T elif self.inflation == 'probit': return approx_fprime(params, self.loglikeobs) return np.hstack((dldw, dldp))
[docs] def score(self, params): return self.score_obs(params).sum(0)
def _hessian_main(self, params): pass def _hessian_logit(self, params): params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] y = self.endog w = self.model_infl.predict(params_infl) w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) score_main = self.model_main.score_obs(params_main) llf_main = self.model_main.loglikeobs(params_main) llf = self.loglikeobs(params) zero_idx = np.nonzero(y == 0)[0] nonzero_idx = np.nonzero(y)[0] hess_arr = np.zeros((self.k_inflate, self.k_exog + self.k_inflate)) pmf = np.exp(llf) #d2l/dw2 for i in range(self.k_inflate): for j in range(i, -1, -1): hess_arr[i, j] = (( self.exog_infl[zero_idx, i] * self.exog_infl[zero_idx, j] * (w[zero_idx] * (1 - w[zero_idx]) * ((1 - np.exp(llf_main[zero_idx])) * (1 - 2 * w[zero_idx]) * np.exp(llf[zero_idx]) - (w[zero_idx] - w[zero_idx]**2) * (1 - np.exp(llf_main[zero_idx]))**2) / pmf[zero_idx]**2)).sum() - (self.exog_infl[nonzero_idx, i] * self.exog_infl[nonzero_idx, j] * w[nonzero_idx] * (1 - w[nonzero_idx])).sum()) #d2l/dpdw for i in range(self.k_inflate): for j in range(self.k_exog): hess_arr[i, j + self.k_inflate] = -(score_main[zero_idx, j] * w[zero_idx] * (1 - w[zero_idx]) * self.exog_infl[zero_idx, i] / pmf[zero_idx]).sum() return hess_arr def _hessian_probit(self, params): pass
[docs] def hessian(self, params): """ Generic Zero Inflated model Hessian matrix of the loglikelihood Parameters ---------- params : array_like The parameters of the model Returns ------- hess : ndarray, (k_vars, k_vars) The Hessian, second derivative of loglikelihood function, evaluated at `params` Notes ----- """ hess_arr_main = self._hessian_main(params) hess_arr_infl = self._hessian_inflate(params) if hess_arr_main is None or hess_arr_infl is None: return approx_hess(params, self.loglike) dim = self.k_exog + self.k_inflate hess_arr = np.zeros((dim, dim)) hess_arr[:self.k_inflate,:] = hess_arr_infl hess_arr[self.k_inflate:,self.k_inflate:] = hess_arr_main tri_idx = np.triu_indices(self.k_exog + self.k_inflate, k=1) hess_arr[tri_idx] = hess_arr.T[tri_idx] return hess_arr
[docs] def predict(self, params, exog=None, exog_infl=None, exposure=None, offset=None, which='mean', y_values=None): """ Predict response variable or other statistic given exogenous variables. Parameters ---------- params : array_like The parameters of the model. exog : ndarray, optional Explanatory variables for the main count model. If ``exog`` is None, then the data from the model will be used. exog_infl : ndarray, optional Explanatory variables for the zero-inflation model. ``exog_infl`` has to be provided if ``exog`` was provided unless ``exog_infl`` in the model is only a constant. offset : ndarray, optional Offset is added to the linear predictor of the mean function with coefficient equal to 1. Default is zero if exog is not None, and the model offset if exog is None. exposure : ndarray, optional Log(exposure) is added to the linear predictor with coefficient equal to 1. If exposure is specified, then it will be logged by the method. The user does not need to log it first. Default is one if exog is is not None, and it is the model exposure if exog is None. which : str (optional) Statitistic to predict. Default is 'mean'. - 'mean' : the conditional expectation of endog E(y | x), i.e. exp of linear predictor. - 'linear' : the linear predictor of the mean function. - 'var' : returns the estimated variance of endog implied by the model. - 'mean-main' : mean of the main count model - 'prob-main' : probability of selecting the main model. The probability of zero inflation is ``1 - prob-main``. - 'mean-nonzero' : expected value conditional on having observation larger than zero, E(y | X, y>0) - 'prob-zero' : probability of observing a zero count. P(y=0 | x) - 'prob' : probabilities of each count from 0 to max(endog), or for y_values if those are provided. This is a multivariate return (2-dim when predicting for several observations). y_values : array_like Values of the random variable endog at which pmf is evaluated. Only used if ``which="prob"`` """ no_exog = False if exog is None: no_exog = True exog = self.exog if exog_infl is None: if no_exog: exog_infl = self.exog_infl else: if self._no_exog_infl: exog_infl = np.ones((len(exog), 1)) else: exog_infl = np.asarray(exog_infl) if exog_infl.ndim == 1 and self.k_inflate == 1: exog_infl = exog_infl[:, None] if exposure is None: if no_exog: exposure = getattr(self, 'exposure', 0) else: exposure = 0 else: exposure = np.log(exposure) if offset is None: if no_exog: offset = getattr(self, 'offset', 0) else: offset = 0 params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] prob_main = 1 - self.model_infl.predict(params_infl, exog_infl) lin_pred = np.dot(exog, params_main[:self.exog.shape[1]]) + exposure + offset # Refactor: This is pretty hacky, # there should be an appropriate predict method in model_main # this is just prob(y=0 | model_main) tmp_exog = self.model_main.exog tmp_endog = self.model_main.endog tmp_offset = getattr(self.model_main, 'offset', False) tmp_exposure = getattr(self.model_main, 'exposure', False) self.model_main.exog = exog self.model_main.endog = np.zeros((exog.shape[0])) self.model_main.offset = offset self.model_main.exposure = exposure llf = self.model_main.loglikeobs(params_main) self.model_main.exog = tmp_exog self.model_main.endog = tmp_endog # tmp_offset might be an array with elementwise equality testing #if np.size(tmp_offset) == 1 and tmp_offset[0] == 'no': if tmp_offset is False: del self.model_main.offset else: self.model_main.offset = tmp_offset #if np.size(tmp_exposure) == 1 and tmp_exposure[0] == 'no': if tmp_exposure is False: del self.model_main.exposure else: self.model_main.exposure = tmp_exposure # end hack prob_zero = (1 - prob_main) + prob_main * np.exp(llf) if which == 'mean': return prob_main * np.exp(lin_pred) elif which == 'mean-main': return np.exp(lin_pred) elif which == 'linear': return lin_pred elif which == 'mean-nonzero': return prob_main * np.exp(lin_pred) / (1 - prob_zero) elif which == 'prob-zero': return prob_zero elif which == 'prob-main': return prob_main elif which == 'var': mu = np.exp(lin_pred) return self._predict_var(params, mu, 1 - prob_main) elif which == 'prob': return self._predict_prob(params, exog, exog_infl, exposure, offset, y_values=y_values) else: raise ValueError('which = %s is not available' % which)
def _derivative_predict(self, params, exog=None, transform='dydx'): """NotImplemented """ raise NotImplementedError def _derivative_exog(self, params, exog=None, transform="dydx", dummy_idx=None, count_idx=None): """NotImplemented """ raise NotImplementedError def _deriv_mean_dparams(self, params): """ Derivative of the expected endog with respect to the parameters. Parameters ---------- params : ndarray parameter at which score is evaluated Returns ------- The value of the derivative of the expected endog with respect to the parameter vector. """ params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] w = self.model_infl.predict(params_infl) w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) mu = self.model_main.predict(params_main) score_infl = self.model_infl._deriv_mean_dparams(params_infl) score_main = self.model_main._deriv_mean_dparams(params_main) dmat_infl = - mu[:, None] * score_infl dmat_main = (1 - w[:, None]) * score_main dmat = np.column_stack((dmat_infl, dmat_main)) return dmat def _deriv_score_obs_dendog(self, params): """derivative of score_obs w.r.t. endog Parameters ---------- params : ndarray parameter at which score is evaluated Returns ------- derivative : ndarray_2d The derivative of the score_obs with respect to endog. """ raise NotImplementedError # The below currently does not work, discontinuity at zero # see https://github.com/statsmodels/statsmodels/pull/7951#issuecomment-996355875 # noqa from statsmodels.tools.numdiff import _approx_fprime_scalar endog_original = self.endog def f(y): if y.ndim == 2 and y.shape[1] == 1: y = y[:, 0] self.endog = y self.model_main.endog = y sf = self.score_obs(params) self.endog = endog_original self.model_main.endog = endog_original return sf ds = _approx_fprime_scalar(self.endog[:, None], f, epsilon=1e-2) return ds
[docs]class ZeroInflatedPoisson(GenericZeroInflated): __doc__ = """ Poisson Zero Inflated Model %(params)s %(extra_params)s Attributes ---------- endog : ndarray A reference to the endogenous response variable exog : ndarray A reference to the exogenous design. exog_infl : ndarray A reference to the zero-inflated exogenous design. """ % {'params' : base._model_params_doc, 'extra_params' : _doc_zi_params + base._missing_param_doc} def __init__(self, endog, exog, exog_infl=None, offset=None, exposure=None, inflation='logit', missing='none', **kwargs): super(ZeroInflatedPoisson, self).__init__(endog, exog, offset=offset, inflation=inflation, exog_infl=exog_infl, exposure=exposure, missing=missing, **kwargs) self.model_main = Poisson(self.endog, self.exog, offset=offset, exposure=exposure) self.distribution = zipoisson self.result_class = ZeroInflatedPoissonResults self.result_class_wrapper = ZeroInflatedPoissonResultsWrapper self.result_class_reg = L1ZeroInflatedPoissonResults self.result_class_reg_wrapper = L1ZeroInflatedPoissonResultsWrapper def _hessian_main(self, params): params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] y = self.endog w = self.model_infl.predict(params_infl) w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) score = self.score(params) zero_idx = np.nonzero(y == 0)[0] nonzero_idx = np.nonzero(y)[0] mu = self.model_main.predict(params_main) hess_arr = np.zeros((self.k_exog, self.k_exog)) coeff = (1 + w[zero_idx] * (np.exp(mu[zero_idx]) - 1)) #d2l/dp2 for i in range(self.k_exog): for j in range(i, -1, -1): hess_arr[i, j] = (( self.exog[zero_idx, i] * self.exog[zero_idx, j] * mu[zero_idx] * (w[zero_idx] - 1) * (1 / coeff - w[zero_idx] * mu[zero_idx] * np.exp(mu[zero_idx]) / coeff**2)).sum() - (mu[nonzero_idx] * self.exog[nonzero_idx, i] * self.exog[nonzero_idx, j]).sum()) return hess_arr def _predict_prob(self, params, exog, exog_infl, exposure, offset, y_values=None): params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] if y_values is None: y_values = np.atleast_2d(np.arange(0, np.max(self.endog)+1)) if len(exog_infl.shape) < 2: transform = True w = np.atleast_2d( self.model_infl.predict(params_infl, exog_infl))[:, None] else: transform = False w = self.model_infl.predict(params_infl, exog_infl)[:, None] w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) mu = self.model_main.predict(params_main, exog, offset=offset)[:, None] result = self.distribution.pmf(y_values, mu, w) return result[0] if transform else result def _predict_var(self, params, mu, prob_infl): """predict values for conditional variance V(endog | exog) Parameters ---------- params : array_like The model parameters. This is only used to extract extra params like dispersion parameter. mu : array_like Array of mean predictions for main model. prob_inlf : array_like Array of predicted probabilities of zero-inflation `w`. Returns ------- Predicted conditional variance. """ w = prob_infl var_ = (1 - w) * mu * (1 + w * mu) return var_ def _get_start_params(self): start_params = self.model_main.fit(disp=0, method="nm").params start_params = np.append(np.ones(self.k_inflate) * 0.1, start_params) return start_params
[docs] def get_distribution(self, params, exog=None, exog_infl=None, exposure=None, offset=None): """Get frozen instance of distribution based on predicted parameters. Parameters ---------- params : array_like The parameters of the model. exog : ndarray, optional Explanatory variables for the main count model. If ``exog`` is None, then the data from the model will be used. exog_infl : ndarray, optional Explanatory variables for the zero-inflation model. ``exog_infl`` has to be provided if ``exog`` was provided unless ``exog_infl`` in the model is only a constant. offset : ndarray, optional Offset is added to the linear predictor of the mean function with coefficient equal to 1. Default is zero if exog is not None, and the model offset if exog is None. exposure : ndarray, optional Log(exposure) is added to the linear predictor of the mean function with coefficient equal to 1. If exposure is specified, then it will be logged by the method. The user does not need to log it first. Default is one if exog is is not None, and it is the model exposure if exog is None. Returns ------- Instance of frozen scipy distribution subclass. """ mu = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="mean-main") w = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="prob-main") distr = self.distribution(mu[:, None], 1 - w[:, None]) return distr
[docs]class ZeroInflatedGeneralizedPoisson(GenericZeroInflated): __doc__ = """ Zero Inflated Generalized Poisson Model %(params)s %(extra_params)s Attributes ---------- endog : ndarray A reference to the endogenous response variable exog : ndarray A reference to the exogenous design. exog_infl : ndarray A reference to the zero-inflated exogenous design. p : scalar P denotes parametrizations for ZIGP regression. """ % {'params' : base._model_params_doc, 'extra_params' : _doc_zi_params + """p : float dispersion power parameter for the GeneralizedPoisson model. p=1 for ZIGP-1 and p=2 for ZIGP-2. Default is p=2 """ + base._missing_param_doc} def __init__(self, endog, exog, exog_infl=None, offset=None, exposure=None, inflation='logit', p=2, missing='none', **kwargs): super(ZeroInflatedGeneralizedPoisson, self).__init__(endog, exog, offset=offset, inflation=inflation, exog_infl=exog_infl, exposure=exposure, missing=missing, **kwargs) self.model_main = GeneralizedPoisson(self.endog, self.exog, offset=offset, exposure=exposure, p=p) self.distribution = zigenpoisson self.k_exog += 1 self.k_extra += 1 self.exog_names.append("alpha") self.result_class = ZeroInflatedGeneralizedPoissonResults self.result_class_wrapper = ZeroInflatedGeneralizedPoissonResultsWrapper self.result_class_reg = L1ZeroInflatedGeneralizedPoissonResults self.result_class_reg_wrapper = L1ZeroInflatedGeneralizedPoissonResultsWrapper def _get_init_kwds(self): kwds = super(ZeroInflatedGeneralizedPoisson, self)._get_init_kwds() kwds['p'] = self.model_main.parameterization + 1 return kwds def _predict_prob(self, params, exog, exog_infl, exposure, offset, y_values=None): params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] p = self.model_main.parameterization + 1 if y_values is None: y_values = np.atleast_2d(np.arange(0, np.max(self.endog)+1)) if len(exog_infl.shape) < 2: transform = True w = np.atleast_2d( self.model_infl.predict(params_infl, exog_infl))[:, None] else: transform = False w = self.model_infl.predict(params_infl, exog_infl)[:, None] w[w == 1.] = np.nextafter(1, 0) mu = self.model_main.predict(params_main, exog, exposure=exposure, offset=offset)[:, None] result = self.distribution.pmf(y_values, mu, params_main[-1], p, w) return result[0] if transform else result def _predict_var(self, params, mu, prob_infl): """predict values for conditional variance V(endog | exog) Parameters ---------- params : array_like The model parameters. This is only used to extract extra params like dispersion parameter. mu : array_like Array of mean predictions for main model. prob_inlf : array_like Array of predicted probabilities of zero-inflation `w`. Returns ------- Predicted conditional variance. """ alpha = params[-1] w = prob_infl p = self.model_main.parameterization var_ = (1 - w) * mu * ((1 + alpha * mu**p)**2 + w * mu) return var_ def _get_start_params(self): with warnings.catch_warnings(): warnings.simplefilter("ignore", category=ConvergenceWarning) start_params = ZeroInflatedPoisson(self.endog, self.exog, exog_infl=self.exog_infl).fit(disp=0).params start_params = np.append(start_params, 0.1) return start_params
[docs] @Appender(ZeroInflatedPoisson.get_distribution.__doc__) def get_distribution(self, params, exog=None, exog_infl=None, exposure=None, offset=None): p = self.model_main.parameterization + 1 mu = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="mean-main") w = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="prob-main") distr = self.distribution(mu[:, None], params[-1], p, 1 - w[:, None]) return distr
[docs]class ZeroInflatedNegativeBinomialP(GenericZeroInflated): __doc__ = """ Zero Inflated Generalized Negative Binomial Model %(params)s %(extra_params)s Attributes ---------- endog : ndarray A reference to the endogenous response variable exog : ndarray A reference to the exogenous design. exog_infl : ndarray A reference to the zero-inflated exogenous design. p : scalar P denotes parametrizations for ZINB regression. p=1 for ZINB-1 and p=2 for ZINB-2. Default is p=2 """ % {'params' : base._model_params_doc, 'extra_params' : _doc_zi_params + """p : float dispersion power parameter for the NegativeBinomialP model. p=1 for ZINB-1 and p=2 for ZINM-2. Default is p=2 """ + base._missing_param_doc} def __init__(self, endog, exog, exog_infl=None, offset=None, exposure=None, inflation='logit', p=2, missing='none', **kwargs): super(ZeroInflatedNegativeBinomialP, self).__init__(endog, exog, offset=offset, inflation=inflation, exog_infl=exog_infl, exposure=exposure, missing=missing, **kwargs) self.model_main = NegativeBinomialP(self.endog, self.exog, offset=offset, exposure=exposure, p=p) self.distribution = zinegbin self.k_exog += 1 self.k_extra += 1 self.exog_names.append("alpha") self.result_class = ZeroInflatedNegativeBinomialResults self.result_class_wrapper = ZeroInflatedNegativeBinomialResultsWrapper self.result_class_reg = L1ZeroInflatedNegativeBinomialResults self.result_class_reg_wrapper = L1ZeroInflatedNegativeBinomialResultsWrapper def _get_init_kwds(self): kwds = super(ZeroInflatedNegativeBinomialP, self)._get_init_kwds() kwds['p'] = self.model_main.parameterization return kwds def _predict_prob(self, params, exog, exog_infl, exposure, offset, y_values=None): params_infl = params[:self.k_inflate] params_main = params[self.k_inflate:] p = self.model_main.parameterization if y_values is None: y_values = np.arange(0, np.max(self.endog)+1) if len(exog_infl.shape) < 2: transform = True w = np.atleast_2d( self.model_infl.predict(params_infl, exog_infl))[:, None] else: transform = False w = self.model_infl.predict(params_infl, exog_infl)[:, None] w = np.clip(w, np.finfo(float).eps, 1 - np.finfo(float).eps) mu = self.model_main.predict(params_main, exog, exposure=exposure, offset=offset)[:, None] result = self.distribution.pmf(y_values, mu, params_main[-1], p, w) return result[0] if transform else result def _predict_var(self, params, mu, prob_infl): """predict values for conditional variance V(endog | exog) Parameters ---------- params : array_like The model parameters. This is only used to extract extra params like dispersion parameter. mu : array_like Array of mean predictions for main model. prob_inlf : array_like Array of predicted probabilities of zero-inflation `w`. Returns ------- Predicted conditional variance. """ alpha = params[-1] w = prob_infl p = self.model_main.parameterization var_ = (1 - w) * mu * (1 + alpha * mu**(p - 1) + w * mu) return var_ def _get_start_params(self): with warnings.catch_warnings(): warnings.simplefilter("ignore", category=ConvergenceWarning) start_params = self.model_main.fit(disp=0, method='nm').params start_params = np.append(np.zeros(self.k_inflate), start_params) return start_params
[docs] @Appender(ZeroInflatedPoisson.get_distribution.__doc__) def get_distribution(self, params, exog=None, exog_infl=None, exposure=None, offset=None): p = self.model_main.parameterization mu = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="mean-main") w = self.predict(params, exog=exog, exog_infl=exog_infl, exposure=exposure, offset=offset, which="prob-main") distr = self.distribution(mu[:, None], params[-1], p, 1 - w[:, None]) return distr
class ZeroInflatedResults(CountResults): def get_prediction(self, exog=None, exog_infl=None, exposure=None, offset=None, which='mean', average=False, agg_weights=None, y_values=None, transform=True, row_labels=None): import statsmodels.base._prediction_inference as pred pred_kwds = { 'exog_infl': exog_infl, 'exposure': exposure, 'offset': offset, 'y_values': y_values, } res = pred.get_prediction_delta(self, exog=exog, which=which, average=average, agg_weights=agg_weights, pred_kwds=pred_kwds) return res def get_influence(self): """ Influence and outlier measures See notes section for influence measures that do not apply for zero inflated models. Returns ------- MLEInfluence The instance has methods to calculate the main influence and outlier measures as attributes. See Also -------- statsmodels.stats.outliers_influence.MLEInfluence Notes ----- ZeroInflated models have functions that are not differentiable with respect to sample endog if endog=0. This means that generalized leverage cannot be computed in the usual definition. Currently, both the generalized leverage, in `hat_matrix_diag` attribute and studetized residuals are not available. In the influence plot generalized leverage is replaced by a hat matrix diagonal that only takes combined exog into account, computed in the same way as for OLS. This is a measure for exog outliers but does not take specific features of the model into account. """ # same as sumper in DiscreteResults, only added for docstring from statsmodels.stats.outliers_influence import MLEInfluence return MLEInfluence(self)
[docs]class ZeroInflatedPoissonResults(ZeroInflatedResults): __doc__ = _discrete_results_docs % { "one_line_description": "A results class for Zero Inflated Poisson", "extra_attr": ""} @cache_readonly def _dispersion_factor(self): mu = self.predict(which='linear') w = 1 - self.predict() / np.exp(self.predict(which='linear')) return (1 + w * np.exp(mu))
[docs] def get_margeff(self, at='overall', method='dydx', atexog=None, dummy=False, count=False): """Get marginal effects of the fitted model. Not yet implemented for Zero Inflated Models """ raise NotImplementedError("not yet implemented for zero inflation")
class L1ZeroInflatedPoissonResults(L1CountResults, ZeroInflatedPoissonResults): pass class ZeroInflatedPoissonResultsWrapper(lm.RegressionResultsWrapper): pass wrap.populate_wrapper(ZeroInflatedPoissonResultsWrapper, ZeroInflatedPoissonResults) class L1ZeroInflatedPoissonResultsWrapper(lm.RegressionResultsWrapper): pass wrap.populate_wrapper(L1ZeroInflatedPoissonResultsWrapper, L1ZeroInflatedPoissonResults)
[docs]class ZeroInflatedGeneralizedPoissonResults(ZeroInflatedResults): __doc__ = _discrete_results_docs % { "one_line_description": "A results class for Zero Inflated Generalized Poisson", "extra_attr": ""} @cache_readonly def _dispersion_factor(self): p = self.model.model_main.parameterization alpha = self.params[self.model.k_inflate:][-1] mu = np.exp(self.predict(which='linear')) w = 1 - self.predict() / mu return ((1 + alpha * mu**p)**2 + w * mu)
[docs] def get_margeff(self, at='overall', method='dydx', atexog=None, dummy=False, count=False): """Get marginal effects of the fitted model. Not yet implemented for Zero Inflated Models """ raise NotImplementedError("not yet implemented for zero inflation")
class L1ZeroInflatedGeneralizedPoissonResults(L1CountResults, ZeroInflatedGeneralizedPoissonResults): pass class ZeroInflatedGeneralizedPoissonResultsWrapper( lm.RegressionResultsWrapper): pass wrap.populate_wrapper(ZeroInflatedGeneralizedPoissonResultsWrapper, ZeroInflatedGeneralizedPoissonResults) class L1ZeroInflatedGeneralizedPoissonResultsWrapper( lm.RegressionResultsWrapper): pass wrap.populate_wrapper(L1ZeroInflatedGeneralizedPoissonResultsWrapper, L1ZeroInflatedGeneralizedPoissonResults)
[docs]class ZeroInflatedNegativeBinomialResults(ZeroInflatedResults): __doc__ = _discrete_results_docs % { "one_line_description": "A results class for Zero Inflated Generalized Negative Binomial", "extra_attr": ""} @cache_readonly def _dispersion_factor(self): p = self.model.model_main.parameterization alpha = self.params[self.model.k_inflate:][-1] mu = np.exp(self.predict(which='linear')) w = 1 - self.predict() / mu return (1 + alpha * mu**(p-1) + w * mu)
[docs] def get_margeff(self, at='overall', method='dydx', atexog=None, dummy=False, count=False): """Get marginal effects of the fitted model. Not yet implemented for Zero Inflated Models """ raise NotImplementedError("not yet implemented for zero inflation")
class L1ZeroInflatedNegativeBinomialResults(L1CountResults, ZeroInflatedNegativeBinomialResults): pass class ZeroInflatedNegativeBinomialResultsWrapper( lm.RegressionResultsWrapper): pass wrap.populate_wrapper(ZeroInflatedNegativeBinomialResultsWrapper, ZeroInflatedNegativeBinomialResults) class L1ZeroInflatedNegativeBinomialResultsWrapper( lm.RegressionResultsWrapper): pass wrap.populate_wrapper(L1ZeroInflatedNegativeBinomialResultsWrapper, L1ZeroInflatedNegativeBinomialResults)