Source code for statsmodels.gam.generalized_additive_model

# -*- coding: utf-8 -*-
Generalized Additive Models

Author: Luca Puggini
Author: Josef Perktold

created on 08/07/2015

from import Iterable
import copy  # check if needed when dropping python 2.7

import numpy as np
from scipy import optimize
import pandas as pd

import statsmodels.base.wrapper as wrap

from statsmodels.discrete.discrete_model import Logit
from statsmodels.genmod.generalized_linear_model import (
    GLM, GLMResults, GLMResultsWrapper, _check_convergence)
import statsmodels.regression.linear_model as lm
# import statsmodels.regression._tools as reg_tools  # TODO: use this for pirls
from import (PerfectSeparationError,
from import cache_readonly
from import _is_using_pandas
from import matrix_sqrt

from statsmodels.base._penalized import PenalizedMixin
from statsmodels.gam.gam_penalties import MultivariateGamPenalty
from statsmodels.gam.gam_cross_validation.gam_cross_validation import (
from statsmodels.gam.gam_cross_validation.cross_validators import KFold

def _transform_predict_exog(model, exog, design_info=None):
    """transform exog for predict using design_info

    Note: this is copied from base.model.Results.predict and converted to
    standalone function with additional options.

    is_pandas = _is_using_pandas(exog, None)

    exog_index = exog.index if is_pandas else None

    if design_info is None:
        design_info = getattr(, 'design_info', None)

    if design_info is not None and (exog is not None):
        from patsy import dmatrix
        if isinstance(exog, pd.Series):
            # we are guessing whether it should be column or row
            if (hasattr(exog, 'name') and isinstance(, str) and
           in design_info.describe()):
                # assume we need one column
                exog = pd.DataFrame(exog)
                # assume we need a row
                exog = pd.DataFrame(exog).T
        orig_exog_len = len(exog)
        is_dict = isinstance(exog, dict)
        exog = dmatrix(design_info, exog, return_type="dataframe")
        if orig_exog_len > len(exog) and not is_dict:
            import warnings
            if exog_index is None:
                warnings.warn('nan values have been dropped', ValueWarning)
                exog = exog.reindex(exog_index)
        exog_index = exog.index

    if exog is not None:
        exog = np.asarray(exog)
        if exog.ndim == 1 and (model.exog.ndim == 1 or
                               model.exog.shape[1] == 1):
            exog = exog[:, None]
        exog = np.atleast_2d(exog)  # needed in count model shape[1]

    return exog, exog_index

[docs]class GLMGamResults(GLMResults): """Results class for generalized additive models, GAM. This inherits from GLMResults. Warning: some inherited methods might not correctly take account of the penalization GLMGamResults inherits from GLMResults All methods related to the loglikelihood function return the penalized values. Attributes ---------- edf list of effective degrees of freedom for each column of the design matrix. hat_matrix_diag diagonal of hat matrix gcv generalized cross-validation criterion computed as ``gcv = scale / (1. - hat_matrix_trace / self.nobs)**2`` cv cross-validation criterion computed as ``cv = ((resid_pearson / (1 - hat_matrix_diag))**2).sum() / nobs`` Notes ----- status: experimental """ def __init__(self, model, params, normalized_cov_params, scale, **kwds): # this is a messy way to compute edf and update scale # need several attributes to compute edf self.model = model self.params = params self.normalized_cov_params = normalized_cov_params self.scale = scale edf = self.edf.sum() self.df_model = edf - 1 # assume constant # need to use nobs or wnobs attribute self.df_resid = self.model.endog.shape[0] - edf # we are setting the model df for the case when super is using it # df in model will be incorrect state when alpha/pen_weight changes self.model.df_model = self.df_model self.model.df_resid = self.df_resid mu = self.fittedvalues self.scale = scale = self.model.estimate_scale(mu) super(GLMGamResults, self).__init__(model, params, normalized_cov_params, scale, **kwds) def _tranform_predict_exog(self, exog=None, exog_smooth=None, transform=True): """Transform original explanatory variables for prediction Parameters ---------- exog : array_like, optional The values for the linear explanatory variables. exog_smooth : array_like values for the variables in the smooth terms transform : bool, optional If transform is False, then ``exog`` is returned unchanged and ``x`` is ignored. It is assumed that exog contains the full design matrix for the predict observations. If transform is True, then the basis representation of the smooth term will be constructed from the provided ``x``. Returns ------- exog_transformed : ndarray design matrix for the prediction """ if exog_smooth is not None: exog_smooth = np.asarray(exog_smooth) exog_index = None if transform is False: # the following allows that either or both exog are not None if exog_smooth is None: # exog could be None or array ex = exog else: if exog is None: ex = exog_smooth else: ex = np.column_stack((exog, exog_smooth)) else: # transform exog_linear if needed if exog is not None and hasattr(self.model, 'design_info_linear'): exog, exog_index = _transform_predict_exog( self.model, exog, self.model.design_info_linear) # create smooth basis if exog_smooth is not None: ex_smooth = self.model.smoother.transform(exog_smooth) if exog is None: ex = ex_smooth else: # TODO: there might be problems is exog_smooth is 1-D ex = np.column_stack((exog, ex_smooth)) else: ex = exog return ex, exog_index
[docs] def predict(self, exog=None, exog_smooth=None, transform=True, **kwargs): """" compute prediction Parameters ---------- exog : array_like, optional The values for the linear explanatory variables exog_smooth : array_like values for the variables in the smooth terms transform : bool, optional If transform is True, then the basis representation of the smooth term will be constructed from the provided ``exog``. kwargs : Some models can take additional arguments or keywords, see the predict method of the model for the details. Returns ------- prediction : ndarray, pandas.Series or pandas.DataFrame predicted values """ ex, exog_index = self._tranform_predict_exog(exog=exog, exog_smooth=exog_smooth, transform=transform) predict_results = super(GLMGamResults, self).predict(ex, transform=False, **kwargs) if exog_index is not None and not hasattr( predict_results, 'predicted_values'): if predict_results.ndim == 1: return pd.Series(predict_results, index=exog_index) else: return pd.DataFrame(predict_results, index=exog_index) else: return predict_results
[docs] def get_prediction(self, exog=None, exog_smooth=None, transform=True, **kwargs): """compute prediction results Parameters ---------- exog : array_like, optional The values for which you want to predict. exog_smooth : array_like values for the variables in the smooth terms transform : bool, optional If transform is True, then the basis representation of the smooth term will be constructed from the provided ``x``. kwargs : Some models can take additional arguments or keywords, see the predict method of the model for the details. Returns ------- prediction_results : generalized_linear_model.PredictionResults The prediction results instance contains prediction and prediction variance and can on demand calculate confidence intervals and summary tables for the prediction of the mean and of new observations. """ ex, exog_index = self._tranform_predict_exog(exog=exog, exog_smooth=exog_smooth, transform=transform) return super(GLMGamResults, self).get_prediction(ex, transform=False, **kwargs)
[docs] def partial_values(self, smooth_index, include_constant=True): """contribution of a smooth term to the linear prediction Warning: This will be replaced by a predict method Parameters ---------- smooth_index : int index of the smooth term within list of smooth terms include_constant : bool If true, then the estimated intercept is added to the prediction and its standard errors. This avoids that the confidence interval has zero width at the imposed identification constraint, e.g. either at a reference point or at the mean. Returns ------- predicted : nd_array predicted value of linear term. This is not the expected response if the link function is not linear. se_pred : nd_array standard error of linear prediction """ variable = smooth_index smoother = self.model.smoother mask = smoother.mask[variable] start_idx = self.model.k_exog_linear idx = start_idx + np.nonzero(mask)[0] # smoother has only smooth parts, not exog_linear exog_part = smoother.basis[:, mask] const_idx = if include_constant and const_idx is not None: idx = np.concatenate(([const_idx], idx)) exog_part = self.model.exog[:, idx] linpred =, self.params[idx]) # select the submatrix corresponding to a single variable partial_cov_params = self.cov_params(column=idx) covb = partial_cov_params var = (exog_part *, exog_part.T).T).sum(1) se = np.sqrt(var) return linpred, se
[docs] def plot_partial(self, smooth_index, plot_se=True, cpr=False, include_constant=True, ax=None): """plot the contribution of a smooth term to the linear prediction Parameters ---------- smooth_index : int index of the smooth term within list of smooth terms plot_se : bool If plot_se is true, then the confidence interval for the linear prediction will be added to the plot. cpr : bool If cpr (component plus residual) is true, the a scatter plot of the partial working residuals will be added to the plot. include_constant : bool If true, then the estimated intercept is added to the prediction and its standard errors. This avoids that the confidence interval has zero width at the imposed identification constraint, e.g. either at a reference point or at the mean. ax : None or matplotlib axis instance If ax is not None, then the plot will be added to it. Returns ------- Figure If `ax` is None, the created figure. Otherwise the Figure to which `ax` is connected. """ from import _import_mpl, create_mpl_ax _import_mpl() variable = smooth_index y_est, se = self.partial_values(variable, include_constant=include_constant) smoother = self.model.smoother x = smoother.smoothers[variable].x sort_index = np.argsort(x) x = x[sort_index] y_est = y_est[sort_index] se = se[sort_index] fig, ax = create_mpl_ax(ax) ax.plot(x, y_est, c='blue', lw=2) if plot_se: ax.plot(x, y_est + 1.96 * se, '-', c='blue') ax.plot(x, y_est - 1.96 * se, '-', c='blue') if cpr: # TODO: resid_response does not make sense with nonlinear link # use resid_working ? residual = self.resid_working[sort_index] cpr_ = y_est + residual ax.plot(x, cpr_, '.', lw=2) ax.set_xlabel(smoother.smoothers[variable].variable_name) return fig
[docs] def test_significance(self, smooth_index): """hypothesis test that a smooth component is zero. This calls `wald_test` to compute the hypothesis test, but uses effective degrees of freedom. Parameters ---------- smooth_index : int index of the smooth term within list of smooth terms Returns ------- wald_test : ContrastResults instance the results instance created by `wald_test` """ variable = smooth_index smoother = self.model.smoother start_idx = self.model.k_exog_linear k_params = len(self.params) # a bit messy, we need first index plus length of smooth term mask = smoother.mask[variable] k_constraints = mask.sum() idx = start_idx + np.nonzero(mask)[0][0] constraints = np.eye(k_constraints, k_params, idx) df_constraints = self.edf[idx: idx + k_constraints].sum() return self.wald_test(constraints, df_constraints=df_constraints)
[docs] def get_hat_matrix_diag(self, observed=True, _axis=1): """ Compute the diagonal of the hat matrix Parameters ---------- observed : bool If true, then observed hessian is used in the hat matrix computation. If false, then the expected hessian is used. In the case of a canonical link function both are the same. This is only relevant for models that implement both observed and expected Hessian, which is currently only GLM. Other models only use the observed Hessian. _axis : int This is mainly for internal use. By default it returns the usual diagonal of the hat matrix. If _axis is zero, then the result corresponds to the effective degrees of freedom, ``edf`` for each column of exog. Returns ------- hat_matrix_diag : ndarray The diagonal of the hat matrix computed from the observed or expected hessian. """ weights = self.model.hessian_factor(self.params, scale=self.scale, observed=observed) wexog = np.sqrt(weights)[:, None] * self.model.exog # we can use inverse hessian directly instead of computing it from # WLS/IRLS as in GLM # TODO: does `normalized_cov_params * scale` work in all cases? # this avoids recomputing hessian, check when used for other models. hess_inv = self.normalized_cov_params * self.scale # this is in GLM equivalent to the more generic and direct # hess_inv = np.linalg.inv(-self.model.hessian(self.params)) hd = (wexog * return hd
@cache_readonly def edf(self): return self.get_hat_matrix_diag(_axis=0) @cache_readonly def hat_matrix_trace(self): return self.hat_matrix_diag.sum() @cache_readonly def hat_matrix_diag(self): return self.get_hat_matrix_diag(observed=True) @cache_readonly def gcv(self): return self.scale / (1. - self.hat_matrix_trace / self.nobs)**2 @cache_readonly def cv(self): cv_ = ((self.resid_pearson / (1. - self.hat_matrix_diag))**2).sum() cv_ /= self.nobs return cv_
class GLMGamResultsWrapper(GLMResultsWrapper): pass wrap.populate_wrapper(GLMGamResultsWrapper, GLMGamResults)
[docs]class GLMGam(PenalizedMixin, GLM): """ Generalized Additive Models (GAM) This inherits from `GLM`. Warning: Not all inherited methods might take correctly account of the penalization. Not all options including offset and exposure have been verified yet. Parameters ---------- endog : array_like The response variable. exog : array_like or None This explanatory variables are treated as linear. The model in this case is a partial linear model. smoother : instance of additive smoother class Examples of smoother instances include Bsplines or CyclicCubicSplines. alpha : float or list of floats Penalization weights for smooth terms. The length of the list needs to be the same as the number of smooth terms in the ``smoother``. family : instance of GLM family See GLM. offset : None or array_like See GLM. exposure : None or array_like See GLM. missing : 'none' Missing value handling is not supported in this class. **kwargs Extra keywords are used in call to the super classes. Notes ----- Status: experimental. This has full unit test coverage for the core results with Gaussian and Poisson (without offset and exposure). Other options and additional results might not be correctly supported yet. (Binomial with counts, i.e. with n_trials, is most likely wrong in pirls. User specified var or freq weights are most likely also not correct for all results.) """ _results_class = GLMGamResults _results_class_wrapper = GLMGamResultsWrapper def __init__(self, endog, exog=None, smoother=None, alpha=0, family=None, offset=None, exposure=None, missing='none', **kwargs): # TODO: check usage of hasconst hasconst = kwargs.get('hasconst', None) xnames_linear = None if hasattr(exog, 'design_info'): self.design_info_linear = exog.design_info xnames_linear = self.design_info_linear.column_names is_pandas = _is_using_pandas(exog, None) # TODO: handle data is experimental, see #5469 # This is a bit wasteful because we need to `handle_data twice` self.data_linear = self._handle_data(endog, exog, missing, hasconst) if xnames_linear is None: xnames_linear = self.data_linear.xnames if exog is not None: exog_linear = self.data_linear.exog k_exog_linear = exog_linear.shape[1] else: exog_linear = None k_exog_linear = 0 self.k_exog_linear = k_exog_linear # We need exog_linear for k-fold cross validation # TODO: alternative is to take columns from combined exog self.exog_linear = exog_linear self.smoother = smoother self.k_smooths = smoother.k_variables self.alpha = self._check_alpha(alpha) penal = MultivariateGamPenalty(smoother, alpha=self.alpha, start_idx=k_exog_linear) kwargs.pop('penal', None) if exog_linear is not None: exog = np.column_stack((exog_linear, smoother.basis)) else: exog = smoother.basis # TODO: check: xnames_linear will be None instead of empty list # if no exog_linear # can smoother be empty ? I guess not allowed. if xnames_linear is None: xnames_linear = [] xnames = xnames_linear + self.smoother.col_names if is_pandas and exog_linear is not None: # we a dataframe so we can get a PandasData instance for wrapping exog = pd.DataFrame(exog, index=self.data_linear.row_labels, columns=xnames) super(GLMGam, self).__init__(endog, exog=exog, family=family, offset=offset, exposure=exposure, penal=penal, missing=missing, **kwargs) if not is_pandas: # set exog nanmes if not given by pandas DataFrame self.exog_names[:] = xnames # TODO: the generic data handling might attach the design_info from the # linear part, but this is incorrect for the full model and # causes problems in wald_test_terms if hasattr(, 'design_info'): del # formula also might be attached which causes problems in predict if hasattr(self, 'formula'): self.formula_linear = self.formula self.formula = None del self.formula def _check_alpha(self, alpha): """check and convert alpha to required list format Parameters ---------- alpha : scalar, list or array_like penalization weight Returns ------- alpha : list penalization weight, list with length equal to the number of smooth terms """ if not isinstance(alpha, Iterable): alpha = [alpha] * len(self.smoother.smoothers) elif not isinstance(alpha, list): # we want alpha to be a list alpha = list(alpha) return alpha
[docs] def fit(self, start_params=None, maxiter=1000, method='pirls', tol=1e-8, scale=None, cov_type='nonrobust', cov_kwds=None, use_t=None, full_output=True, disp=False, max_start_irls=3, **kwargs): """estimate parameters and create instance of GLMGamResults class Parameters ---------- most parameters are the same as for GLM method : optimization method The special optimization method is "pirls" which uses a penalized version of IRLS. Other methods are gradient optimizers as used in base.model.LikelihoodModel. Returns ------- res : instance of wrapped GLMGamResults """ # TODO: temporary hack to remove attribute # formula also might be attached which in inherited from_formula # causes problems in predict if hasattr(self, 'formula'): self.formula_linear = self.formula del self.formula # TODO: alpha not allowed yet, but is in `_fit_pirls` # alpha = self._check_alpha() if method.lower() in ['pirls', 'irls']: res = self._fit_pirls(self.alpha, start_params=start_params, maxiter=maxiter, tol=tol, scale=scale, cov_type=cov_type, cov_kwds=cov_kwds, use_t=use_t, **kwargs) else: if max_start_irls > 0 and (start_params is None): res = self._fit_pirls(self.alpha, start_params=start_params, maxiter=max_start_irls, tol=tol, scale=scale, cov_type=cov_type, cov_kwds=cov_kwds, use_t=use_t, **kwargs) start_params = res.params del res res = super(GLMGam, self).fit(start_params=start_params, maxiter=maxiter, method=method, tol=tol, scale=scale, cov_type=cov_type, cov_kwds=cov_kwds, use_t=use_t, full_output=full_output, disp=disp, max_start_irls=0, **kwargs) return res
# pag 165 4.3 # pag 136 PIRLS def _fit_pirls(self, alpha, start_params=None, maxiter=100, tol=1e-8, scale=None, cov_type='nonrobust', cov_kwds=None, use_t=None, weights=None): """fit model with penalized reweighted least squares """ # TODO: this currently modifies several attributes # self.scale, self.scaletype,, self.weights # self.data_weights, # and possibly self._offset_exposure # several of those might not be necessary, e.g. mu and weights # alpha = alpha * len(y) * self.scale / 100 # TODO: we need to rescale alpha endog = self.endog wlsexog = self.exog # smoother.basis spl_s = self.penal.penalty_matrix(alpha=alpha) nobs, n_columns = wlsexog.shape # TODO what are these values? if weights is None: self.data_weights = np.array([1.] * nobs) else: self.data_weights = weights if not hasattr(self, '_offset_exposure'): self._offset_exposure = 0 self.scaletype = scale # TODO: check default scale types # self.scaletype = 'dev' # during iteration self.scale = 1 if start_params is None: mu = lin_pred = else: lin_pred =, start_params) + self._offset_exposure mu = dev =, mu) history = dict(params=[None, start_params], deviance=[np.inf, dev]) converged = False criterion = history['deviance'] # This special case is used to get the likelihood for a specific # params vector. if maxiter == 0: mu = self.scale = self.estimate_scale(mu) wls_results = lm.RegressionResults(self, start_params, None) iteration = 0 for iteration in range(maxiter): # TODO: is this equivalent to point 1 of page 136: # w = 1 / (V(mu) * g'(mu)) ? self.weights = self.data_weights * # TODO: is this equivalent to point 1 of page 136: # z = g(mu)(y - mu) + X beta ? wlsendog = (lin_pred + * (endog - mu) - self._offset_exposure) # this defines the augmented matrix point 2a on page 136 wls_results = penalized_wls(wlsendog, wlsexog, spl_s, self.weights) lin_pred =, wls_results.params).ravel() lin_pred += self._offset_exposure mu = # We do not need to update scale in GLM/LEF models # We might need it in dispersion models. # self.scale = self.estimate_scale(mu) history = self._update_history(wls_results, mu, history) if endog.squeeze().ndim == 1 and np.allclose(mu - endog, 0): msg = "Perfect separation detected, results not available" raise PerfectSeparationError(msg) # TODO need atol, rtol # args of _check_convergence: (criterion, iteration, atol, rtol) converged = _check_convergence(criterion, iteration, tol, 0) if converged: break = mu self.scale = self.estimate_scale(mu) glm_results = GLMGamResults(self, wls_results.params, wls_results.normalized_cov_params, self.scale, cov_type=cov_type, cov_kwds=cov_kwds, use_t=use_t) glm_results.method = "PIRLS" history['iteration'] = iteration + 1 glm_results.fit_history = history glm_results.converged = converged return GLMGamResultsWrapper(glm_results)
[docs] def select_penweight(self, criterion='aic', start_params=None, start_model_params=None, method='basinhopping', **fit_kwds): """find alpha by minimizing results criterion The objective for the minimization can be results attributes like ``gcv``, ``aic`` or ``bic`` where the latter are based on effective degrees of freedom. Warning: In many case the optimization might converge to a local optimum or near optimum. Different start_params or using a global optimizer is recommended, default is basinhopping. Parameters ---------- criterion='aic' name of results attribute to be minimized. Default is 'aic', other options are 'gcv', 'cv' or 'bic'. start_params : None or array starting parameters for alpha in the penalization weight minimization. The parameters are internally exponentiated and the minimization is with respect to ``exp(alpha)`` start_model_params : None or array starting parameter for the ``model._fit_pirls``. method : 'basinhopping', 'nm' or 'minimize' 'basinhopping' and 'nm' directly use the underlying scipy.optimize functions `basinhopping` and `fmin`. 'minimize' provides access to the high level interface, `scipy.optimize.minimize`. fit_kwds : keyword arguments additional keyword arguments will be used in the call to the scipy optimizer. Which keywords are supported depends on the scipy optimization function. Returns ------- alpha : ndarray penalization parameter found by minimizing the criterion. Note that this can be only a local (near) optimum. fit_res : tuple results returned by the scipy optimization routine. The parameters in the optimization problem are `log(alpha)` history : dict history of calls to pirls and contains alpha, the fit criterion and the parameters to which pirls converged to for the given alpha. Notes ----- In the test cases Nelder-Mead and bfgs often converge to local optima, see also This does not use any analytical derivatives for the criterion minimization. Status: experimental, It is possible that defaults change if there is a better way to find a global optimum. API (e.g. type of return) might also change. """ # copy attributes that are changed, so we can reset them scale_keep = self.scale scaletype_keep = self.scaletype # TODO: use .copy() method when available for all types alpha_keep = copy.copy(self.alpha) if start_params is None: start_params = np.zeros(self.k_smooths) else: start_params = np.log(1e-20 + start_params) history = {} history['alpha'] = [] history['params'] = [start_model_params] history['criterion'] = [] def fun(p): a = np.exp(p) res_ = self._fit_pirls(start_params=history['params'][-1], alpha=a) history['alpha'].append(a) history['params'].append(np.asarray(res_.params)) return getattr(res_, criterion) if method == 'nm': kwds = dict(full_output=True, maxiter=1000, maxfun=2000) kwds.update(fit_kwds) fit_res = optimize.fmin(fun, start_params, **kwds) opt = fit_res[0] elif method == 'basinhopping': kwds = dict(minimizer_kwargs={'method': 'Nelder-Mead', 'options': {'maxiter': 100, 'maxfev': 500}}, niter=10) kwds.update(fit_kwds) fit_res = optimize.basinhopping(fun, start_params, **kwds) opt = fit_res.x elif method == 'minimize': fit_res = optimize.minimize(fun, start_params, **fit_kwds) opt = fit_res.x else: raise ValueError('method not recognized') del history['params'][0] # remove the model start_params alpha = np.exp(opt) # reset attributes that have or might have changed self.scale = scale_keep self.scaletype = scaletype_keep self.alpha = alpha_keep return alpha, fit_res, history
[docs] def select_penweight_kfold(self, alphas=None, cv_iterator=None, cost=None, k_folds=5, k_grid=11): """find alphas by k-fold cross-validation Warning: This estimates ``k_folds`` models for each point in the grid of alphas. Parameters ---------- alphas : None or list of arrays cv_iterator : instance instance of a cross-validation iterator, by default this is a KFold instance cost : function default is mean squared error. The cost function to evaluate the prediction error for the left out sample. This should take two arrays as argument and return one float. k_folds : int number of folds if default Kfold iterator is used. This is ignored if ``cv_iterator`` is not None. Returns ------- alpha_cv : list of float Best alpha in grid according to cross-validation res_cv : instance of MultivariateGAMCVPath The instance was used for cross-validation and holds the results Notes ----- The default alphas are defined as ``alphas = [np.logspace(0, 7, k_grid) for _ in range(k_smooths)]`` """ if cost is None: def cost(x1, x2): return np.linalg.norm(x1 - x2) / len(x1) if alphas is None: alphas = [np.logspace(0, 7, k_grid) for _ in range(self.k_smooths)] if cv_iterator is None: cv_iterator = KFold(k_folds=k_folds, shuffle=True) gam_cv = MultivariateGAMCVPath(smoother=self.smoother, alphas=alphas, gam=GLMGam, cost=cost, endog=self.endog, exog=self.exog_linear, cv_iterator=cv_iterator) gam_cv_res = return gam_cv_res.alpha_cv, gam_cv_res
[docs]class LogitGam(PenalizedMixin, Logit): """Generalized Additive model for discrete Logit This subclasses discrete_model Logit. Warning: not all inherited methods might take correctly account of the penalization not verified yet. """ def __init__(self, endog, smoother, alpha, *args, **kwargs): if not isinstance(alpha, Iterable): alpha = np.array([alpha] * len(smoother.smoothers)) self.smoother = smoother self.alpha = alpha self.pen_weight = 1 # TODO: pen weight should not be defined here!! penal = MultivariateGamPenalty(smoother, alpha=alpha) super(LogitGam, self).__init__(endog, smoother.basis, penal=penal, *args, **kwargs)
def penalized_wls(endog, exog, penalty_matrix, weights): """weighted least squares with quadratic penalty Parameters ---------- endog : ndarray response or endogenous variable exog : ndarray design matrix, matrix of exogenous or explanatory variables penalty_matrix : ndarray, 2-Dim square penality matrix for quadratic penalization. Note, the penalty_matrix is multiplied by two to match non-pirls fitting methods. weights : ndarray weights for WLS Returns ------- results : Results instance of WLS """ y, x, s = endog, exog, penalty_matrix # TODO: I do not understand why I need 2 * s aug_y, aug_x, aug_weights = make_augmented_matrix(y, x, 2 * s, weights) wls_results = lm.WLS(aug_y, aug_x, aug_weights).fit() # TODO: use MinimalWLS during iterations, less overhead # However, MinimalWLS does not return normalized_cov_params # which we need at the end of the iterations # call would be # wls_results = reg_tools._MinimalWLS(aug_y, aug_x, aug_weights).fit() wls_results.params = wls_results.params.ravel() return wls_results def make_augmented_matrix(endog, exog, penalty_matrix, weights): """augment endog, exog and weights with stochastic restriction matrix Parameters ---------- endog : ndarray response or endogenous variable exog : ndarray design matrix, matrix of exogenous or explanatory variables penalty_matrix : ndarray, 2-Dim square penality matrix for quadratic penalization weights : ndarray weights for WLS Returns ------- endog_aug : ndarray augmented response variable exog_aug : ndarray augmented design matrix weights_aug : ndarray augmented weights for WLS """ y, x, s, = endog, exog, penalty_matrix nobs = x.shape[0] # TODO: needs full because of broadcasting with weights # check what weights should be doing rs = matrix_sqrt(s) x1 = np.vstack([x, rs]) # augmented x n_samp1es_x1 = x1.shape[0] y1 = np.array([0.] * n_samp1es_x1) # augmented y y1[:nobs] = y id1 = np.array([1.] * rs.shape[0]) w1 = np.concatenate([weights, id1]) return y1, x1, w1