def plot_ceres_residuals(results, focus_exog, frac=0.66, cond_means=None, ax=None): # Docstring attached below model = results.model focus_exog, focus_col = utils.maybe_name_or_idx(focus_exog, model) presid = ceres_resids(results, focus_exog, frac=frac, cond_means=cond_means) focus_exog_vals = model.exog[:, focus_col] fig, ax = utils.create_mpl_ax(ax) ax.plot(focus_exog_vals, presid, 'o', alpha=0.6) ax.set_title('CERES residuals plot', fontsize='large') ax.set_xlabel(focus_exog, size=15) ax.set_ylabel("Component plus residual", size=15) return fig
def plot_ccpr(results, exog_idx, ax=None): """Plot CCPR against one regressor. Generates a CCPR (component and component-plus-residual) plot. Parameters ---------- results : result instance A regression results instance. exog_idx : int or string Exogenous, explanatory variable. If string is given, it should be the variable name that you want to use, and you can use arbitrary translations as with a formula. ax : Matplotlib AxesSubplot instance, optional If given, it is used to plot in instead of a new figure being created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. See Also -------- plot_ccpr_grid : Creates CCPR plot for multiple regressors in a plot grid. Notes ----- The CCPR plot provides a way to judge the effect of one regressor on the response variable by taking into account the effects of the other independent variables. The partial residuals plot is defined as Residuals + B_i*X_i versus X_i. The component adds the B_i*X_i versus X_i to show where the fitted line would lie. Care should be taken if X_i is highly correlated with any of the other independent variables. If this is the case, the variance evident in the plot will be an underestimate of the true variance. References ---------- http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) x1 = results.model.exog[:, exog_idx] #namestr = ' for %s' % self.name if self.name else '' x1beta = x1*results._results.params[exog_idx] ax.plot(x1, x1beta + results.resid, 'o') from statsmodels.tools.tools import add_constant mod = OLS(x1beta, add_constant(x1)).fit() params = mod.params fig = abline_plot(*params, **dict(ax=ax)) #ax.plot(x1, x1beta, '-') ax.set_title('Component and component plus residual plot') ax.set_ylabel("Residual + %s*beta_%d" % (exog_name, exog_idx)) ax.set_xlabel("%s" % exog_name) return fig
def ccpr_data(results, exog_idx): exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) x1 = results.model.exog[:, exog_idx] x1beta = x1 * results.params[exog_idx] return x1, x1beta + results.resid
def plot_fit(results, exog_idx, y_true=None, ax=None, **kwargs): """Plot fit against one regressor. This creates one graph with the scatterplot of observed values compared to fitted values. Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes x_var : int or str Name or index of regressor in exog matrix. y_true : array_like (optional) If this is not None, then the array is added to the plot ax : Matplotlib AxesSubplot instance, optional If given, this subplot is used to plot in instead of a new figure being created. kwargs The keyword arguments are passed to the plot command for the fitted values points. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y = results.model.endog x1 = results.model.exog[:, exog_idx] x1_argsort = np.argsort(x1) y = y[x1_argsort] x1 = x1[x1_argsort] ax.plot(x1, y, 'bo', label=results.model.endog_names) if not y_true is None: ax.plot(x1, y_true[x1_argsort], 'b-', label='True values') title = 'Fitted values versus %s' % exog_name prstd, iv_l, iv_u = wls_prediction_std(results) ax.plot(x1, results.fittedvalues[x1_argsort], 'D', color='r', label='fitted', **kwargs) ax.vlines(x1, iv_l[x1_argsort], iv_u[x1_argsort], linewidth=1, color='k', alpha=.7) #ax.fill_between(x1, iv_l[x1_argsort], iv_u[x1_argsort], alpha=0.1, # color='k') ax.set_title(title) ax.set_xlabel(exog_name) ax.set_ylabel(results.model.endog_names) ax.legend(loc='best') return fig
def ccpr_data(results, exog_idx): exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) x1 = results.model.exog[:, exog_idx] x1beta = x1*results.params[exog_idx] return x1, x1beta + results.resid
def _variable_pos(self, var, model): if model == 'mediator': mod = self.mediator_model else: mod = self.outcome_model if var == 'mediator': return maybe_name_or_idx(self.mediator, mod)[1] exp = self.exposure exp_is_2 = ((len(exp) == 2) and not isinstance(exp, string_types)) if exp_is_2: if model == 'outcome': return exp[0] elif model == 'mediator': return exp[1] else: return maybe_name_or_idx(exp, mod)[1]
def _variable_pos(self, var, model): if model == 'mediator': mod = self.mediator_model else: mod = self.outcome_model if var == 'mediator': return maybe_name_or_idx(self.mediator, mod)[1] exp = self.exposure exp_is_2 = ((len(exp) == 2) and (type(exp) != type(''))) if exp_is_2: if model == 'outcome': return exp[0] elif model == 'mediator': return exp[1] else: return maybe_name_or_idx(exp, mod)[1]
def retrieve_ols_predictions_and_errors(ols_results, regressor): ''' This function retrieves OLS predictions and errors from OLS results for each dataset given in ols_results. Final dict has the following pattern: { <first_variable>: { 'x': <array>, 'predictions': <array> 'errors': { 'min': <array> 'max': <array> } } [, <second_variable>: { 'x': <array>, 'predictions': <array> 'errors': { 'min': <array> 'max': <array> } }, ...] } Parameters - ols_results: Dictionary containing results for each dataset on which OLS has been run (see run_ols_test) - regressor: Name or index of regressor in exog matrix (see statsmodels documentation if needed) Return - results: Dictionary containing predictions and errors for each dataset given in ols_results ''' results = {} for key, ols_results in ols_results.items(): name, index = utils.maybe_name_or_idx(regressor, ols_results.model) x = ols_results.model.exog[:, index] x_argsort = np.argsort(x) x = x[x_argsort] prstd, iv_l, iv_u = wls_prediction_std(ols_results) predictions = ols_results.fittedvalues results[key] = {'x': x, 'predictions': predictions, 'errors': {'min': iv_l, 'max': iv_u}} return results
def plot_partial_residuals(results, focus_exog, ax=None): # Docstring attached below model = results.model focus_exog, focus_col = utils.maybe_name_or_idx(focus_exog, model) pr = partial_resids(results, focus_exog) focus_exog_vals = results.model.exog[:, focus_col] fig, ax = utils.create_mpl_ax(ax) ax.plot(focus_exog_vals, pr, 'o', alpha=0.6) ax.set_title('Partial residuals plot', fontsize='large') if type(focus_exog) is str: xname = focus_exog else: xname = model.exog_names[focus_exog] ax.set_xlabel(xname, size=15) ax.set_ylabel("Component plus residual", size=15) return fig
def plot_ccpr_grid(results, exog_idx=None, grid=None, fig=None): """Generate CCPR plots against a set of regressors, plot in a grid. Generates a grid of CCPR (component and component-plus-residual) plots. Parameters ---------- results : result instance uses exog and params of the result instance exog_idx : None or list of int (column) indices of the exog used in the plot grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Notes ----- Partial residual plots are formed as:: Res + Betahat(i)*Xi versus Xi and CCPR adds:: Betahat(i)*Xi versus Xi See Also -------- plot_ccpr : Creates CCPR plot for a single regressor. References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx) / 2.)) ncols = 2 else: nrows = len(exog_idx) ncols = 1 seen_constant = 0 for i, idx in enumerate(exog_idx): if results.model.exog[:, idx].var() == 0: seen_constant = 1 continue ax = fig.add_subplot(nrows, ncols, i + 1 - seen_constant) fig = plot_ccpr(results, exog_idx=idx, ax=ax) ax.set_title("") fig.suptitle("Component-Component Plus Residual Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def added_variable_resids(results, focus_exog, resid_type=None, use_glm_weights=True, fit_kwargs=None): """ Residualize the endog variable and a 'focus' exog variable in a regression model with respect to the other exog variables. Parameters ---------- results : regression results instance A fitted model including the focus exog and all other predictors of interest. focus_exog : integer or string The column of results.model.exog or a variable name that is to be residualized against the other predictors. resid_type : string The type of residuals to use for the dependent variable. If None, uses `resid_deviance` for GLM/GEE and `resid` otherwise. use_glm_weights : bool Only used if the model is a GLM or GEE. If True, the residuals for the focus predictor are computed using WLS, with the weights obtained from the IRLS calculations for fitting the GLM. If False, unweighted regression is used. fit_kwargs : dict, optional Keyword arguments to be passed to fit when refitting the model. Returns ------- endog_resid : array-like The residuals for the original exog focus_exog_resid : array-like The residuals for the focus predictor Notes ----- The 'focus variable' residuals are always obtained using linear regression. Currently only GLM, GEE, and OLS models are supported. """ model = results.model if not isinstance(model, (GEE, GLM, OLS)): raise ValueError("model type %s not supported for added variable residuals" % model.__class__.__name__) exog = model.exog endog = model.endog focus_exog, focus_col = utils.maybe_name_or_idx(focus_exog, model) focus_exog_vals = exog[:, focus_col] # Default residuals if resid_type is None: if isinstance(model, (GEE, GLM)): resid_type = "resid_deviance" else: resid_type = "resid" ii = range(exog.shape[1]) ii = list(ii) ii.pop(focus_col) reduced_exog = exog[:, ii] start_params = results.params[ii] klass = model.__class__ kwargs = model._get_init_kwds() new_model = klass(endog, reduced_exog, **kwargs) args = {"start_params": start_params} if fit_kwargs is not None: args.update(fit_kwargs) new_result = new_model.fit(**args) if not new_result.converged: raise ValueError("fit did not converge when calculating added variable residuals") try: endog_resid = getattr(new_result, resid_type) except AttributeError: raise ValueError("'%s' residual type not available" % resid_type) import statsmodels.regression.linear_model as lm if isinstance(model, (GLM, GEE)) and use_glm_weights: weights = model.family.weights(results.fittedvalues) if hasattr(model, "data_weights"): weights = weights * model.data_weights lm_results = lm.WLS(focus_exog_vals, reduced_exog, weights).fit() else: lm_results = lm.OLS(focus_exog_vals, reduced_exog).fit() focus_exog_resid = lm_results.resid return endog_resid, focus_exog_resid
def plot_partregress_grid(results, exog_idx=None, grid=None, fig=None): """Plot partial regression for a set of regressors. Parameters ---------- results : #1lab_results instance A regression model #1lab_results instance exog_idx : None, list of ints, list of strings (column) indices of the exog used in the plot, default is all. grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `fig` is None, the created figure. Otherwise `fig` itself. Notes ----- A subplot is created for each explanatory variable given by exog_idx. The partial regression plot shows the relationship between the response and the given explanatory variable after removing the effect of all other explanatory variables in exog. See Also -------- plot_partregress : Plot partial regression for a single regressor. plot_ccpr References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/partregr.htm """ import pandas fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) #maybe add option for using wendog, wexog instead y = pandas.Series(results.model.endog, name=results.model.endog_names) exog = results.model.exog k_vars = exog.shape[1] #this function doesn't make sense if k_vars=1 if not grid is None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx) / 2.)) ncols = 2 title_kwargs = {"fontdict": {"fontsize": 'small'}} else: nrows = len(exog_idx) ncols = 1 title_kwargs = {} # for indexing purposes other_names = np.array(results.model.exog_names) for i, idx in enumerate(exog_idx): others = lrange(k_vars) others.pop(idx) exog_others = pandas.DataFrame(exog[:, others], columns=other_names[others]) ax = fig.add_subplot(nrows, ncols, i + 1) plot_partregress(y, pandas.Series(exog[:, idx], name=other_names[idx]), exog_others, ax=ax, title_kwargs=title_kwargs, obs_labels=False) ax.set_title("") fig.suptitle("Partial Regression Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_partregress_grid(results, exog_idx=None, grid=None, fig=None): """Plot partial regression for a set of regressors. Parameters ---------- results : results instance A regression model results instance exog_idx : None, list of ints, list of strings (column) indices of the exog used in the plot, default is all. grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `fig` is None, the created figure. Otherwise `fig` itself. Notes ----- A subplot is created for each explanatory variable given by exog_idx. The partial regression plot shows the relationship between the response and the given explanatory variable after removing the effect of all other explanatory variables in exog. See Also -------- plot_partregress : Plot partial regression for a single regressor. plot_ccpr : Plot CCPR against one regressor Examples -------- Using the state crime dataset seperately plot the effect of the each variable on the on the outcome, murder rate while accounting for the effect of all other variables in the model visualized with a grid of partial regression plots. >>> from statsmodels.graphics.regressionplots import plot_partregress_grid >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> import statsmodels.formula.api as smf >>> fig = plt.figure(figsize=(8, 6)) >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> plot_partregress_grid(results, fig=fig) >>> plt.show() .. plot:: plots/graphics_regression_partregress_grid.py References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/partregr.htm """ import pandas fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) #maybe add option for using wendog, wexog instead y = pandas.Series(results.model.endog, name=results.model.endog_names) exog = results.model.exog k_vars = exog.shape[1] #this function doesn't make sense if k_vars=1 if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx) / 2.)) ncols = 2 title_kwargs = {"fontdict": {"fontsize": 'small'}} else: nrows = len(exog_idx) ncols = 1 title_kwargs = {} # for indexing purposes other_names = np.array(results.model.exog_names) for i, idx in enumerate(exog_idx): others = lrange(k_vars) others.pop(idx) exog_others = pandas.DataFrame(exog[:, others], columns=other_names[others]) ax = fig.add_subplot(nrows, ncols, i + 1) plot_partregress(y, pandas.Series(exog[:, idx], name=other_names[idx]), exog_others, ax=ax, title_kwargs=title_kwargs, obs_labels=False) ax.set_title("") fig.suptitle("Partial Regression Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_ccpr_grid(results, exog_idx=None, grid=None, fig=None): """Generate CCPR plots against a set of regressors, plot in a grid. Generates a grid of CCPR (component and component-plus-residual) plots. Parameters ---------- results : result instance uses exog and params of the result instance exog_idx : None or list of int (column) indices of the exog used in the plot grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Notes ----- Partial residual plots are formed as:: Res + Betahat(i)*Xi versus Xi and CCPR adds:: Betahat(i)*Xi versus Xi See Also -------- plot_ccpr : Creates CCPR plot for a single regressor. Examples -------- Using the state crime dataset seperately plot the effect of the each variable on the on the outcome, murder rate while accounting for the effect of all other variables in the model. >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> import statsmodels.formula.api as smf >>> fig = plt.figure(figsize=(8, 8)) >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> sm.graphics.plot_ccpr_grid(results, fig=fig) >>> plt.show() .. plot:: plots/graphics_regression_ccpr_grid.py References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx) / 2.)) ncols = 2 else: nrows = len(exog_idx) ncols = 1 seen_constant = 0 for i, idx in enumerate(exog_idx): if results.model.exog[:, idx].var() == 0: seen_constant = 1 continue ax = fig.add_subplot(nrows, ncols, i + 1 - seen_constant) fig = plot_ccpr(results, exog_idx=idx, ax=ax) ax.set_title("") fig.suptitle("Component-Component Plus Residual Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_ccpr(results, exog_idx, ax=None): """Plot CCPR against one regressor. Generates a CCPR (component and component-plus-residual) plot. Parameters ---------- results : result instance A regression results instance. exog_idx : int or string Exogenous, explanatory variable. If string is given, it should be the variable name that you want to use, and you can use arbitrary translations as with a formula. ax : Matplotlib AxesSubplot instance, optional If given, it is used to plot in instead of a new figure being created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. See Also -------- plot_ccpr_grid : Creates CCPR plot for multiple regressors in a plot grid. Notes ----- The CCPR plot provides a way to judge the effect of one regressor on the response variable by taking into account the effects of the other independent variables. The partial residuals plot is defined as Residuals + B_i*X_i versus X_i. The component adds the B_i*X_i versus X_i to show where the fitted line would lie. Care should be taken if X_i is highly correlated with any of the other independent variables. If this is the case, the variance evident in the plot will be an underestimate of the true variance. Examples -------- Using the state crime dataset plot the effect of the rate of single households ('single') on the murder rate while accounting for high school graduation rate ('hs_grad'), percentage of people in an urban area, and rate of poverty ('poverty'). >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plot >>> import statsmodels.formula.api as smf >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> sm.graphics.plot_ccpr(results, 'single') >>> plt.show() .. plot:: plots/graphics_regression_ccpr.py References ---------- http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) x1 = results.model.exog[:, exog_idx] #namestr = ' for %s' % self.name if self.name else '' x1beta = x1*results.params[exog_idx] ax.plot(x1, x1beta + results.resid, 'o') from statsmodels.tools.tools import add_constant mod = OLS(x1beta, add_constant(x1)).fit() params = mod.params fig = abline_plot(*params, **dict(ax=ax)) #ax.plot(x1, x1beta, '-') ax.set_title('Component and component plus residual plot') ax.set_ylabel("Residual + %s*beta_%d" % (exog_name, exog_idx)) ax.set_xlabel("%s" % exog_name) return fig
def added_variable_resids(results, focus_exog, resid_type=None, use_glm_weights=True, fit_kwargs=None): """ Residualize the endog variable and a 'focus' exog variable in a regression model with respect to the other exog variables. Parameters ---------- results : regression results instance A fitted model including the focus exog and all other predictors of interest. focus_exog : integer or string The column of results.model.exog or a variable name that is to be residualized against the other predictors. resid_type : string The type of residuals to use for the dependent variable. If None, uses `resid_deviance` for GLM/GEE and `resid` otherwise. use_glm_weights : bool Only used if the model is a GLM or GEE. If True, the residuals for the focus predictor are computed using WLS, with the weights obtained from the IRLS calculations for fitting the GLM. If False, unweighted regression is used. fit_kwargs : dict, optional Keyword arguments to be passed to fit when refitting the model. Returns ------- endog_resid : array-like The residuals for the original exog focus_exog_resid : array-like The residuals for the focus predictor Notes ----- The 'focus variable' residuals are always obtained using linear regression. Currently only GLM, GEE, and OLS models are supported. """ model = results.model if not isinstance(model, (GEE, GLM, OLS)): raise ValueError( "model type %s not supported for added variable residuals" % model.__class__.__name__) exog = model.exog endog = model.endog focus_exog, focus_col = utils.maybe_name_or_idx(focus_exog, model) focus_exog_vals = exog[:, focus_col] # Default residuals if resid_type is None: if isinstance(model, (GEE, GLM)): resid_type = "resid_deviance" else: resid_type = "resid" ii = range(exog.shape[1]) ii = list(ii) ii.pop(focus_col) reduced_exog = exog[:, ii] start_params = results.params[ii] klass = model.__class__ kwargs = model._get_init_kwds() new_model = klass(endog, reduced_exog, **kwargs) args = {"start_params": start_params} if fit_kwargs is not None: args.update(fit_kwargs) new_result = new_model.fit(**args) if not new_result.converged: raise ValueError( "fit did not converge when calculating added variable residuals") try: endog_resid = getattr(new_result, resid_type) except AttributeError: raise ValueError("'%s' residual type not available" % resid_type) import statsmodels.regression.linear_model as lm if isinstance(model, (GLM, GEE)) and use_glm_weights: weights = model.family.weights(results.fittedvalues) if hasattr(model, "data_weights"): weights = weights * model.data_weights lm_results = lm.WLS(focus_exog_vals, reduced_exog, weights).fit() else: lm_results = lm.OLS(focus_exog_vals, reduced_exog).fit() focus_exog_resid = lm_results.resid return endog_resid, focus_exog_resid
def plot_fit(results, exog_idx, y_true=None, ax=None, **kwargs): """Plot fit against one regressor. This creates one graph with the scatterplot of observed values compared to fitted values. Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes x_var : int or str Name or index of regressor in exog matrix. y_true : array_like (optional) If this is not None, then the array is added to the plot ax : Matplotlib AxesSubplot instance, optional If given, this subplot is used to plot in instead of a new figure being created. kwargs The keyword arguments are passed to the plot command for the fitted values points. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Examples -------- Load the Statewide Crime data set and perform linear regression with `poverty` and `hs_grad` as variables and `murder` as the response >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> data = sm.datasets.statecrime.load_pandas().data >>> murder = data['murder'] >>> X = data[['poverty', 'hs_grad']] >>> X["constant"] = 1 >>> y = murder >>> model = sm.OLS(y, X) >>> results = model.fit() Create a plot just for the variable 'Poverty': >>> fig, ax = plt.subplots() >>> fig = sm.graphics.plot_fit(results, 0, ax=ax) >>> ax.set_ylabel("Murder Rate") >>> ax.set_xlabel("Poverty Level") >>> ax.set_title("Linear Regression") >>> plt.show() .. plot:: plots/graphics_plot_fit_ex.py """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y = results.model.endog x1 = results.model.exog[:, exog_idx] x1_argsort = np.argsort(x1) y = y[x1_argsort] x1 = x1[x1_argsort] ax.plot(x1, y, 'bo', label=results.model.endog_names) if not y_true is None: ax.plot(x1, y_true[x1_argsort], 'b-', label='True values') title = 'Fitted values versus %s' % exog_name prstd, iv_l, iv_u = wls_prediction_std(results) ax.plot(x1, results.fittedvalues[x1_argsort], 'D', color='r', label='fitted', **kwargs) ax.vlines(x1, iv_l[x1_argsort], iv_u[x1_argsort], linewidth=1, color='k', alpha=.7) #ax.fill_between(x1, iv_l[x1_argsort], iv_u[x1_argsort], alpha=0.1, # color='k') ax.set_title(title) ax.set_xlabel(exog_name) ax.set_ylabel(results.model.endog_names) ax.legend(loc='best', numpoints=1) return fig
def plot_ccpr_grid(results, exog_idx=None, grid=None, fig=None): """Generate CCPR plots against a set of regressors, plot in a grid. Generates a grid of CCPR (component and component-plus-residual) plots. Parameters ---------- results : result instance uses exog and params of the result instance exog_idx : None or list of int (column) indices of the exog used in the plot grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Notes ----- Partial residual plots are formed as:: Res + Betahat(i)*Xi versus Xi and CCPR adds:: Betahat(i)*Xi versus Xi See Also -------- plot_ccpr : Creates CCPR plot for a single regressor. References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx)/2.)) ncols = 2 else: nrows = len(exog_idx) ncols = 1 seen_constant = 0 for i, idx in enumerate(exog_idx): if results.model.exog[:, idx].var() == 0: seen_constant = 1 continue ax = fig.add_subplot(nrows, ncols, i+1-seen_constant) fig = plot_ccpr(results, exog_idx=idx, ax=ax) ax.set_title("") fig.suptitle("Component-Component Plus Residual Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_partregress_grid(results, exog_idx=None, grid=None, fig=None): """Plot partial regression for a set of regressors. Parameters ---------- results : results instance A regression model results instance exog_idx : None, list of ints, list of strings (column) indices of the exog used in the plot, default is all. grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `fig` is None, the created figure. Otherwise `fig` itself. Notes ----- A subplot is created for each explanatory variable given by exog_idx. The partial regression plot shows the relationship between the response and the given explanatory variable after removing the effect of all other explanatory variables in exog. See Also -------- plot_partregress : Plot partial regression for a single regressor. plot_ccpr References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/partregr.htm """ import pandas fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) #maybe add option for using wendog, wexog instead y = pandas.Series(results.model.endog, name=results.model.endog_names) exog = results.model.exog k_vars = exog.shape[1] #this function doesn't make sense if k_vars=1 if not grid is None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx)/2.)) ncols = 2 title_kwargs = {"fontdict" : {"fontsize" : 'small'}} else: nrows = len(exog_idx) ncols = 1 title_kwargs = {} # for indexing purposes other_names = np.array(results.model.exog_names) for i, idx in enumerate(exog_idx): others = lrange(k_vars) others.pop(idx) exog_others = pandas.DataFrame(exog[:, others], columns=other_names[others]) ax = fig.add_subplot(nrows, ncols, i+1) plot_partregress(y, pandas.Series(exog[:, idx], name=other_names[idx]), exog_others, ax=ax, title_kwargs=title_kwargs, obs_labels=False) ax.set_title("") fig.suptitle("Partial Regression Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_regress_exog(results, exog_idx, fig=None): """Plot regression results against one regressor. This plots four graphs in a 2 by 2 figure: 'endog versus exog', 'residuals versus exog', 'fitted versus exog' and 'fitted plus residual versus exog' Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes exog_idx : int index of regressor in exog matrix fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : matplotlib figure instance """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y_name = results.model.endog_names x1 = results.model.exog[:, exog_idx] prstd, iv_l, iv_u = wls_prediction_std(results) ax = fig.add_subplot(2, 2, 1) ax.plot(x1, results.model.endog, 'o', color='b', alpha=0.9, label=y_name) ax.plot(x1, results.fittedvalues, 'D', color='r', label='fitted', alpha=.5) ax.vlines(x1, iv_l, iv_u, linewidth=1, color='k', alpha=.7) ax.set_title('Y and Fitted vs. X', fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel(y_name) ax.legend(loc='best') ax = fig.add_subplot(2, 2, 2) ax.plot(x1, results.resid, 'o') ax.axhline(y=0, color='black') ax.set_title('Residuals versus %s' % exog_name, fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel("resid") ax = fig.add_subplot(2, 2, 3) exog_noti = np.ones(results.model.exog.shape[1], bool) exog_noti[exog_idx] = False exog_others = results.model.exog[:, exog_noti] from pandas import Series fig = plot_partregress(results.model.data.orig_endog, Series(x1, name=exog_name, index=results.model.data.row_labels), exog_others, obs_labels=False, ax=ax) ax.set_title('Partial regression plot', fontsize='large') #ax.set_ylabel("Fitted values") #ax.set_xlabel(exog_name) ax = fig.add_subplot(2, 2, 4) fig = plot_ccpr(results, exog_idx, ax=ax) ax.set_title('CCPR Plot', fontsize='large') #ax.set_xlabel(exog_name) #ax.set_ylabel("Fitted values + resids") fig.suptitle('Regression Plots for %s' % exog_name, fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.90) return fig
def feature_regression_summary(df, feat_idx, target, model_fit_results, display_regress_diagnostics=False): feat = df.columns[feat_idx] v = vif(np.matrix(df), feat_idx) colinear = v > 10 if display_regress_diagnostics: # ‘endog versus exog’, ‘residuals versus exog’, ‘fitted versus exog’ and ‘fitted plus residual versus exog’ fig = plt.figure(constrained_layout=True, figsize=(2.25 * plot_edge, 4 * plot_edge)) fig = smgrpu.create_mpl_fig(fig) gs = GridSpec(3, 2, figure=fig) ax_fit = fig.add_subplot(gs[0, 0]) ax_partial_residuals = fig.add_subplot(gs[0, 1]) ax_partregress = fig.add_subplot(gs[1, 0]) ax_ccpr = fig.add_subplot(gs[1, 1]) ax_dist = fig.add_subplot(gs[2:4, 0:2]) exog_name, exog_idx = smgrpu.maybe_name_or_idx(feat, model_fit_results.model) smresults = smtt.maybe_unwrap_results(model_fit_results) y_name = smresults.model.endog_names x1 = smresults.model.exog[:, exog_idx] prstd, iv_l, iv_u = wls_prediction_std(smresults) # endog versus exog # use wrapper since it's availab;e! sm.graphics.plot_fit(model_fit_results, feat, ax=ax_fit) # residuals versus exog ax_partial_residuals.plot(x1, smresults.resid, 'o') ax_partial_residuals.axhline(y=0, color='black') ax_partial_residuals.set_title('Residuals versus %s' % exog_name, fontsize='large') ax_partial_residuals.set_xlabel(exog_name) ax_partial_residuals.set_ylabel("resid") # Partial Regression plot: fitted versus exog exog_noti = np.ones(smresults.model.exog.shape[1], bool) exog_noti[exog_idx] = False exog_others = smresults.model.exog[:, exog_noti] from pandas import Series smgrp.plot_partregress(smresults.model.data.orig_endog, Series(x1, name=exog_name, index=smresults.model.data.row_labels), exog_others, obs_labels=False, ax=ax_partregress) # CCPR: fitted plus residual versus exog # use wrapper since it's availab;e! sm.graphics.plot_ccpr(model_fit_results, feat, ax=ax_ccpr) ax_ccpr.set_title('CCPR Plot', fontsize='large') sns.distplot(df[feat], ax=ax_dist) fig.suptitle('Regression Plots for %s' % exog_name, fontsize="large") #fig.tight_layout() #fig.subplots_adjust(top=.90) plt.show() display( HTML( "Variance Inflation Factor (<i>VIF</i>) for <b>{}</b>: <b>{}</b> {}" .format( feat, round(v, 2), "$\\le 10 \\iff$ low colinearity" if not colinear else "$> 10 \\iff$ <b>HIGH COLINEARITY</b>"))) display( HTML( "<b><i>p-value</i></b> (<i>VIF</i>) for <b>{}</b>: <b>{}</b><br><br>" .format(feat, model_fit_results.pvalues[feat_idx + 1]))) return v
def ceres_resids(results, focus_exog, frac=0.66, cond_means=None): """ Calculate the CERES residuals (Conditional Expectation Partial Residuals) for a fitted model. Parameters ---------- results : model results instance The fitted model for which the CERES residuals are calculated. focus_exog : int The column of results.model.exog used as the 'focus variable'. frac : float, optional Lowess smoothing parameter for estimating the conditional means. Not used if `cond_means` is provided. cond_means : array-like, optional If provided, the columns of this array are the conditional means E[exog | focus exog], where exog ranges over some or all of the columns of exog other than focus exog. If this is an empty nx0 array, the conditional means are treated as being zero. If None, the conditional means are estimated. Returns ------- An array containing the CERES residuals. Notes ----- If `cond_means` is not provided, it is obtained by smoothing each column of exog (except the focus column) against the focus column. Currently only supports GLM, GEE, and OLS models. """ model = results.model if not isinstance(model, (GLM, GEE, OLS)): raise ValueError("ceres residuals not available for %s" % model.__class__.__name__) focus_exog, focus_col = utils.maybe_name_or_idx(focus_exog, model) # Indices of non-focus columns ix_nf = range(len(results.params)) ix_nf = list(ix_nf) ix_nf.pop(focus_col) nnf = len(ix_nf) # Estimate the conditional means if not provided. if cond_means is None: # Below we calculate E[x | focus] where x is each column other # than the focus column. We don't want the intercept when we do # this so we remove it here. pexog = model.exog[:, ix_nf] pexog -= pexog.mean(0) u, s, vt = np.linalg.svd(pexog, 0) ii = np.flatnonzero(s > 1e-6) pexog = u[:, ii] fcol = model.exog[:, focus_col] cond_means = np.empty((len(fcol), pexog.shape[1])) for j in range(pexog.shape[1]): # Get the fitted values for column i given the other # columns (skip the intercept). y0 = pexog[:, j] cf = lowess(y0, fcol, frac=frac, return_sorted=False) cond_means[:, j] = cf new_exog = np.concatenate((model.exog[:, ix_nf], cond_means), axis=1) # Refit the model using the adjusted exog values klass = model.__class__ init_kwargs = model._get_init_kwds() new_model = klass(model.endog, new_exog, **init_kwargs) new_result = new_model.fit() # The partial residual, with respect to l(x2) (notation of Cook 1998) presid = model.endog - new_result.fittedvalues if isinstance(model, (GLM, GEE)): presid *= model.family.link.deriv(new_result.fittedvalues) if new_exog.shape[1] > nnf: presid += np.dot(new_exog[:, nnf:], new_result.params[nnf:]) return presid
def plot_partregress_grid(results, exog_idx=None, grid=None, fig=None): """Plot partial regression for a set of regressors. Parameters ---------- results : results instance A regression model results instance exog_idx : None, list of ints, list of strings (column) indices of the exog used in the plot, default is all. grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `fig` is None, the created figure. Otherwise `fig` itself. Notes ----- A subplot is created for each explanatory variable given by exog_idx. The partial regression plot shows the relationship between the response and the given explanatory variable after removing the effect of all other explanatory variables in exog. See Also -------- plot_partregress : Plot partial regression for a single regressor. plot_ccpr : Plot CCPR against one regressor Examples -------- Using the state crime dataset seperately plot the effect of the each variable on the on the outcome, murder rate while accounting for the effect of all other variables in the model visualized with a grid of partial regression plots. >>> from statsmodels.graphics.regressionplots import plot_partregress_grid >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> import statsmodels.formula.api as smf >>> fig = plt.figure(figsize=(8, 6)) >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> plot_partregress_grid(results, fig=fig) >>> plt.show() .. plot:: plots/graphics_regression_partregress_grid.py References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/partregr.htm """ import pandas fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) #maybe add option for using wendog, wexog instead y = pandas.Series(results.model.endog, name=results.model.endog_names) exog = results.model.exog k_vars = exog.shape[1] #this function doesn't make sense if k_vars=1 if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx)/2.)) ncols = 2 title_kwargs = {"fontdict" : {"fontsize" : 'small'}} else: nrows = len(exog_idx) ncols = 1 title_kwargs = {} # for indexing purposes other_names = np.array(results.model.exog_names) for i, idx in enumerate(exog_idx): others = lrange(k_vars) others.pop(idx) exog_others = pandas.DataFrame(exog[:, others], columns=other_names[others]) ax = fig.add_subplot(nrows, ncols, i+1) plot_partregress(y, pandas.Series(exog[:, idx], name=other_names[idx]), exog_others, ax=ax, title_kwargs=title_kwargs, obs_labels=False) ax.set_title("") fig.suptitle("Partial Regression Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig
def plot_regress_exog(results, exog_idx, fig=None): """Plot regression results against one regressor. This plots four graphs in a 2 by 2 figure: 'endog versus exog', 'residuals versus exog', 'fitted versus exog' and 'fitted plus residual versus exog' Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes exog_idx : int or str Name or index of regressor in exog matrix fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : matplotlib figure instance Examples -------- Load the Statewide Crime data set and build a model with regressors including the rate of high school graduation (hs_grad), population in urban areas (urban), households below poverty line (poverty), and single person households (single). Outcome variable is the muder rate (murder). Build a 2 by 2 figure based on poverty showing fitted versus actual murder rate, residuals versus the poverty rate, partial regression plot of poverty, and CCPR plot for poverty rate. >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plot >>> import statsmodels.formula.api as smf >>> fig = plt.figure(figsize=(8, 6)) >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> sm.graphics.plot_regress_exog(results, 'poverty', fig=fig) >>> plt.show() .. plot:: plots/graphics_regression_regress_exog.py """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y_name = results.model.endog_names x1 = results.model.exog[:, exog_idx] prstd, iv_l, iv_u = wls_prediction_std(results) ax = fig.add_subplot(2, 2, 1) ax.plot(x1, results.model.endog, 'o', color='b', alpha=0.9, label=y_name) ax.plot(x1, results.fittedvalues, 'D', color='r', label='fitted', alpha=.5) ax.vlines(x1, iv_l, iv_u, linewidth=1, color='k', alpha=.7) ax.set_title('Y and Fitted vs. X', fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel(y_name) ax.legend(loc='best') ax = fig.add_subplot(2, 2, 2) ax.plot(x1, results.resid, 'o') ax.axhline(y=0, color='black') ax.set_title('Residuals versus %s' % exog_name, fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel("resid") ax = fig.add_subplot(2, 2, 3) exog_noti = np.ones(results.model.exog.shape[1], bool) exog_noti[exog_idx] = False exog_others = results.model.exog[:, exog_noti] from pandas import Series fig = plot_partregress(results.model.data.orig_endog, Series(x1, name=exog_name, index=results.model.data.row_labels), exog_others, obs_labels=False, ax=ax) ax.set_title('Partial regression plot', fontsize='large') #ax.set_ylabel("Fitted values") #ax.set_xlabel(exog_name) ax = fig.add_subplot(2, 2, 4) fig = plot_ccpr(results, exog_idx, ax=ax) ax.set_title('CCPR Plot', fontsize='large') #ax.set_xlabel(exog_name) #ax.set_ylabel("Fitted values + resids") fig.suptitle('Regression Plots for %s' % exog_name, fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.90) return fig
def plot_ccpr(results, exog_idx, ax=None): """Plot CCPR against one regressor. Generates a CCPR (component and component-plus-residual) plot. Parameters ---------- results : result instance A regression results instance. exog_idx : int or string Exogenous, explanatory variable. If string is given, it should be the variable name that you want to use, and you can use arbitrary translations as with a formula. ax : Matplotlib AxesSubplot instance, optional If given, it is used to plot in instead of a new figure being created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. See Also -------- plot_ccpr_grid : Creates CCPR plot for multiple regressors in a plot grid. Notes ----- The CCPR plot provides a way to judge the effect of one regressor on the response variable by taking into account the effects of the other independent variables. The partial residuals plot is defined as Residuals + B_i*X_i versus X_i. The component adds the B_i*X_i versus X_i to show where the fitted line would lie. Care should be taken if X_i is highly correlated with any of the other independent variables. If this is the case, the variance evident in the plot will be an underestimate of the true variance. Examples -------- Using the state crime dataset plot the effect of the rate of single households ('single') on the murder rate while accounting for high school graduation rate ('hs_grad'), percentage of people in an urban area, and rate of poverty ('poverty'). >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plot >>> import statsmodels.formula.api as smf >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> sm.graphics.plot_ccpr(results, 'single') >>> plt.show() .. plot:: plots/graphics_regression_ccpr.py References ---------- http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) x1 = results.model.exog[:, exog_idx] #namestr = ' for %s' % self.name if self.name else '' x1beta = x1 * results.params[exog_idx] ax.plot(x1, x1beta + results.resid, 'o') from statsmodels.tools.tools import add_constant mod = OLS(x1beta, add_constant(x1)).fit() params = mod.params fig = abline_plot(*params, **dict(ax=ax)) #ax.plot(x1, x1beta, '-') ax.set_title('Component and component plus residual plot') ax.set_ylabel("Residual + %s*beta_%d" % (exog_name, exog_idx)) ax.set_xlabel("%s" % exog_name) return fig
def plot_regress_exog(results, exog_idx, fig=None): """Plot regression #1lab_results against one regressor. This plots four graphs in a 2 by 2 figure: 'endog versus exog', 'residuals versus exog', 'fitted versus exog' and 'fitted plus residual versus exog' Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes exog_idx : int index of regressor in exog matrix fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : matplotlib figure instance """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y_name = results.model.endog_names x1 = results.model.exog[:, exog_idx] prstd, iv_l, iv_u = wls_prediction_std(results) ax = fig.add_subplot(2, 2, 1) ax.plot(x1, results.model.endog, 'o', color='b', alpha=0.9, label=y_name) ax.plot(x1, results.fittedvalues, 'D', color='r', label='fitted', alpha=.5) ax.vlines(x1, iv_l, iv_u, linewidth=1, color='k', alpha=.7) ax.set_title('Y and Fitted vs. X', fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel(y_name) ax.legend(loc='best') ax = fig.add_subplot(2, 2, 2) ax.plot(x1, results.resid, 'o') ax.axhline(y=0, color='black') ax.set_title('Residuals versus %s' % exog_name, fontsize='large') ax.set_xlabel(exog_name) ax.set_ylabel("resid") ax = fig.add_subplot(2, 2, 3) exog_noti = np.ones(results.model.exog.shape[1], bool) exog_noti[exog_idx] = False exog_others = results.model.exog[:, exog_noti] from pandas import Series fig = plot_partregress(results.model.data.orig_endog, Series(x1, name=exog_name, index=results.model.data.row_labels), exog_others, obs_labels=False, ax=ax) ax.set_title('Partial regression plot', fontsize='large') #ax.set_ylabel("Fitted values") #ax.set_xlabel(exog_name) ax = fig.add_subplot(2, 2, 4) fig = plot_ccpr(results, exog_idx, ax=ax) ax.set_title('CCPR Plot', fontsize='large') #ax.set_xlabel(exog_name) #ax.set_ylabel("Fitted values + resids") fig.suptitle('Regression Plots for %s' % exog_name, fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.90) return fig
def plot_fit(results, exog_idx, y_true=None, ax=None, **kwargs): """Plot fit against one regressor. This creates one graph with the scatterplot of observed values compared to fitted values. Parameters ---------- results : result instance result instance with resid, model.endog and model.exog as attributes x_var : int or str Name or index of regressor in exog matrix. y_true : array_like (optional) If this is not None, then the array is added to the plot ax : Matplotlib AxesSubplot instance, optional If given, this subplot is used to plot in instead of a new figure being created. kwargs The keyword arguments are passed to the plot command for the fitted values points. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Examples -------- Load the Statewide Crime data set and perform linear regression with `poverty` and `hs_grad` as variables and `murder` as the response >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> data = sm.datasets.statecrime.load_pandas().data >>> murder = data['murder'] >>> X = data[['poverty', 'hs_grad']] >>> X["constant"] = 1 >>> y = murder >>> model = sm.OLS(y, X) >>> results = model.fit() Create a plot just for the variable 'Poverty': >>> fig, ax = plt.subplots() >>> fig = sm.graphics.plot_fit(results, 0, ax=ax) >>> ax.set_ylabel("Murder Rate") >>> ax.set_xlabel("Poverty Level") >>> ax.set_title("Linear Regression") >>> plt.show() .. plot:: plots/graphics_plot_fit_ex.py """ fig, ax = utils.create_mpl_ax(ax) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) results = maybe_unwrap_results(results) #maybe add option for wendog, wexog y = results.model.endog x1 = results.model.exog[:, exog_idx] x1_argsort = np.argsort(x1) y = y[x1_argsort] x1 = x1[x1_argsort] ax.plot(x1, y, 'bo', label=results.model.endog_names) if y_true is not None: ax.plot(x1, y_true[x1_argsort], 'b-', label='True values') title = 'Fitted values versus %s' % exog_name prstd, iv_l, iv_u = wls_prediction_std(results) ax.plot(x1, results.fittedvalues[x1_argsort], 'D', color='r', label='fitted', **kwargs) ax.vlines(x1, iv_l[x1_argsort], iv_u[x1_argsort], linewidth=1, color='k', alpha=.7) #ax.fill_between(x1, iv_l[x1_argsort], iv_u[x1_argsort], alpha=0.1, # color='k') ax.set_title(title) ax.set_xlabel(exog_name) ax.set_ylabel(results.model.endog_names) ax.legend(loc='best', numpoints=1) return fig
def plot_ccpr_grid(results, exog_idx=None, grid=None, fig=None): """Generate CCPR plots against a set of regressors, plot in a grid. Generates a grid of CCPR (component and component-plus-residual) plots. Parameters ---------- results : result instance uses exog and params of the result instance exog_idx : None or list of int (column) indices of the exog used in the plot grid : None or tuple of int (nrows, ncols) If grid is given, then it is used for the arrangement of the subplots. If grid is None, then ncol is one, if there are only 2 subplots, and the number of columns is two otherwise. fig : Matplotlib figure instance, optional If given, this figure is simply returned. Otherwise a new figure is created. Returns ------- fig : Matplotlib figure instance If `ax` is None, the created figure. Otherwise the figure to which `ax` is connected. Notes ----- Partial residual plots are formed as:: Res + Betahat(i)*Xi versus Xi and CCPR adds:: Betahat(i)*Xi versus Xi See Also -------- plot_ccpr : Creates CCPR plot for a single regressor. Examples -------- Using the state crime dataset seperately plot the effect of the each variable on the on the outcome, murder rate while accounting for the effect of all other variables in the model. >>> import statsmodels.api as sm >>> import matplotlib.pyplot as plt >>> import statsmodels.formula.api as smf >>> fig = plt.figure(figsize=(8, 8)) >>> crime_data = sm.datasets.statecrime.load_pandas() >>> results = smf.ols('murder ~ hs_grad + urban + poverty + single', ... data=crime_data.data).fit() >>> sm.graphics.plot_ccpr_grid(results, fig=fig) >>> plt.show() .. plot:: plots/graphics_regression_ccpr_grid.py References ---------- See http://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/ccpr.htm """ fig = utils.create_mpl_fig(fig) exog_name, exog_idx = utils.maybe_name_or_idx(exog_idx, results.model) if grid is not None: nrows, ncols = grid else: if len(exog_idx) > 2: nrows = int(np.ceil(len(exog_idx)/2.)) ncols = 2 else: nrows = len(exog_idx) ncols = 1 seen_constant = 0 for i, idx in enumerate(exog_idx): if results.model.exog[:, idx].var() == 0: seen_constant = 1 continue ax = fig.add_subplot(nrows, ncols, i+1-seen_constant) fig = plot_ccpr(results, exog_idx=idx, ax=ax) ax.set_title("") fig.suptitle("Component-Component Plus Residual Plot", fontsize="large") fig.tight_layout() fig.subplots_adjust(top=.95) return fig