""" Procedures for fitting marginal regression models to dependent data using Generalized Estimating Equations. References ---------- KY Liang and S Zeger. "Longitudinal data analysis using generalized linear models". Biometrika (1986) 73 (1): 13-22. S Zeger and KY Liang. "Longitudinal Data Analysis for Discrete and Continuous Outcomes". Biometrics Vol. 42, No. 1 (Mar., 1986), pp. 121-130 A Rotnitzky and NP Jewell (1990). "Hypothesis testing of regression parameters in semiparametric generalized linear models for cluster correlated data", Biometrika, 77, 485-497. Xu Guo and Wei Pan (2002). "Small sample performance of the score test in GEE". http://www.sph.umn.edu/faculty1/wp-content/uploads/2012/11/rr2002-013.pdf LA Mancl LA, TA DeRouen (2001). A covariance estimator for GEE with improved small-sample properties. Biometrics. 2001 Mar;57(1):126-34. """ from statsmodels.compat.python import lzip from statsmodels.compat.pandas import Appender import numpy as np from scipy import stats import pandas as pd import patsy from collections import defaultdict from statsmodels.tools.decorators import cache_readonly import statsmodels.base.model as base # used for wrapper: import statsmodels.regression.linear_model as lm import statsmodels.base.wrapper as wrap from statsmodels.genmod import families from statsmodels.genmod.generalized_linear_model import GLM, GLMResults from statsmodels.genmod import cov_struct as cov_structs import statsmodels.genmod.families.varfuncs as varfuncs from statsmodels.genmod.families.links import Link from statsmodels.tools.sm_exceptions import (ConvergenceWarning, DomainWarning, IterationLimitWarning, ValueWarning) import warnings from statsmodels.graphics._regressionplots_doc import ( _plot_added_variable_doc, _plot_partial_residuals_doc, _plot_ceres_residuals_doc) from statsmodels.discrete.discrete_margins import ( _get_margeff_exog, _check_margeff_args, _effects_at, margeff_cov_with_se, _check_at_is_all, _transform_names, _check_discrete_args, _get_dummy_index, _get_count_index) class ParameterConstraint: """ A class for managing linear equality constraints for a parameter vector. """ def __init__(self, lhs, rhs, exog): """ Parameters ---------- lhs : ndarray A q x p matrix which is the left hand side of the constraint lhs * param = rhs. The number of constraints is q >= 1 and p is the dimension of the parameter vector. rhs : ndarray A 1-dimensional vector of length q which is the right hand side of the constraint equation. exog : ndarray The n x p exognenous data for the full model. """ # In case a row or column vector is passed (patsy linear # constraints passes a column vector). rhs = np.atleast_1d(rhs.squeeze()) if rhs.ndim > 1: raise ValueError("The right hand side of the constraint " "must be a vector.") if len(rhs) != lhs.shape[0]: raise ValueError("The number of rows of the left hand " "side constraint matrix L must equal " "the length of the right hand side " "constraint vector R.") self.lhs = lhs self.rhs = rhs # The columns of lhs0 are an orthogonal basis for the # orthogonal complement to row(lhs), the columns of lhs1 are # an orthogonal basis for row(lhs). The columns of lhsf = # [lhs0, lhs1] are mutually orthogonal. lhs_u, lhs_s, lhs_vt = np.linalg.svd(lhs.T, full_matrices=1) self.lhs0 = lhs_u[:, len(lhs_s):] self.lhs1 = lhs_u[:, 0:len(lhs_s)] self.lhsf = np.hstack((self.lhs0, self.lhs1)) # param0 is one solution to the underdetermined system # L * param = R. self.param0 = np.dot(self.lhs1, np.dot(lhs_vt, self.rhs) / lhs_s) self._offset_increment = np.dot(exog, self.param0) self.orig_exog = exog self.exog_fulltrans = np.dot(exog, self.lhsf) def offset_increment(self): """ Returns a vector that should be added to the offset vector to accommodate the constraint. Parameters ---------- exog : array_like The exogeneous data for the model. """ return self._offset_increment def reduced_exog(self): """ Returns a linearly transformed exog matrix whose columns span the constrained model space. Parameters ---------- exog : array_like The exogeneous data for the model. """ return self.exog_fulltrans[:, 0:self.lhs0.shape[1]] def restore_exog(self): """ Returns the full exog matrix before it was reduced to satisfy the constraint. """ return self.orig_exog def unpack_param(self, params): """ Converts the parameter vector `params` from reduced to full coordinates. """ return self.param0 + np.dot(self.lhs0, params) def unpack_cov(self, bcov): """ Converts the covariance matrix `bcov` from reduced to full coordinates. """ return np.dot(self.lhs0, np.dot(bcov, self.lhs0.T)) _gee_init_doc = """ Marginal regression model fit using Generalized Estimating Equations. GEE can be used to fit Generalized Linear Models (GLMs) when the data have a grouped structure, and the observations are possibly correlated within groups but not between groups. Parameters ---------- endog : array_like 1d array of endogenous values (i.e. responses, outcomes, dependent variables, or 'Y' values). exog : array_like 2d array of exogeneous values (i.e. covariates, predictors, independent variables, regressors, or 'X' values). A `nobs x k` array where `nobs` is the number of observations and `k` is the number of regressors. An intercept is not included by default and should be added by the user. See `statsmodels.tools.add_constant`. groups : array_like A 1d array of length `nobs` containing the group labels. time : array_like A 2d array of time (or other index) values, used by some dependence structures to define similarity relationships among observations within a cluster. family : family class instance %(family_doc)s cov_struct : CovStruct class instance The default is Independence. To specify an exchangeable structure use cov_struct = Exchangeable(). See statsmodels.genmod.cov_struct.CovStruct for more information. offset : array_like An offset to be included in the fit. If provided, must be an array whose length is the number of rows in exog. dep_data : array_like Additional data passed to the dependence structure. constraint : (ndarray, ndarray) If provided, the constraint is a tuple (L, R) such that the model parameters are estimated under the constraint L * param = R, where L is a q x p matrix and R is a q-dimensional vector. If constraint is provided, a score test is performed to compare the constrained model to the unconstrained model. update_dep : bool If true, the dependence parameters are optimized, otherwise they are held fixed at their starting values. weights : array_like An array of case weights to use in the analysis. %(extra_params)s See Also -------- statsmodels.genmod.families.family :ref:`families` :ref:`links` Notes ----- Only the following combinations make sense for family and link :: + ident log logit probit cloglog pow opow nbinom loglog logc Gaussian | x x x inv Gaussian | x x x binomial | x x x x x x x x x Poisson | x x x neg binomial | x x x x gamma | x x x Not all of these link functions are currently available. Endog and exog are references so that if the data they refer to are already arrays and these arrays are changed, endog and exog will change. The "robust" covariance type is the standard "sandwich estimator" (e.g. Liang and Zeger (1986)). It is the default here and in most other packages. The "naive" estimator gives smaller standard errors, but is only correct if the working correlation structure is correctly specified. The "bias reduced" estimator of Mancl and DeRouen (Biometrics, 2001) reduces the downward bias of the robust estimator. The robust covariance provided here follows Liang and Zeger (1986) and agrees with R's gee implementation. To obtain the robust standard errors reported in Stata, multiply by sqrt(N / (N - g)), where N is the total sample size, and g is the average group size. %(notes)s Examples -------- %(example)s """ _gee_nointercept = """ The nominal and ordinal GEE models should not have an intercept (either implicit or explicit). Use "0 + " in a formula to suppress the intercept. """ _gee_family_doc = """\ The default is Gaussian. To specify the binomial distribution use `family=sm.families.Binomial()`. Each family can take a link instance as an argument. See statsmodels.genmod.families.family for more information.""" _gee_ordinal_family_doc = """\ The only family supported is `Binomial`. The default `Logit` link may be replaced with `probit` if desired.""" _gee_nominal_family_doc = """\ The default value `None` uses a multinomial logit family specifically designed for use with GEE. Setting this argument to a non-default value is not currently supported.""" _gee_fit_doc = """ Fits a marginal regression model using generalized estimating equations (GEE). Parameters ---------- maxiter : int The maximum number of iterations ctol : float The convergence criterion for stopping the Gauss-Seidel iterations start_params : array_like A vector of starting values for the regression coefficients. If None, a default is chosen. params_niter : int The number of Gauss-Seidel updates of the mean structure parameters that take place prior to each update of the dependence structure. first_dep_update : int No dependence structure updates occur before this iteration number. cov_type : str One of "robust", "naive", or "bias_reduced". ddof_scale : scalar or None The scale parameter is estimated as the sum of squared Pearson residuals divided by `N - ddof_scale`, where N is the total sample size. If `ddof_scale` is None, the number of covariates (including an intercept if present) is used. scaling_factor : scalar The estimated covariance of the parameter estimates is scaled by this value. Default is 1, Stata uses N / (N - g), where N is the total sample size and g is the average group size. scale : str or float, optional `scale` can be None, 'X2', or a float If a float, its value is used as the scale parameter. The default value is None, which uses `X2` (Pearson's chi-square) for Gamma, Gaussian, and Inverse Gaussian. The default is 1 for the Binomial and Poisson families. Returns ------- An instance of the GEEResults class or subclass Notes ----- If convergence difficulties occur, increase the values of `first_dep_update` and/or `params_niter`. Setting `first_dep_update` to a greater value (e.g. ~10-20) causes the algorithm to move close to the GLM solution before attempting to identify the dependence structure. For the Gaussian family, there is no benefit to setting `params_niter` to a value greater than 1, since the mean structure parameters converge in one step. """ _gee_results_doc = """ Attributes ---------- cov_params_default : ndarray default covariance of the parameter estimates. Is chosen among one of the following three based on `cov_type` cov_robust : ndarray covariance of the parameter estimates that is robust cov_naive : ndarray covariance of the parameter estimates that is not robust to correlation or variance misspecification cov_robust_bc : ndarray covariance of the parameter estimates that is robust and bias reduced converged : bool indicator for convergence of the optimization. True if the norm of the score is smaller than a threshold cov_type : str string indicating whether a "robust", "naive" or "bias_reduced" covariance is used as default fit_history : dict Contains information about the iterations. fittedvalues : ndarray Linear predicted values for the fitted model. dot(exog, params) model : class instance Pointer to GEE model instance that called `fit`. normalized_cov_params : ndarray See GEE docstring params : ndarray The coefficients of the fitted model. Note that interpretation of the coefficients often depends on the distribution family and the data. scale : float The estimate of the scale / dispersion for the model fit. See GEE.fit for more information. score_norm : float norm of the score at the end of the iterative estimation. bse : ndarray The standard errors of the fitted GEE parameters. """ _gee_example = """ Logistic regression with autoregressive working dependence: >>> import statsmodels.api as sm >>> family = sm.families.Binomial() >>> va = sm.cov_struct.Autoregressive() >>> model = sm.GEE(endog, exog, group, family=family, cov_struct=va) >>> result = model.fit() >>> print(result.summary()) Use formulas to fit a Poisson GLM with independent working dependence: >>> import statsmodels.api as sm >>> fam = sm.families.Poisson() >>> ind = sm.cov_struct.Independence() >>> model = sm.GEE.from_formula("y ~ age + trt + base", "subject", data, cov_struct=ind, family=fam) >>> result = model.fit() >>> print(result.summary()) Equivalent, using the formula API: >>> import statsmodels.api as sm >>> import statsmodels.formula.api as smf >>> fam = sm.families.Poisson() >>> ind = sm.cov_struct.Independence() >>> model = smf.gee("y ~ age + trt + base", "subject", data, cov_struct=ind, family=fam) >>> result = model.fit() >>> print(result.summary()) """ _gee_ordinal_example = """ Fit an ordinal regression model using GEE, with "global odds ratio" dependence: >>> import statsmodels.api as sm >>> gor = sm.cov_struct.GlobalOddsRatio("ordinal") >>> model = sm.OrdinalGEE(endog, exog, groups, cov_struct=gor) >>> result = model.fit() >>> print(result.summary()) Using formulas: >>> import statsmodels.formula.api as smf >>> model = smf.ordinal_gee("y ~ 0 + x1 + x2", groups, data, cov_struct=gor) >>> result = model.fit() >>> print(result.summary()) """ _gee_nominal_example = """ Fit a nominal regression model using GEE: >>> import statsmodels.api as sm >>> import statsmodels.formula.api as smf >>> gor = sm.cov_struct.GlobalOddsRatio("nominal") >>> model = sm.NominalGEE(endog, exog, groups, cov_struct=gor) >>> result = model.fit() >>> print(result.summary()) Using formulas: >>> import statsmodels.api as sm >>> model = sm.NominalGEE.from_formula("y ~ 0 + x1 + x2", groups, data, cov_struct=gor) >>> result = model.fit() >>> print(result.summary()) Using the formula API: >>> import statsmodels.formula.api as smf >>> model = smf.nominal_gee("y ~ 0 + x1 + x2", groups, data, cov_struct=gor) >>> result = model.fit() >>> print(result.summary()) """ def _check_args(endog, exog, groups, time, offset, exposure): if endog.size != exog.shape[0]: raise ValueError("Leading dimension of 'exog' should match " "length of 'endog'") if groups.size != endog.size: raise ValueError("'groups' and 'endog' should have the same size") if time is not None and (time.size != endog.size): raise ValueError("'time' and 'endog' should have the same size") if offset is not None and (offset.size != endog.size): raise ValueError("'offset and 'endog' should have the same size") if exposure is not None and (exposure.size != endog.size): raise ValueError("'exposure' and 'endog' should have the same size") class GEE(GLM): __doc__ = ( " Marginal Regression Model using Generalized Estimating " "Equations.\n" + _gee_init_doc % {'extra_params': base._missing_param_doc, 'family_doc': _gee_family_doc, 'example': _gee_example, 'notes': ""}) cached_means = None def __init__(self, endog, exog, groups, time=None, family=None, cov_struct=None, missing='none', offset=None, exposure=None, dep_data=None, constraint=None, update_dep=True, weights=None, **kwargs): if type(self) is GEE: self._check_kwargs(kwargs) if family is not None: if not isinstance(family.link, tuple(family.safe_links)): msg = ("The {0} link function does not respect the " "domain of the {1} family.") warnings.warn(msg.format(family.link.__class__.__name__, family.__class__.__name__), DomainWarning) groups = np.asarray(groups) # in case groups is pandas if "missing_idx" in kwargs and kwargs["missing_idx"] is not None: # If here, we are entering from super.from_formula; missing # has already been dropped from endog and exog, but not from # the other variables. ii = ~kwargs["missing_idx"] groups = groups[ii] if time is not None: time = time[ii] if offset is not None: offset = offset[ii] if exposure is not None: exposure = exposure[ii] del kwargs["missing_idx"] self.missing = missing self.dep_data = dep_data self.constraint = constraint self.update_dep = update_dep self._fit_history = defaultdict(list) # Pass groups, time, offset, and dep_data so they are # processed for missing data along with endog and exog. # Calling super creates self.exog, self.endog, etc. as # ndarrays and the original exog, endog, etc. are # self.data.endog, etc. super().__init__(endog, exog, groups=groups, time=time, offset=offset, exposure=exposure, weights=weights, dep_data=dep_data, missing=missing, family=family, **kwargs) _check_args( self.endog, self.exog, self.groups, self.time, getattr(self, "offset", None), getattr(self, "exposure", None), ) self._init_keys.extend(["update_dep", "constraint", "family", "cov_struct"]) # remove keys added by super that are not supported try: self._init_keys.remove("freq_weights") self._init_keys.remove("var_weights") except ValueError: pass # Handle the family argument if family is None: family = families.Gaussian() else: if not issubclass(family.__class__, families.Family): raise ValueError("GEE: `family` must be a genmod " "family instance") self.family = family # Handle the cov_struct argument if cov_struct is None: cov_struct = cov_structs.Independence() else: if not issubclass(cov_struct.__class__, cov_structs.CovStruct): raise ValueError("GEE: `cov_struct` must be a genmod " "cov_struct instance") self.cov_struct = cov_struct # Handle the constraint self.constraint = None if constraint is not None: if len(constraint) != 2: raise ValueError("GEE: `constraint` must be a 2-tuple.") if constraint[0].shape[1] != self.exog.shape[1]: raise ValueError( "GEE: the left hand side of the constraint must have " "the same number of columns as the exog matrix.") self.constraint = ParameterConstraint(constraint[0], constraint[1], self.exog) if self._offset_exposure is not None: self._offset_exposure += self.constraint.offset_increment() else: self._offset_exposure = ( self.constraint.offset_increment().copy()) self.exog = self.constraint.reduced_exog() # Create list of row indices for each group group_labels, ix = np.unique(self.groups, return_inverse=True) se = pd.Series(index=np.arange(len(ix)), dtype="int") gb = se.groupby(ix).groups dk = [(lb, np.asarray(gb[k])) for k, lb in enumerate(group_labels)] self.group_indices = dict(dk) self.group_labels = group_labels # Convert the data to the internal representation, which is a # list of arrays, corresponding to the groups. self.endog_li = self.cluster_list(self.endog) self.exog_li = self.cluster_list(self.exog) if self.weights is not None: self.weights_li = self.cluster_list(self.weights) self.num_group = len(self.endog_li) # Time defaults to a 1d grid with equal spacing if self.time is not None: if self.time.ndim == 1: self.time = self.time[:, None] self.time_li = self.cluster_list(self.time) else: self.time_li = \ [np.arange(len(y), dtype=np.float64)[:, None] for y in self.endog_li] self.time = np.concatenate(self.time_li) if (self._offset_exposure is None or (np.isscalar(self._offset_exposure) and self._offset_exposure == 0.)): self.offset_li = None else: self.offset_li = self.cluster_list(self._offset_exposure) if constraint is not None: self.constraint.exog_fulltrans_li = \ self.cluster_list(self.constraint.exog_fulltrans) self.family = family self.cov_struct.initialize(self) # Total sample size group_ns = [len(y) for y in self.endog_li] self.nobs = sum(group_ns) # The following are column based, not on rank see #1928 self.df_model = self.exog.shape[1] - 1 # assumes constant self.df_resid = self.nobs - self.exog.shape[1] # Skip the covariance updates if all groups have a single # observation (reduces to fitting a GLM). maxgroup = max([len(x) for x in self.endog_li]) if maxgroup == 1: self.update_dep = False # Override to allow groups and time to be passed as variable # names. @classmethod def from_formula(cls, formula, groups, data, subset=None, time=None, offset=None, exposure=None, *args, **kwargs): """ Create a GEE model instance from a formula and dataframe. Parameters ---------- formula : str or generic Formula object The formula specifying the model groups : array_like or string Array of grouping labels. If a string, this is the name of a variable in `data` that contains the grouping labels. data : array_like The data for the model. subset : array_like An array-like object of booleans, integers, or index values that indicate the subset of the data to used when fitting the model. time : array_like or string The time values, used for dependence structures involving distances between observations. If a string, this is the name of a variable in `data` that contains the time values. offset : array_like or string The offset values, added to the linear predictor. If a string, this is the name of a variable in `data` that contains the offset values. exposure : array_like or string The exposure values, only used if the link function is the logarithm function, in which case the log of `exposure` is added to the offset (if any). If a string, this is the name of a variable in `data` that contains the offset values. {missing_param_doc} args : extra arguments These are passed to the model kwargs : extra keyword arguments These are passed to the model with two exceptions. `dep_data` is processed as described below. The ``eval_env`` keyword is passed to patsy. It can be either a :class:`patsy:patsy.EvalEnvironment` object or an integer indicating the depth of the namespace to use. For example, the default ``eval_env=0`` uses the calling namespace. If you wish to use a "clean" environment set ``eval_env=-1``. Optional arguments ------------------ dep_data : str or array_like Data used for estimating the dependence structure. See specific dependence structure classes (e.g. Nested) for details. If `dep_data` is a string, it is interpreted as a formula that is applied to `data`. If it is an array, it must be an array of strings corresponding to column names in `data`. Otherwise it must be an array-like with the same number of rows as data. Returns ------- model : GEE model instance Notes ----- `data` must define __getitem__ with the keys in the formula terms args and kwargs are passed on to the model instantiation. E.g., a numpy structured or rec array, a dictionary, or a pandas DataFrame. """.format(missing_param_doc=base._missing_param_doc) groups_name = "Groups" if isinstance(groups, str): groups_name = groups groups = data[groups] if isinstance(time, str): time = data[time] if isinstance(offset, str): offset = data[offset] if isinstance(exposure, str): exposure = data[exposure] dep_data = kwargs.get("dep_data") dep_data_names = None if dep_data is not None: if isinstance(dep_data, str): dep_data = patsy.dmatrix(dep_data, data, return_type='dataframe') dep_data_names = dep_data.columns.tolist() else: dep_data_names = list(dep_data) dep_data = data[dep_data] kwargs["dep_data"] = np.asarray(dep_data) family = None if "family" in kwargs: family = kwargs["family"] del kwargs["family"] model = super().from_formula(formula, data=data, subset=subset, groups=groups, time=time, offset=offset, exposure=exposure, family=family, *args, **kwargs) if dep_data_names is not None: model._dep_data_names = dep_data_names model._groups_name = groups_name return model def cluster_list(self, array): """ Returns `array` split into subarrays corresponding to the cluster structure. """ if array.ndim == 1: return [np.array(array[self.group_indices[k]]) for k in self.group_labels] else: return [np.array(array[self.group_indices[k], :]) for k in self.group_labels] def compare_score_test(self, submodel): """ Perform a score test for the given submodel against this model. Parameters ---------- submodel : GEEResults instance A fitted GEE model that is a submodel of this model. Returns ------- A dictionary with keys "statistic", "p-value", and "df", containing the score test statistic, its chi^2 p-value, and the degrees of freedom used to compute the p-value. Notes ----- The score test can be performed without calling 'fit' on the larger model. The provided submodel must be obtained from a fitted GEE. This method performs the same score test as can be obtained by fitting the GEE with a linear constraint and calling `score_test` on the results. References ---------- Xu Guo and Wei Pan (2002). "Small sample performance of the score test in GEE". http://www.sph.umn.edu/faculty1/wp-content/uploads/2012/11/rr2002-013.pdf """ # Since the model has not been fit, its scaletype has not been # set. So give it the scaletype of the submodel. self.scaletype = submodel.model.scaletype # Check consistency between model and submodel (not a comprehensive # check) submod = submodel.model if self.exog.shape[0] != submod.exog.shape[0]: msg = "Model and submodel have different numbers of cases." raise ValueError(msg) if self.exog.shape[1] == submod.exog.shape[1]: msg = "Model and submodel have the same number of variables" warnings.warn(msg) if not isinstance(self.family, type(submod.family)): msg = "Model and submodel have different GLM families." warnings.warn(msg) if not isinstance(self.cov_struct, type(submod.cov_struct)): warnings.warn("Model and submodel have different GEE covariance " "structures.") if not np.equal(self.weights, submod.weights).all(): msg = "Model and submodel should have the same weights." warnings.warn(msg) # Get the positions of the submodel variables in the # parent model qm, qc = _score_test_submodel(self, submodel.model) if qm is None: msg = "The provided model is not a submodel." raise ValueError(msg) # Embed the submodel params into a params vector for the # parent model params_ex = np.dot(qm, submodel.params) # Attempt to preserve the state of the parent model cov_struct_save = self.cov_struct import copy cached_means_save = copy.deepcopy(self.cached_means) # Get the score vector of the submodel params in # the parent model self.cov_struct = submodel.cov_struct self.update_cached_means(params_ex) _, score = self._update_mean_params() if score is None: msg = "Singular matrix encountered in GEE score test" warnings.warn(msg, ConvergenceWarning) return None if not hasattr(self, "ddof_scale"): self.ddof_scale = self.exog.shape[1] if not hasattr(self, "scaling_factor"): self.scaling_factor = 1 _, ncov1, cmat = self._covmat() score2 = np.dot(qc.T, score) try: amat = np.linalg.inv(ncov1) except np.linalg.LinAlgError: amat = np.linalg.pinv(ncov1) bmat_11 = np.dot(qm.T, np.dot(cmat, qm)) bmat_22 = np.dot(qc.T, np.dot(cmat, qc)) bmat_12 = np.dot(qm.T, np.dot(cmat, qc)) amat_11 = np.dot(qm.T, np.dot(amat, qm)) amat_12 = np.dot(qm.T, np.dot(amat, qc)) try: ab = np.linalg.solve(amat_11, bmat_12) except np.linalg.LinAlgError: ab = np.dot(np.linalg.pinv(amat_11), bmat_12) score_cov = bmat_22 - np.dot(amat_12.T, ab) try: aa = np.linalg.solve(amat_11, amat_12) except np.linalg.LinAlgError: aa = np.dot(np.linalg.pinv(amat_11), amat_12) score_cov -= np.dot(bmat_12.T, aa) try: ab = np.linalg.solve(amat_11, bmat_11) except np.linalg.LinAlgError: ab = np.dot(np.linalg.pinv(amat_11), bmat_11) try: aa = np.linalg.solve(amat_11, amat_12) except np.linalg.LinAlgError: aa = np.dot(np.linalg.pinv(amat_11), amat_12) score_cov += np.dot(amat_12.T, np.dot(ab, aa)) # Attempt to restore state self.cov_struct = cov_struct_save self.cached_means = cached_means_save from scipy.stats.distributions import chi2 try: sc2 = np.linalg.solve(score_cov, score2) except np.linalg.LinAlgError: sc2 = np.dot(np.linalg.pinv(score_cov), score2) score_statistic = np.dot(score2, sc2) score_df = len(score2) score_pvalue = 1 - chi2.cdf(score_statistic, score_df) return {"statistic": score_statistic, "df": score_df, "p-value": score_pvalue} def estimate_scale(self): """ Estimate the dispersion/scale. """ if self.scaletype is None: if isinstance(self.family, (families.Binomial, families.Poisson, families.NegativeBinomial, _Multinomial)): return 1. elif isinstance(self.scaletype, float): return np.array(self.scaletype) endog = self.endog_li cached_means = self.cached_means nobs = self.nobs varfunc = self.family.variance scale = 0. fsum = 0. for i in range(self.num_group): if len(endog[i]) == 0: continue expval, _ = cached_means[i] sdev = np.sqrt(varfunc(expval)) resid = (endog[i] - expval) / sdev if self.weights is not None: f = self.weights_li[i] scale += np.sum(f * (resid ** 2)) fsum += f.sum() else: scale += np.sum(resid ** 2) fsum += len(resid) scale /= (fsum * (nobs - self.ddof_scale) / float(nobs)) return scale def mean_deriv(self, exog, lin_pred): """ Derivative of the expected endog with respect to the parameters. Parameters ---------- exog : array_like The exogeneous data at which the derivative is computed. lin_pred : array_like The values of the linear predictor. Returns ------- The value of the derivative of the expected endog with respect to the parameter vector. Notes ----- If there is an offset or exposure, it should be added to `lin_pred` prior to calling this function. """ idl = self.family.link.inverse_deriv(lin_pred) dmat = exog * idl[:, None] return dmat def mean_deriv_exog(self, exog, params, offset_exposure=None): """ Derivative of the expected endog with respect to exog. Parameters ---------- exog : array_like Values of the independent variables at which the derivative is calculated. params : array_like Parameter values at which the derivative is calculated. offset_exposure : array_like, optional Combined offset and exposure. Returns ------- The derivative of the expected endog with respect to exog. """ lin_pred = np.dot(exog, params) if offset_exposure is not None: lin_pred += offset_exposure idl = self.family.link.inverse_deriv(lin_pred) dmat = np.outer(idl, params) return dmat def _update_mean_params(self): """ Returns ------- update : array_like The update vector such that params + update is the next iterate when solving the score equations. score : array_like The current value of the score equations, not incorporating the scale parameter. If desired, multiply this vector by the scale parameter to incorporate the scale. """ endog = self.endog_li exog = self.exog_li weights = getattr(self, "weights_li", None) cached_means = self.cached_means varfunc = self.family.variance bmat, score = 0, 0 for i in range(self.num_group): expval, lpr = cached_means[i] resid = endog[i] - expval dmat = self.mean_deriv(exog[i], lpr) sdev = np.sqrt(varfunc(expval)) if weights is not None: w = weights[i] wresid = resid * w wdmat = dmat * w[:, None] else: wresid = resid wdmat = dmat rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (wdmat, wresid)) if rslt is None: return None, None vinv_d, vinv_resid = tuple(rslt) bmat += np.dot(dmat.T, vinv_d) score += np.dot(dmat.T, vinv_resid) try: update = np.linalg.solve(bmat, score) except np.linalg.LinAlgError: update = np.dot(np.linalg.pinv(bmat), score) self._fit_history["cov_adjust"].append( self.cov_struct.cov_adjust) return update, score def update_cached_means(self, mean_params): """ cached_means should always contain the most recent calculation of the group-wise mean vectors. This function should be called every time the regression parameters are changed, to keep the cached means up to date. """ endog = self.endog_li exog = self.exog_li offset = self.offset_li linkinv = self.family.link.inverse self.cached_means = [] for i in range(self.num_group): if len(endog[i]) == 0: continue lpr = np.dot(exog[i], mean_params) if offset is not None: lpr += offset[i] expval = linkinv(lpr) self.cached_means.append((expval, lpr)) def _covmat(self): """ Returns the sampling covariance matrix of the regression parameters and related quantities. Returns ------- cov_robust : array_like The robust, or sandwich estimate of the covariance, which is meaningful even if the working covariance structure is incorrectly specified. cov_naive : array_like The model-based estimate of the covariance, which is meaningful if the covariance structure is correctly specified. cmat : array_like The center matrix of the sandwich expression, used in obtaining score test results. """ endog = self.endog_li exog = self.exog_li weights = getattr(self, "weights_li", None) varfunc = self.family.variance cached_means = self.cached_means # Calculate the naive (model-based) and robust (sandwich) # covariances. bmat, cmat = 0, 0 for i in range(self.num_group): expval, lpr = cached_means[i] resid = endog[i] - expval dmat = self.mean_deriv(exog[i], lpr) sdev = np.sqrt(varfunc(expval)) if weights is not None: w = weights[i] wresid = resid * w wdmat = dmat * w[:, None] else: wresid = resid wdmat = dmat rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (wdmat, wresid)) if rslt is None: return None, None, None, None vinv_d, vinv_resid = tuple(rslt) bmat += np.dot(dmat.T, vinv_d) dvinv_resid = np.dot(dmat.T, vinv_resid) cmat += np.outer(dvinv_resid, dvinv_resid) scale = self.estimate_scale() try: bmati = np.linalg.inv(bmat) except np.linalg.LinAlgError: bmati = np.linalg.pinv(bmat) cov_naive = bmati * scale cov_robust = np.dot(bmati, np.dot(cmat, bmati)) cov_naive *= self.scaling_factor cov_robust *= self.scaling_factor return cov_robust, cov_naive, cmat # Calculate the bias-corrected sandwich estimate of Mancl and # DeRouen. def _bc_covmat(self, cov_naive): cov_naive = cov_naive / self.scaling_factor endog = self.endog_li exog = self.exog_li varfunc = self.family.variance cached_means = self.cached_means scale = self.estimate_scale() bcm = 0 for i in range(self.num_group): expval, lpr = cached_means[i] resid = endog[i] - expval dmat = self.mean_deriv(exog[i], lpr) sdev = np.sqrt(varfunc(expval)) rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (dmat,)) if rslt is None: return None vinv_d = rslt[0] vinv_d /= scale hmat = np.dot(vinv_d, cov_naive) hmat = np.dot(hmat, dmat.T).T f = self.weights_li[i] if self.weights is not None else 1. aresid = np.linalg.solve(np.eye(len(resid)) - hmat, resid) rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (aresid,)) if rslt is None: return None srt = rslt[0] srt = f * np.dot(dmat.T, srt) / scale bcm += np.outer(srt, srt) cov_robust_bc = np.dot(cov_naive, np.dot(bcm, cov_naive)) cov_robust_bc *= self.scaling_factor return cov_robust_bc def _starting_params(self): if np.isscalar(self._offset_exposure): offset = None else: offset = self._offset_exposure model = GLM(self.endog, self.exog, family=self.family, offset=offset, freq_weights=self.weights) result = model.fit() return result.params @Appender(_gee_fit_doc) def fit(self, maxiter=60, ctol=1e-6, start_params=None, params_niter=1, first_dep_update=0, cov_type='robust', ddof_scale=None, scaling_factor=1., scale=None): self.scaletype = scale # Subtract this number from the total sample size when # normalizing the scale parameter estimate. if ddof_scale is None: self.ddof_scale = self.exog.shape[1] else: if not ddof_scale >= 0: raise ValueError( "ddof_scale must be a non-negative number or None") self.ddof_scale = ddof_scale self.scaling_factor = scaling_factor self._fit_history = defaultdict(list) if self.weights is not None and cov_type == 'naive': raise ValueError("when using weights, cov_type may not be naive") if start_params is None: mean_params = self._starting_params() else: start_params = np.asarray(start_params) mean_params = start_params.copy() self.update_cached_means(mean_params) del_params = -1. num_assoc_updates = 0 for itr in range(maxiter): update, score = self._update_mean_params() if update is None: warnings.warn("Singular matrix encountered in GEE update", ConvergenceWarning) break mean_params += update self.update_cached_means(mean_params) # L2 norm of the change in mean structure parameters at # this iteration. del_params = np.sqrt(np.sum(score ** 2)) self._fit_history['params'].append(mean_params.copy()) self._fit_history['score'].append(score) self._fit_history['dep_params'].append( self.cov_struct.dep_params) # Do not exit until the association parameters have been # updated at least once. if (del_params < ctol and (num_assoc_updates > 0 or self.update_dep is False)): break # Update the dependence structure if (self.update_dep and (itr % params_niter) == 0 and (itr >= first_dep_update)): self._update_assoc(mean_params) num_assoc_updates += 1 if del_params >= ctol: warnings.warn("Iteration limit reached prior to convergence", IterationLimitWarning) if mean_params is None: warnings.warn("Unable to estimate GEE parameters.", ConvergenceWarning) return None bcov, ncov, _ = self._covmat() if bcov is None: warnings.warn("Estimated covariance structure for GEE " "estimates is singular", ConvergenceWarning) return None bc_cov = None if cov_type == "bias_reduced": bc_cov = self._bc_covmat(ncov) if self.constraint is not None: x = mean_params.copy() mean_params, bcov = self._handle_constraint(mean_params, bcov) if mean_params is None: warnings.warn("Unable to estimate constrained GEE " "parameters.", ConvergenceWarning) return None y, ncov = self._handle_constraint(x, ncov) if y is None: warnings.warn("Unable to estimate constrained GEE " "parameters.", ConvergenceWarning) return None if bc_cov is not None: y, bc_cov = self._handle_constraint(x, bc_cov) if x is None: warnings.warn("Unable to estimate constrained GEE " "parameters.", ConvergenceWarning) return None scale = self.estimate_scale() # kwargs to add to results instance, need to be available in __init__ res_kwds = dict(cov_type=cov_type, cov_robust=bcov, cov_naive=ncov, cov_robust_bc=bc_cov) # The superclass constructor will multiply the covariance # matrix argument bcov by scale, which we do not want, so we # divide bcov by the scale parameter here results = GEEResults(self, mean_params, bcov / scale, scale, cov_type=cov_type, use_t=False, attr_kwds=res_kwds) # attributes not needed during results__init__ results.fit_history = self._fit_history self.fit_history = defaultdict(list) results.score_norm = del_params results.converged = (del_params < ctol) results.cov_struct = self.cov_struct results.params_niter = params_niter results.first_dep_update = first_dep_update results.ctol = ctol results.maxiter = maxiter # These will be copied over to subclasses when upgrading. results._props = ["cov_type", "use_t", "cov_params_default", "cov_robust", "cov_naive", "cov_robust_bc", "fit_history", "score_norm", "converged", "cov_struct", "params_niter", "first_dep_update", "ctol", "maxiter"] return GEEResultsWrapper(results) def _update_regularized(self, params, pen_wt, scad_param, eps): sn, hm = 0, 0 for i in range(self.num_group): expval, _ = self.cached_means[i] resid = self.endog_li[i] - expval sdev = np.sqrt(self.family.variance(expval)) ex = self.exog_li[i] * sdev[:, None]**2 rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (resid, ex)) sn0 = rslt[0] sn += np.dot(ex.T, sn0) hm0 = rslt[1] hm += np.dot(ex.T, hm0) # Wang et al. divide sn here by num_group, but that # seems to be incorrect ap = np.abs(params) clipped = np.clip(scad_param * pen_wt - ap, 0, np.inf) en = pen_wt * clipped * (ap > pen_wt) en /= (scad_param - 1) * pen_wt en += pen_wt * (ap <= pen_wt) en /= eps + ap hm.flat[::hm.shape[0] + 1] += self.num_group * en sn -= self.num_group * en * params try: update = np.linalg.solve(hm, sn) except np.linalg.LinAlgError: update = np.dot(np.linalg.pinv(hm), sn) msg = "Encountered singularity in regularized GEE update" warnings.warn(msg) hm *= self.estimate_scale() return update, hm def _regularized_covmat(self, mean_params): self.update_cached_means(mean_params) ma = 0 for i in range(self.num_group): expval, _ = self.cached_means[i] resid = self.endog_li[i] - expval sdev = np.sqrt(self.family.variance(expval)) ex = self.exog_li[i] * sdev[:, None]**2 rslt = self.cov_struct.covariance_matrix_solve( expval, i, sdev, (resid,)) ma0 = np.dot(ex.T, rslt[0]) ma += np.outer(ma0, ma0) return ma def fit_regularized(self, pen_wt, scad_param=3.7, maxiter=100, ddof_scale=None, update_assoc=5, ctol=1e-5, ztol=1e-3, eps=1e-6, scale=None): """ Regularized estimation for GEE. Parameters ---------- pen_wt : float The penalty weight (a non-negative scalar). scad_param : float Non-negative scalar determining the shape of the Scad penalty. maxiter : int The maximum number of iterations. ddof_scale : int Value to subtract from `nobs` when calculating the denominator degrees of freedom for t-statistics, defaults to the number of columns in `exog`. update_assoc : int The dependence parameters are updated every `update_assoc` iterations of the mean structure parameter updates. ctol : float Convergence criterion, default is one order of magnitude smaller than proposed in section 3.1 of Wang et al. ztol : float Coefficients smaller than this value are treated as being zero, default is based on section 5 of Wang et al. eps : non-negative scalar Numerical constant, see section 3.2 of Wang et al. scale : float or string If a float, this value is used as the scale parameter. If "X2", the scale parameter is always estimated using Pearson's chi-square method (e.g. as in a quasi-Poisson analysis). If None, the default approach for the family is used to estimate the scale parameter. Returns ------- GEEResults instance. Note that not all methods of the results class make sense when the model has been fit with regularization. Notes ----- This implementation assumes that the link is canonical. References ---------- Wang L, Zhou J, Qu A. (2012). Penalized generalized estimating equations for high-dimensional longitudinal data analysis. Biometrics. 2012 Jun;68(2):353-60. doi: 10.1111/j.1541-0420.2011.01678.x. https://www.ncbi.nlm.nih.gov/pubmed/21955051 http://users.stat.umn.edu/~wangx346/research/GEE_selection.pdf """ self.scaletype = scale mean_params = np.zeros(self.exog.shape[1]) self.update_cached_means(mean_params) converged = False fit_history = defaultdict(list) # Subtract this number from the total sample size when # normalizing the scale parameter estimate. if ddof_scale is None: self.ddof_scale = self.exog.shape[1] else: if not ddof_scale >= 0: raise ValueError( "ddof_scale must be a non-negative number or None") self.ddof_scale = ddof_scale # Keep this private for now. In some cases the early steps are # very small so it seems necessary to ensure a certain minimum # number of iterations before testing for convergence. miniter = 20 for itr in range(maxiter): update, hm = self._update_regularized( mean_params, pen_wt, scad_param, eps) if update is None: msg = "Singular matrix encountered in regularized GEE update" warnings.warn(msg, ConvergenceWarning) break if itr > miniter and np.sqrt(np.sum(update**2)) < ctol: converged = True break mean_params += update fit_history['params'].append(mean_params.copy()) self.update_cached_means(mean_params) if itr != 0 and (itr % update_assoc == 0): self._update_assoc(mean_params) if not converged: msg = "GEE.fit_regularized did not converge" warnings.warn(msg) mean_params[np.abs(mean_params) < ztol] = 0 self._update_assoc(mean_params) ma = self._regularized_covmat(mean_params) cov = np.linalg.solve(hm, ma) cov = np.linalg.solve(hm, cov.T) # kwargs to add to results instance, need to be available in __init__ res_kwds = dict(cov_type="robust", cov_robust=cov) scale = self.estimate_scale() rslt = GEEResults(self, mean_params, cov, scale, regularized=True, attr_kwds=res_kwds) rslt.fit_history = fit_history return GEEResultsWrapper(rslt) def _handle_constraint(self, mean_params, bcov): """ Expand the parameter estimate `mean_params` and covariance matrix `bcov` to the coordinate system of the unconstrained model. Parameters ---------- mean_params : array_like A parameter vector estimate for the reduced model. bcov : array_like The covariance matrix of mean_params. Returns ------- mean_params : array_like The input parameter vector mean_params, expanded to the coordinate system of the full model bcov : array_like The input covariance matrix bcov, expanded to the coordinate system of the full model """ # The number of variables in the full model red_p = len(mean_params) full_p = self.constraint.lhs.shape[1] mean_params0 = np.r_[mean_params, np.zeros(full_p - red_p)] # Get the score vector under the full model. save_exog_li = self.exog_li self.exog_li = self.constraint.exog_fulltrans_li import copy save_cached_means = copy.deepcopy(self.cached_means) self.update_cached_means(mean_params0) _, score = self._update_mean_params() if score is None: warnings.warn("Singular matrix encountered in GEE score test", ConvergenceWarning) return None, None _, ncov1, cmat = self._covmat() scale = self.estimate_scale() cmat = cmat / scale ** 2 score2 = score[red_p:] / scale amat = np.linalg.inv(ncov1) bmat_11 = cmat[0:red_p, 0:red_p] bmat_22 = cmat[red_p:, red_p:] bmat_12 = cmat[0:red_p, red_p:] amat_11 = amat[0:red_p, 0:red_p] amat_12 = amat[0:red_p, red_p:] score_cov = bmat_22 - np.dot(amat_12.T, np.linalg.solve(amat_11, bmat_12)) score_cov -= np.dot(bmat_12.T, np.linalg.solve(amat_11, amat_12)) score_cov += np.dot(amat_12.T, np.dot(np.linalg.solve(amat_11, bmat_11), np.linalg.solve(amat_11, amat_12))) from scipy.stats.distributions import chi2 score_statistic = np.dot(score2, np.linalg.solve(score_cov, score2)) score_df = len(score2) score_pvalue = 1 - chi2.cdf(score_statistic, score_df) self.score_test_results = {"statistic": score_statistic, "df": score_df, "p-value": score_pvalue} mean_params = self.constraint.unpack_param(mean_params) bcov = self.constraint.unpack_cov(bcov) self.exog_li = save_exog_li self.cached_means = save_cached_means self.exog = self.constraint.restore_exog() return mean_params, bcov def _update_assoc(self, params): """ Update the association parameters """ self.cov_struct.update(params) def _derivative_exog(self, params, exog=None, transform='dydx', dummy_idx=None, count_idx=None): """ For computing marginal effects, returns dF(XB) / dX where F(.) is the fitted mean. transform can be 'dydx', 'dyex', 'eydx', or 'eyex'. Not all of these make sense in the presence of discrete regressors, but checks are done in the results in get_margeff. """ # This form should be appropriate for group 1 probit, logit, # logistic, cloglog, heckprob, xtprobit. offset_exposure = None if exog is None: exog = self.exog offset_exposure = self._offset_exposure margeff = self.mean_deriv_exog(exog, params, offset_exposure) if 'ex' in transform: margeff *= exog if 'ey' in transform: margeff /= self.predict(params, exog)[:, None] if count_idx is not None: from statsmodels.discrete.discrete_margins import ( _get_count_effects) margeff = _get_count_effects(margeff, exog, count_idx, transform, self, params) if dummy_idx is not None: from statsmodels.discrete.discrete_margins import ( _get_dummy_effects) margeff = _get_dummy_effects(margeff, exog, dummy_idx, transform, self, params) return margeff def qic(self, params, scale, cov_params, n_step=1000): """ Returns quasi-information criteria and quasi-likelihood values. Parameters ---------- params : array_like The GEE estimates of the regression parameters. scale : scalar Estimated scale parameter cov_params : array_like An estimate of the covariance matrix for the model parameters. Conventionally this is the robust covariance matrix. n_step : integer The number of points in the trapezoidal approximation to the quasi-likelihood function. Returns ------- ql : scalar The quasi-likelihood value qic : scalar A QIC that can be used to compare the mean and covariance structures of the model. qicu : scalar A simplified QIC that can be used to compare mean structures but not covariance structures Notes ----- The quasi-likelihood used here is obtained by numerically evaluating Wedderburn's integral representation of the quasi-likelihood function. This approach is valid for all families and links. Many other packages use analytical expressions for quasi-likelihoods that are valid in special cases where the link function is canonical. These analytical expressions may omit additive constants that only depend on the data. Therefore, the numerical values of our QL and QIC values will differ from the values reported by other packages. However only the differences between two QIC values calculated for different models using the same data are meaningful. Our QIC should produce the same QIC differences as other software. When using the QIC for models with unknown scale parameter, use a common estimate of the scale parameter for all models being compared. References ---------- .. [*] W. Pan (2001). Akaike's information criterion in generalized estimating equations. Biometrics (57) 1. """ varfunc = self.family.variance means = [] omega = 0.0 # omega^-1 is the model-based covariance assuming independence for i in range(self.num_group): expval, lpr = self.cached_means[i] means.append(expval) dmat = self.mean_deriv(self.exog_li[i], lpr) omega += np.dot(dmat.T, dmat) / scale means = np.concatenate(means) # The quasi-likelihood, use change of variables so the integration is # from -1 to 1. endog_li = np.concatenate(self.endog_li) du = means - endog_li qv = np.empty(n_step) xv = np.linspace(-0.99999, 1, n_step) for i, g in enumerate(xv): u = endog_li + (g + 1) * du / 2.0 vu = varfunc(u) qv[i] = -np.sum(du**2 * (g + 1) / vu) qv /= (4 * scale) try: from scipy.integrate import trapezoid except ImportError: # Remove after minimum is SciPy 1.7 from scipy.integrate import trapz as trapezoid ql = trapezoid(qv, dx=xv[1] - xv[0]) qicu = -2 * ql + 2 * self.exog.shape[1] qic = -2 * ql + 2 * np.trace(np.dot(omega, cov_params)) return ql, qic, qicu class GEEResults(GLMResults): __doc__ = ( "This class summarizes the fit of a marginal regression model " "using GEE.\n" + _gee_results_doc) def __init__(self, model, params, cov_params, scale, cov_type='robust', use_t=False, regularized=False, **kwds): super().__init__( model, params, normalized_cov_params=cov_params, scale=scale ) # not added by super self.df_resid = model.df_resid self.df_model = model.df_model self.family = model.family attr_kwds = kwds.pop('attr_kwds', {}) self.__dict__.update(attr_kwds) # we do not do this if the cov_type has already been set # subclasses can set it through attr_kwds if not (hasattr(self, 'cov_type') and hasattr(self, 'cov_params_default')): self.cov_type = cov_type # keep alias covariance_type = self.cov_type.lower() allowed_covariances = ["robust", "naive", "bias_reduced"] if covariance_type not in allowed_covariances: msg = ("GEE: `cov_type` must be one of " + ", ".join(allowed_covariances)) raise ValueError(msg) if cov_type == "robust": cov = self.cov_robust elif cov_type == "naive": cov = self.cov_naive elif cov_type == "bias_reduced": cov = self.cov_robust_bc self.cov_params_default = cov else: if self.cov_type != cov_type: raise ValueError('cov_type in argument is different from ' 'already attached cov_type') @cache_readonly def resid(self): """ The response residuals. """ return self.resid_response def standard_errors(self, cov_type="robust"): """ This is a convenience function that returns the standard errors for any covariance type. The value of `bse` is the standard errors for whichever covariance type is specified as an argument to `fit` (defaults to "robust"). Parameters ---------- cov_type : str One of "robust", "naive", or "bias_reduced". Determines the covariance used to compute standard errors. Defaults to "robust". """ # Check covariance_type covariance_type = cov_type.lower() allowed_covariances = ["robust", "naive", "bias_reduced"] if covariance_type not in allowed_covariances: msg = ("GEE: `covariance_type` must be one of " + ", ".join(allowed_covariances)) raise ValueError(msg) if covariance_type == "robust": return np.sqrt(np.diag(self.cov_robust)) elif covariance_type == "naive": return np.sqrt(np.diag(self.cov_naive)) elif covariance_type == "bias_reduced": if self.cov_robust_bc is None: raise ValueError( "GEE: `bias_reduced` covariance not available") return np.sqrt(np.diag(self.cov_robust_bc)) # Need to override to allow for different covariance types. @cache_readonly def bse(self): return self.standard_errors(self.cov_type) def score_test(self): """ Return the results of a score test for a linear constraint. Returns ------- Adictionary containing the p-value, the test statistic, and the degrees of freedom for the score test. Notes ----- See also GEE.compare_score_test for an alternative way to perform a score test. GEEResults.score_test is more general, in that it supports testing arbitrary linear equality constraints. However GEE.compare_score_test might be easier to use when comparing two explicit models. References ---------- Xu Guo and Wei Pan (2002). "Small sample performance of the score test in GEE". http://www.sph.umn.edu/faculty1/wp-content/uploads/2012/11/rr2002-013.pdf """ if not hasattr(self.model, "score_test_results"): msg = "score_test on results instance only available when " msg += " model was fit with constraints" raise ValueError(msg) return self.model.score_test_results @cache_readonly def resid_split(self): """ Returns the residuals, the endogeneous data minus the fitted values from the model. The residuals are returned as a list of arrays containing the residuals for each cluster. """ sresid = [] for v in self.model.group_labels: ii = self.model.group_indices[v] sresid.append(self.resid[ii]) return sresid @cache_readonly def resid_centered(self): """ Returns the residuals centered within each group. """ cresid = self.resid.copy() for v in self.model.group_labels: ii = self.model.group_indices[v] cresid[ii] -= cresid[ii].mean() return cresid @cache_readonly def resid_centered_split(self): """ Returns the residuals centered within each group. The residuals are returned as a list of arrays containing the centered residuals for each cluster. """ sresid = [] for v in self.model.group_labels: ii = self.model.group_indices[v] sresid.append(self.centered_resid[ii]) return sresid def qic(self, scale=None, n_step=1000): """ Returns the QIC and QICu information criteria. See GEE.qic for documentation. """ # It is easy to forget to set the scale parameter. Sometimes # this is intentional, so we warn. if scale is None: warnings.warn("QIC values obtained using scale=None are not " "appropriate for comparing models") if scale is None: scale = self.scale _, qic, qicu = self.model.qic(self.params, scale, self.cov_params(), n_step=n_step) return qic, qicu # FIXME: alias to be removed, temporary backwards compatibility split_resid = resid_split centered_resid = resid_centered split_centered_resid = resid_centered_split @Appender(_plot_added_variable_doc % {'extra_params_doc': ''}) def plot_added_variable(self, focus_exog, resid_type=None, use_glm_weights=True, fit_kwargs=None, ax=None): from statsmodels.graphics.regressionplots import plot_added_variable fig = plot_added_variable(self, focus_exog, resid_type=resid_type, use_glm_weights=use_glm_weights, fit_kwargs=fit_kwargs, ax=ax) return fig @Appender(_plot_partial_residuals_doc % {'extra_params_doc': ''}) def plot_partial_residuals(self, focus_exog, ax=None): from statsmodels.graphics.regressionplots import plot_partial_residuals return plot_partial_residuals(self, focus_exog, ax=ax) @Appender(_plot_ceres_residuals_doc % {'extra_params_doc': ''}) def plot_ceres_residuals(self, focus_exog, frac=0.66, cond_means=None, ax=None): from statsmodels.graphics.regressionplots import plot_ceres_residuals return plot_ceres_residuals(self, focus_exog, frac, cond_means=cond_means, ax=ax) def conf_int(self, alpha=.05, cols=None, cov_type=None): """ Returns confidence intervals for the fitted parameters. Parameters ---------- alpha : float, optional The `alpha` level for the confidence interval. i.e., The default `alpha` = .05 returns a 95% confidence interval. cols : array_like, optional `cols` specifies which confidence intervals to return cov_type : str The covariance type used for computing standard errors; must be one of 'robust', 'naive', and 'bias reduced'. See `GEE` for details. Notes ----- The confidence interval is based on the Gaussian distribution. """ # super does not allow to specify cov_type and method is not # implemented, # FIXME: remove this method here if cov_type is None: bse = self.bse else: bse = self.standard_errors(cov_type=cov_type) params = self.params dist = stats.norm q = dist.ppf(1 - alpha / 2) if cols is None: lower = self.params - q * bse upper = self.params + q * bse else: cols = np.asarray(cols) lower = params[cols] - q * bse[cols] upper = params[cols] + q * bse[cols] return np.asarray(lzip(lower, upper)) def summary(self, yname=None, xname=None, title=None, alpha=.05): """ Summarize the GEE regression results Parameters ---------- yname : str, optional Default is `y` xname : list[str], optional Names for the exogenous variables, default is `var_#` for ## in the number of regressors. Must match the number of parameters in the model title : str, optional Title for the top table. If not None, then this replaces the default title alpha : float significance level for the confidence intervals cov_type : str The covariance type used to compute the standard errors; one of 'robust' (the usual robust sandwich-type covariance estimate), 'naive' (ignores dependence), and 'bias reduced' (the Mancl/DeRouen estimate). Returns ------- smry : Summary instance this holds the summary tables and text, which can be printed or converted to various output formats. See Also -------- statsmodels.iolib.summary.Summary : class to hold summary results """ top_left = [('Dep. Variable:', None), ('Model:', None), ('Method:', ['Generalized']), ('', ['Estimating Equations']), ('Family:', [self.model.family.__class__.__name__]), ('Dependence structure:', [self.model.cov_struct.__class__.__name__]), ('Date:', None), ('Covariance type: ', [self.cov_type, ]) ] NY = [len(y) for y in self.model.endog_li] top_right = [('No. Observations:', [sum(NY)]), ('No. clusters:', [len(self.model.endog_li)]), ('Min. cluster size:', [min(NY)]), ('Max. cluster size:', [max(NY)]), ('Mean cluster size:', ["%.1f" % np.mean(NY)]), ('Num. iterations:', ['%d' % len(self.fit_history['params'])]), ('Scale:', ["%.3f" % self.scale]), ('Time:', None), ] # The skew of the residuals skew1 = stats.skew(self.resid) kurt1 = stats.kurtosis(self.resid) skew2 = stats.skew(self.centered_resid) kurt2 = stats.kurtosis(self.centered_resid) diagn_left = [('Skew:', ["%12.4f" % skew1]), ('Centered skew:', ["%12.4f" % skew2])] diagn_right = [('Kurtosis:', ["%12.4f" % kurt1]), ('Centered kurtosis:', ["%12.4f" % kurt2]) ] if title is None: title = self.model.__class__.__name__ + ' ' +\ "Regression Results" # Override the exog variable names if xname is provided as an # argument. if xname is None: xname = self.model.exog_names if yname is None: yname = self.model.endog_names # Create summary table instance from statsmodels.iolib.summary import Summary smry = Summary() smry.add_table_2cols(self, gleft=top_left, gright=top_right, yname=yname, xname=xname, title=title) smry.add_table_params(self, yname=yname, xname=xname, alpha=alpha, use_t=False) smry.add_table_2cols(self, gleft=diagn_left, gright=diagn_right, yname=yname, xname=xname, title="") return smry def get_margeff(self, at='overall', method='dydx', atexog=None, dummy=False, count=False): """Get marginal effects of the fitted model. Parameters ---------- at : str, optional Options are: - 'overall', The average of the marginal effects at each observation. - 'mean', The marginal effects at the mean of each regressor. - 'median', The marginal effects at the median of each regressor. - 'zero', The marginal effects at zero for each regressor. - 'all', The marginal effects at each observation. If `at` is 'all' only margeff will be available. Note that if `exog` is specified, then marginal effects for all variables not specified by `exog` are calculated using the `at` option. method : str, optional Options are: - 'dydx' - dy/dx - No transformation is made and marginal effects are returned. This is the default. - 'eyex' - estimate elasticities of variables in `exog` -- d(lny)/d(lnx) - 'dyex' - estimate semi-elasticity -- dy/d(lnx) - 'eydx' - estimate semi-elasticity -- d(lny)/dx Note that tranformations are done after each observation is calculated. Semi-elasticities for binary variables are computed using the midpoint method. 'dyex' and 'eyex' do not make sense for discrete variables. atexog : array_like, optional Optionally, you can provide the exogenous variables over which to get the marginal effects. This should be a dictionary with the key as the zero-indexed column number and the value of the dictionary. Default is None for all independent variables less the constant. dummy : bool, optional If False, treats binary variables (if present) as continuous. This is the default. Else if True, treats binary variables as changing from 0 to 1. Note that any variable that is either 0 or 1 is treated as binary. Each binary variable is treated separately for now. count : bool, optional If False, treats count variables (if present) as continuous. This is the default. Else if True, the marginal effect is the change in probabilities when each observation is increased by one. Returns ------- effects : ndarray the marginal effect corresponding to the input options Notes ----- When using after Poisson, returns the expected number of events per period, assuming that the model is loglinear. """ if self.model.constraint is not None: warnings.warn("marginal effects ignore constraints", ValueWarning) return GEEMargins(self, (at, method, atexog, dummy, count)) def plot_isotropic_dependence(self, ax=None, xpoints=10, min_n=50): """ Create a plot of the pairwise products of within-group residuals against the corresponding time differences. This plot can be used to assess the possible form of an isotropic covariance structure. Parameters ---------- ax : AxesSubplot An axes on which to draw the graph. If None, new figure and axes objects are created xpoints : scalar or array_like If scalar, the number of points equally spaced points on the time difference axis used to define bins for calculating local means. If an array, the specific points that define the bins. min_n : int The minimum sample size in a bin for the mean residual product to be included on the plot. """ from statsmodels.graphics import utils as gutils resid = self.model.cluster_list(self.resid) time = self.model.cluster_list(self.model.time) # All within-group pairwise time distances (xdt) and the # corresponding products of scaled residuals (xre). xre, xdt = [], [] for re, ti in zip(resid, time): ix = np.tril_indices(re.shape[0], 0) re = re[ix[0]] * re[ix[1]] / self.scale ** 2 xre.append(re) dists = np.sqrt(((ti[ix[0], :] - ti[ix[1], :]) ** 2).sum(1)) xdt.append(dists) xre = np.concatenate(xre) xdt = np.concatenate(xdt) if ax is None: fig, ax = gutils.create_mpl_ax(ax) else: fig = ax.get_figure() # Convert to a correlation ii = np.flatnonzero(xdt == 0) v0 = np.mean(xre[ii]) xre /= v0 # Use the simple average to smooth, since fancier smoothers # that trim and downweight outliers give biased results (we # need the actual mean of a skewed distribution). if np.isscalar(xpoints): xpoints = np.linspace(0, max(xdt), xpoints) dg = np.digitize(xdt, xpoints) dgu = np.unique(dg) hist = np.asarray([np.sum(dg == k) for k in dgu]) ii = np.flatnonzero(hist >= min_n) dgu = dgu[ii] dgy = np.asarray([np.mean(xre[dg == k]) for k in dgu]) dgx = np.asarray([np.mean(xdt[dg == k]) for k in dgu]) ax.plot(dgx, dgy, '-', color='orange', lw=5) ax.set_xlabel("Time difference") ax.set_ylabel("Product of scaled residuals") return fig def sensitivity_params(self, dep_params_first, dep_params_last, num_steps): """ Refits the GEE model using a sequence of values for the dependence parameters. Parameters ---------- dep_params_first : array_like The first dep_params in the sequence dep_params_last : array_like The last dep_params in the sequence num_steps : int The number of dep_params in the sequence Returns ------- results : array_like The GEEResults objects resulting from the fits. """ model = self.model import copy cov_struct = copy.deepcopy(self.model.cov_struct) # We are fixing the dependence structure in each run. update_dep = model.update_dep model.update_dep = False dep_params = [] results = [] for x in np.linspace(0, 1, num_steps): dp = x * dep_params_last + (1 - x) * dep_params_first dep_params.append(dp) model.cov_struct = copy.deepcopy(cov_struct) model.cov_struct.dep_params = dp rslt = model.fit(start_params=self.params, ctol=self.ctol, params_niter=self.params_niter, first_dep_update=self.first_dep_update, cov_type=self.cov_type) results.append(rslt) model.update_dep = update_dep return results # FIXME: alias to be removed, temporary backwards compatibility params_sensitivity = sensitivity_params class GEEResultsWrapper(lm.RegressionResultsWrapper): _attrs = { 'centered_resid': 'rows', } _wrap_attrs = wrap.union_dicts(lm.RegressionResultsWrapper._wrap_attrs, _attrs) wrap.populate_wrapper(GEEResultsWrapper, GEEResults) # noqa:E305 class OrdinalGEE(GEE): __doc__ = ( " Ordinal Response Marginal Regression Model using GEE\n" + _gee_init_doc % {'extra_params': base._missing_param_doc, 'family_doc': _gee_ordinal_family_doc, 'example': _gee_ordinal_example, 'notes': _gee_nointercept}) def __init__(self, endog, exog, groups, time=None, family=None, cov_struct=None, missing='none', offset=None, dep_data=None, constraint=None, **kwargs): if family is None: family = families.Binomial() else: if not isinstance(family, families.Binomial): raise ValueError("ordinal GEE must use a Binomial family") if cov_struct is None: cov_struct = cov_structs.OrdinalIndependence() endog, exog, groups, time, offset = self.setup_ordinal( endog, exog, groups, time, offset) super().__init__(endog, exog, groups, time, family, cov_struct, missing, offset, dep_data, constraint) def setup_ordinal(self, endog, exog, groups, time, offset): """ Restructure ordinal data as binary indicators so that they can be analyzed using Generalized Estimating Equations. """ self.endog_orig = endog.copy() self.exog_orig = exog.copy() self.groups_orig = groups.copy() if offset is not None: self.offset_orig = offset.copy() else: self.offset_orig = None offset = np.zeros(len(endog)) if time is not None: self.time_orig = time.copy() else: self.time_orig = None time = np.zeros((len(endog), 1)) exog = np.asarray(exog) endog = np.asarray(endog) groups = np.asarray(groups) time = np.asarray(time) offset = np.asarray(offset) # The unique outcomes, except the greatest one. self.endog_values = np.unique(endog) endog_cuts = self.endog_values[0:-1] ncut = len(endog_cuts) nrows = ncut * len(endog) exog_out = np.zeros((nrows, exog.shape[1]), dtype=np.float64) endog_out = np.zeros(nrows, dtype=np.float64) intercepts = np.zeros((nrows, ncut), dtype=np.float64) groups_out = np.zeros(nrows, dtype=groups.dtype) time_out = np.zeros((nrows, time.shape[1]), dtype=np.float64) offset_out = np.zeros(nrows, dtype=np.float64) jrow = 0 zipper = zip(exog, endog, groups, time, offset) for (exog_row, endog_value, group_value, time_value, offset_value) in zipper: # Loop over thresholds for the indicators for thresh_ix, thresh in enumerate(endog_cuts): exog_out[jrow, :] = exog_row endog_out[jrow] = int(np.squeeze(endog_value > thresh)) intercepts[jrow, thresh_ix] = 1 groups_out[jrow] = group_value time_out[jrow] = time_value offset_out[jrow] = offset_value jrow += 1 exog_out = np.concatenate((intercepts, exog_out), axis=1) # exog column names, including intercepts xnames = ["I(y>%.1f)" % v for v in endog_cuts] if type(self.exog_orig) is pd.DataFrame: xnames.extend(self.exog_orig.columns) else: xnames.extend(["x%d" % k for k in range(1, exog.shape[1] + 1)]) exog_out = pd.DataFrame(exog_out, columns=xnames) # Preserve the endog name if there is one if type(self.endog_orig) is pd.Series: endog_out = pd.Series(endog_out, name=self.endog_orig.name) return endog_out, exog_out, groups_out, time_out, offset_out def _starting_params(self): exposure = getattr(self, "exposure", None) model = GEE(self.endog, self.exog, self.groups, time=self.time, family=families.Binomial(), offset=self.offset, exposure=exposure) result = model.fit() return result.params @Appender(_gee_fit_doc) def fit(self, maxiter=60, ctol=1e-6, start_params=None, params_niter=1, first_dep_update=0, cov_type='robust'): rslt = super().fit(maxiter, ctol, start_params, params_niter, first_dep_update, cov_type=cov_type) rslt = rslt._results # use unwrapped instance res_kwds = {k: getattr(rslt, k) for k in rslt._props} # Convert the GEEResults to an OrdinalGEEResults ord_rslt = OrdinalGEEResults(self, rslt.params, rslt.cov_params() / rslt.scale, rslt.scale, cov_type=cov_type, attr_kwds=res_kwds) # for k in rslt._props: # setattr(ord_rslt, k, getattr(rslt, k)) # TODO: document or delete return OrdinalGEEResultsWrapper(ord_rslt) class OrdinalGEEResults(GEEResults): __doc__ = ( "This class summarizes the fit of a marginal regression model" "for an ordinal response using GEE.\n" + _gee_results_doc) def plot_distribution(self, ax=None, exog_values=None): """ Plot the fitted probabilities of endog in an ordinal model, for specified values of the predictors. Parameters ---------- ax : AxesSubplot An axes on which to draw the graph. If None, new figure and axes objects are created exog_values : array_like A list of dictionaries, with each dictionary mapping variable names to values at which the variable is held fixed. The values P(endog=y | exog) are plotted for all possible values of y, at the given exog value. Variables not included in a dictionary are held fixed at the mean value. Example: -------- We have a model with covariates 'age' and 'sex', and wish to plot the probabilities P(endog=y | exog) for males (sex=0) and for females (sex=1), as separate paths on the plot. Since 'age' is not included below in the map, it is held fixed at its mean value. >>> ev = [{"sex": 1}, {"sex": 0}] >>> rslt.distribution_plot(exog_values=ev) """ from statsmodels.graphics import utils as gutils if ax is None: fig, ax = gutils.create_mpl_ax(ax) else: fig = ax.get_figure() # If no covariate patterns are specified, create one with all # variables set to their mean values. if exog_values is None: exog_values = [{}, ] exog_means = self.model.exog.mean(0) ix_icept = [i for i, x in enumerate(self.model.exog_names) if x.startswith("I(")] for ev in exog_values: for k in ev.keys(): if k not in self.model.exog_names: raise ValueError("%s is not a variable in the model" % k) # Get the fitted probability for each level, at the given # covariate values. pr = [] for j in ix_icept: xp = np.zeros_like(self.params) xp[j] = 1. for i, vn in enumerate(self.model.exog_names): if i in ix_icept: continue # User-specified value if vn in ev: xp[i] = ev[vn] # Mean value else: xp[i] = exog_means[i] p = 1 / (1 + np.exp(-np.dot(xp, self.params))) pr.append(p) pr.insert(0, 1) pr.append(0) pr = np.asarray(pr) prd = -np.diff(pr) ax.plot(self.model.endog_values, prd, 'o-') ax.set_xlabel("Response value") ax.set_ylabel("Probability") ax.set_ylim(0, 1) return fig def _score_test_submodel(par, sub): """ Return transformation matrices for design matrices. Parameters ---------- par : instance The parent model sub : instance The sub-model Returns ------- qm : array_like Matrix mapping the design matrix of the parent to the design matrix for the sub-model. qc : array_like Matrix mapping the design matrix of the parent to the orthogonal complement of the columnspace of the submodel in the columnspace of the parent. Notes ----- Returns None, None if the provided submodel is not actually a submodel. """ x1 = par.exog x2 = sub.exog u, s, vt = np.linalg.svd(x1, 0) v = vt.T # Get the orthogonal complement of col(x2) in col(x1). a, _ = np.linalg.qr(x2) a = u - np.dot(a, np.dot(a.T, u)) x2c, sb, _ = np.linalg.svd(a, 0) x2c = x2c[:, sb > 1e-12] # x1 * qm = x2 ii = np.flatnonzero(np.abs(s) > 1e-12) qm = np.dot(v[:, ii], np.dot(u[:, ii].T, x2) / s[ii, None]) e = np.max(np.abs(x2 - np.dot(x1, qm))) if e > 1e-8: return None, None # x1 * qc = x2c qc = np.dot(v[:, ii], np.dot(u[:, ii].T, x2c) / s[ii, None]) return qm, qc class OrdinalGEEResultsWrapper(GEEResultsWrapper): pass wrap.populate_wrapper(OrdinalGEEResultsWrapper, OrdinalGEEResults) # noqa:E305 class NominalGEE(GEE): __doc__ = ( " Nominal Response Marginal Regression Model using GEE.\n" + _gee_init_doc % {'extra_params': base._missing_param_doc, 'family_doc': _gee_nominal_family_doc, 'example': _gee_nominal_example, 'notes': _gee_nointercept}) def __init__(self, endog, exog, groups, time=None, family=None, cov_struct=None, missing='none', offset=None, dep_data=None, constraint=None, **kwargs): endog, exog, groups, time, offset = self.setup_nominal( endog, exog, groups, time, offset) if family is None: family = _Multinomial(self.ncut + 1) if cov_struct is None: cov_struct = cov_structs.NominalIndependence() super().__init__( endog, exog, groups, time, family, cov_struct, missing, offset, dep_data, constraint) def _starting_params(self): exposure = getattr(self, "exposure", None) model = GEE(self.endog, self.exog, self.groups, time=self.time, family=families.Binomial(), offset=self.offset, exposure=exposure) result = model.fit() return result.params def setup_nominal(self, endog, exog, groups, time, offset): """ Restructure nominal data as binary indicators so that they can be analyzed using Generalized Estimating Equations. """ self.endog_orig = endog.copy() self.exog_orig = exog.copy() self.groups_orig = groups.copy() if offset is not None: self.offset_orig = offset.copy() else: self.offset_orig = None offset = np.zeros(len(endog)) if time is not None: self.time_orig = time.copy() else: self.time_orig = None time = np.zeros((len(endog), 1)) exog = np.asarray(exog) endog = np.asarray(endog) groups = np.asarray(groups) time = np.asarray(time) offset = np.asarray(offset) # The unique outcomes, except the greatest one. self.endog_values = np.unique(endog) endog_cuts = self.endog_values[0:-1] ncut = len(endog_cuts) self.ncut = ncut nrows = len(endog_cuts) * exog.shape[0] ncols = len(endog_cuts) * exog.shape[1] exog_out = np.zeros((nrows, ncols), dtype=np.float64) endog_out = np.zeros(nrows, dtype=np.float64) groups_out = np.zeros(nrows, dtype=np.float64) time_out = np.zeros((nrows, time.shape[1]), dtype=np.float64) offset_out = np.zeros(nrows, dtype=np.float64) jrow = 0 zipper = zip(exog, endog, groups, time, offset) for (exog_row, endog_value, group_value, time_value, offset_value) in zipper: # Loop over thresholds for the indicators for thresh_ix, thresh in enumerate(endog_cuts): u = np.zeros(len(endog_cuts), dtype=np.float64) u[thresh_ix] = 1 exog_out[jrow, :] = np.kron(u, exog_row) endog_out[jrow] = (int(endog_value == thresh)) groups_out[jrow] = group_value time_out[jrow] = time_value offset_out[jrow] = offset_value jrow += 1 # exog names if isinstance(self.exog_orig, pd.DataFrame): xnames_in = self.exog_orig.columns else: xnames_in = ["x%d" % k for k in range(1, exog.shape[1] + 1)] xnames = [] for tr in endog_cuts: xnames.extend([f"{v}[{tr:.1f}]" for v in xnames_in]) exog_out = pd.DataFrame(exog_out, columns=xnames) exog_out = pd.DataFrame(exog_out, columns=xnames) # Preserve endog name if there is one if isinstance(self.endog_orig, pd.Series): endog_out = pd.Series(endog_out, name=self.endog_orig.name) return endog_out, exog_out, groups_out, time_out, offset_out def mean_deriv(self, exog, lin_pred): """ Derivative of the expected endog with respect to the parameters. Parameters ---------- exog : array_like The exogeneous data at which the derivative is computed, number of rows must be a multiple of `ncut`. lin_pred : array_like The values of the linear predictor, length must be multiple of `ncut`. Returns ------- The derivative of the expected endog with respect to the parameters. """ expval = np.exp(lin_pred) # Reshape so that each row contains all the indicators # corresponding to one multinomial observation. expval_m = np.reshape(expval, (len(expval) // self.ncut, self.ncut)) # The normalizing constant for the multinomial probabilities. denom = 1 + expval_m.sum(1) denom = np.kron(denom, np.ones(self.ncut, dtype=np.float64)) # The multinomial probabilities mprob = expval / denom # First term of the derivative: denom * expval' / denom^2 = # expval' / denom. dmat = mprob[:, None] * exog # Second term of the derivative: -expval * denom' / denom^2 ddenom = expval[:, None] * exog dmat -= mprob[:, None] * ddenom / denom[:, None] return dmat def mean_deriv_exog(self, exog, params, offset_exposure=None): """ Derivative of the expected endog with respect to exog for the multinomial model, used in analyzing marginal effects. Parameters ---------- exog : array_like The exogeneous data at which the derivative is computed, number of rows must be a multiple of `ncut`. lpr : array_like The linear predictor values, length must be multiple of `ncut`. Returns ------- The value of the derivative of the expected endog with respect to exog. Notes ----- offset_exposure must be set at None for the multinomial family. """ if offset_exposure is not None: warnings.warn("Offset/exposure ignored for the multinomial family", ValueWarning) lpr = np.dot(exog, params) expval = np.exp(lpr) expval_m = np.reshape(expval, (len(expval) // self.ncut, self.ncut)) denom = 1 + expval_m.sum(1) denom = np.kron(denom, np.ones(self.ncut, dtype=np.float64)) bmat0 = np.outer(np.ones(exog.shape[0]), params) # Masking matrix qmat = [] for j in range(self.ncut): ee = np.zeros(self.ncut, dtype=np.float64) ee[j] = 1 qmat.append(np.kron(ee, np.ones(len(params) // self.ncut))) qmat = np.array(qmat) qmat = np.kron(np.ones((exog.shape[0] // self.ncut, 1)), qmat) bmat = bmat0 * qmat dmat = expval[:, None] * bmat / denom[:, None] expval_mb = np.kron(expval_m, np.ones((self.ncut, 1))) expval_mb = np.kron(expval_mb, np.ones((1, self.ncut))) dmat -= expval[:, None] * (bmat * expval_mb) / denom[:, None] ** 2 return dmat @Appender(_gee_fit_doc) def fit(self, maxiter=60, ctol=1e-6, start_params=None, params_niter=1, first_dep_update=0, cov_type='robust'): rslt = super().fit(maxiter, ctol, start_params, params_niter, first_dep_update, cov_type=cov_type) if rslt is None: warnings.warn("GEE updates did not converge", ConvergenceWarning) return None rslt = rslt._results # use unwrapped instance res_kwds = {k: getattr(rslt, k) for k in rslt._props} # Convert the GEEResults to a NominalGEEResults nom_rslt = NominalGEEResults(self, rslt.params, rslt.cov_params() / rslt.scale, rslt.scale, cov_type=cov_type, attr_kwds=res_kwds) # TODO: document or delete # for k in rslt._props: # setattr(nom_rslt, k, getattr(rslt, k)) return NominalGEEResultsWrapper(nom_rslt) class NominalGEEResults(GEEResults): __doc__ = ( "This class summarizes the fit of a marginal regression model" "for a nominal response using GEE.\n" + _gee_results_doc) def plot_distribution(self, ax=None, exog_values=None): """ Plot the fitted probabilities of endog in an nominal model, for specified values of the predictors. Parameters ---------- ax : AxesSubplot An axes on which to draw the graph. If None, new figure and axes objects are created exog_values : array_like A list of dictionaries, with each dictionary mapping variable names to values at which the variable is held fixed. The values P(endog=y | exog) are plotted for all possible values of y, at the given exog value. Variables not included in a dictionary are held fixed at the mean value. Example: -------- We have a model with covariates 'age' and 'sex', and wish to plot the probabilities P(endog=y | exog) for males (sex=0) and for females (sex=1), as separate paths on the plot. Since 'age' is not included below in the map, it is held fixed at its mean value. >>> ex = [{"sex": 1}, {"sex": 0}] >>> rslt.distribution_plot(exog_values=ex) """ from statsmodels.graphics import utils as gutils if ax is None: fig, ax = gutils.create_mpl_ax(ax) else: fig = ax.get_figure() # If no covariate patterns are specified, create one with all # variables set to their mean values. if exog_values is None: exog_values = [{}, ] link = self.model.family.link.inverse ncut = self.model.family.ncut k = int(self.model.exog.shape[1] / ncut) exog_means = self.model.exog.mean(0)[0:k] exog_names = self.model.exog_names[0:k] exog_names = [x.split("[")[0] for x in exog_names] params = np.reshape(self.params, (ncut, len(self.params) // ncut)) for ev in exog_values: exog = exog_means.copy() for k in ev.keys(): if k not in exog_names: raise ValueError("%s is not a variable in the model" % k) ii = exog_names.index(k) exog[ii] = ev[k] lpr = np.dot(params, exog) pr = link(lpr) pr = np.r_[pr, 1 - pr.sum()] ax.plot(self.model.endog_values, pr, 'o-') ax.set_xlabel("Response value") ax.set_ylabel("Probability") ax.set_xticks(self.model.endog_values) ax.set_xticklabels(self.model.endog_values) ax.set_ylim(0, 1) return fig class NominalGEEResultsWrapper(GEEResultsWrapper): pass wrap.populate_wrapper(NominalGEEResultsWrapper, NominalGEEResults) # noqa:E305 class _MultinomialLogit(Link): """ The multinomial logit transform, only for use with GEE. Notes ----- The data are assumed coded as binary indicators, where each observed multinomial value y is coded as I(y == S[0]), ..., I(y == S[-1]), where S is the set of possible response labels, excluding the largest one. Thererefore functions in this class should only be called using vector argument whose length is a multiple of |S| = ncut, which is an argument to be provided when initializing the class. call and derivative use a private method _clean to trim p by 1e-10 so that p is in (0, 1) """ def __init__(self, ncut): self.ncut = ncut def inverse(self, lpr): """ Inverse of the multinomial logit transform, which gives the expected values of the data as a function of the linear predictors. Parameters ---------- lpr : array_like (length must be divisible by `ncut`) The linear predictors Returns ------- prob : ndarray Probabilities, or expected values """ expval = np.exp(lpr) denom = 1 + np.reshape(expval, (len(expval) // self.ncut, self.ncut)).sum(1) denom = np.kron(denom, np.ones(self.ncut, dtype=np.float64)) prob = expval / denom return prob class _Multinomial(families.Family): """ Pseudo-link function for fitting nominal multinomial models with GEE. Not for use outside the GEE class. """ links = [_MultinomialLogit, ] variance = varfuncs.binary safe_links = [_MultinomialLogit, ] def __init__(self, nlevels, check_link=True): """ Parameters ---------- nlevels : int The number of distinct categories for the multinomial distribution. """ self._check_link = check_link self.initialize(nlevels) def initialize(self, nlevels): self.ncut = nlevels - 1 self.link = _MultinomialLogit(self.ncut) class GEEMargins: """ Estimated marginal effects for a regression model fit with GEE. Parameters ---------- results : GEEResults instance The results instance of a fitted discrete choice model args : tuple Args are passed to `get_margeff`. This is the same as results.get_margeff. See there for more information. kwargs : dict Keyword args are passed to `get_margeff`. This is the same as results.get_margeff. See there for more information. """ def __init__(self, results, args, kwargs={}): self._cache = {} self.results = results self.get_margeff(*args, **kwargs) def _reset(self): self._cache = {} @cache_readonly def tvalues(self): _check_at_is_all(self.margeff_options) return self.margeff / self.margeff_se def summary_frame(self, alpha=.05): """ Returns a DataFrame summarizing the marginal effects. Parameters ---------- alpha : float Number between 0 and 1. The confidence intervals have the probability 1-alpha. Returns ------- frame : DataFrames A DataFrame summarizing the marginal effects. """ _check_at_is_all(self.margeff_options) from pandas import DataFrame names = [_transform_names[self.margeff_options['method']], 'Std. Err.', 'z', 'Pr(>|z|)', 'Conf. Int. Low', 'Cont. Int. Hi.'] ind = self.results.model.exog.var(0) != 0 # True if not a constant exog_names = self.results.model.exog_names var_names = [name for i, name in enumerate(exog_names) if ind[i]] table = np.column_stack((self.margeff, self.margeff_se, self.tvalues, self.pvalues, self.conf_int(alpha))) return DataFrame(table, columns=names, index=var_names) @cache_readonly def pvalues(self): _check_at_is_all(self.margeff_options) return stats.norm.sf(np.abs(self.tvalues)) * 2 def conf_int(self, alpha=.05): """ Returns the confidence intervals of the marginal effects Parameters ---------- alpha : float Number between 0 and 1. The confidence intervals have the probability 1-alpha. Returns ------- conf_int : ndarray An array with lower, upper confidence intervals for the marginal effects. """ _check_at_is_all(self.margeff_options) me_se = self.margeff_se q = stats.norm.ppf(1 - alpha / 2) lower = self.margeff - q * me_se upper = self.margeff + q * me_se return np.asarray(lzip(lower, upper)) def summary(self, alpha=.05): """ Returns a summary table for marginal effects Parameters ---------- alpha : float Number between 0 and 1. The confidence intervals have the probability 1-alpha. Returns ------- Summary : SummaryTable A SummaryTable instance """ _check_at_is_all(self.margeff_options) results = self.results model = results.model title = model.__class__.__name__ + " Marginal Effects" method = self.margeff_options['method'] top_left = [('Dep. Variable:', [model.endog_names]), ('Method:', [method]), ('At:', [self.margeff_options['at']]), ] from statsmodels.iolib.summary import (Summary, summary_params, table_extend) exog_names = model.exog_names[:] # copy smry = Summary() const_idx = model.data.const_idx if const_idx is not None: exog_names.pop(const_idx) J = int(getattr(model, "J", 1)) if J > 1: yname, yname_list = results._get_endog_name(model.endog_names, None, all=True) else: yname = model.endog_names yname_list = [yname] smry.add_table_2cols(self, gleft=top_left, gright=[], yname=yname, xname=exog_names, title=title) # NOTE: add_table_params is not general enough yet for margeff # could use a refactor with getattr instead of hard-coded params # tvalues etc. table = [] conf_int = self.conf_int(alpha) margeff = self.margeff margeff_se = self.margeff_se tvalues = self.tvalues pvalues = self.pvalues if J > 1: for eq in range(J): restup = (results, margeff[:, eq], margeff_se[:, eq], tvalues[:, eq], pvalues[:, eq], conf_int[:, :, eq]) tble = summary_params(restup, yname=yname_list[eq], xname=exog_names, alpha=alpha, use_t=False, skip_header=True) tble.title = yname_list[eq] # overwrite coef with method name header = ['', _transform_names[method], 'std err', 'z', 'P>|z|', '[%3.1f%% Conf. Int.]' % (100 - alpha * 100)] tble.insert_header_row(0, header) # from IPython.core.debugger import Pdb; Pdb().set_trace() table.append(tble) table = table_extend(table, keep_headers=True) else: restup = (results, margeff, margeff_se, tvalues, pvalues, conf_int) table = summary_params(restup, yname=yname, xname=exog_names, alpha=alpha, use_t=False, skip_header=True) header = ['', _transform_names[method], 'std err', 'z', 'P>|z|', '[%3.1f%% Conf. Int.]' % (100 - alpha * 100)] table.insert_header_row(0, header) smry.tables.append(table) return smry def get_margeff(self, at='overall', method='dydx', atexog=None, dummy=False, count=False): self._reset() # always reset the cache when this is called # TODO: if at is not all or overall, we can also put atexog values # in summary table head method = method.lower() at = at.lower() _check_margeff_args(at, method) self.margeff_options = dict(method=method, at=at) results = self.results model = results.model params = results.params exog = model.exog.copy() # copy because values are changed effects_idx = exog.var(0) != 0 const_idx = model.data.const_idx if dummy: _check_discrete_args(at, method) dummy_idx, dummy = _get_dummy_index(exog, const_idx) else: dummy_idx = None if count: _check_discrete_args(at, method) count_idx, count = _get_count_index(exog, const_idx) else: count_idx = None # get the exogenous variables exog = _get_margeff_exog(exog, at, atexog, effects_idx) # get base marginal effects, handled by sub-classes effects = model._derivative_exog(params, exog, method, dummy_idx, count_idx) effects = _effects_at(effects, at) if at == 'all': self.margeff = effects[:, effects_idx] else: # Set standard error of the marginal effects by Delta method. margeff_cov, margeff_se = margeff_cov_with_se( model, params, exog, results.cov_params(), at, model._derivative_exog, dummy_idx, count_idx, method, 1) # do not care about at constant self.margeff_cov = margeff_cov[effects_idx][:, effects_idx] self.margeff_se = margeff_se[effects_idx] self.margeff = effects[effects_idx]