diff --git a/docs/quickstart.ipynb b/docs/quickstart.ipynb index 13c3fbfa..716decb4 100644 --- a/docs/quickstart.ipynb +++ b/docs/quickstart.ipynb @@ -34,54 +34,14 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", - "
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a/pyfixest/estimation/feols_.py +++ b/pyfixest/estimation/feols_.py @@ -1426,7 +1426,8 @@ def predict( atol: float = 1e-6, btol: float = 1e-6, type: str = "link", - ) -> np.ndarray: + compute_stdp: bool = False + ) -> pd.DataFrame: """ Predict values of the model on new data. @@ -1451,23 +1452,29 @@ def predict( Another stopping tolerance for scipy.sparse.linalg.lsqr(). See https://docs.scipy.org/doc/ scipy/reference/generated/scipy.sparse.linalg.lsqr.html - link: + type: The type of prediction to be made. Can be either 'link' or 'response'. Defaults to 'link'. 'link' and 'response' lead to identical results for linear models. + compute_stdp: boolean + Whether to compute standard error of the predictions Returns ------- - y_hat : np.ndarray - A flat np.array with predicted values of the regression model. + pred_results : pd.DataFrame + Dataframe with columns "y_hat" and optionally "stdp" (if compute_stdp is True) """ if self._is_iv: raise NotImplementedError( "The predict() method is currently not supported for IV models." ) + prediction_df = pd.DataFrame() if newdata is None: - return self._Y_untransformed.to_numpy().flatten() - self.resid() + prediction_df["yhat"] = self._Y_untransformed.to_numpy().flatten() - self._u_hat.flatten() + if compute_stdp: + prediction_df["stdp"] = self.get_newdata_stdp(self._X) + return prediction_df newdata = _polars_to_pandas(newdata).reset_index(drop=False) @@ -1501,7 +1508,64 @@ def predict( _fixef_mat = _apply_fixef_numpy(df_fe.values, fixef_dicts) y_hat += np.sum(_fixef_mat, axis=1) - return y_hat.flatten() + prediction_df["yhat"] = y_hat.flatten() + if compute_stdp: + stdp_df = np.full(newdata.shape[0], np.nan) + stdp_df[X_index] = self.get_newdata_stdp(X) + prediction_df["stdp"] = stdp_df + + return prediction_df + + + def get_newdata_stdp(self, X): + """ + Get standard error of predictions for new data. + + Parameters + ---------- + X : np.ndarray + Covariates for new data points. + + Returns + ------- + list + Standard errors for each prediction + """ + # for now only compute prediction error if model has no fixed effects + # TODO: implement for fixed effects + if not self._has_fixef: + if not self._X_is_empty: + return list(map(self.get_single_row_stdp, X)) + else: + warnings.warn( + """ + Standard error of the prediction cannot be computed if X is empty. + Prediction dataframe stdp column will be None. + """ + ) + else: + warnings.warn( + """ + Standard error of the prediction is not implemented for fixed effects models. + Prediction dataframe stdp column will be None. + """ + ) + + def get_single_row_stdp(self, row): + """ + Get standard error of predictions for a single row. + + Parameters + ---------- + row : np.ndarray + Single row of new covariate data + + Returns + ------- + np.ndarray + Standard error of prediction for single row + """ + return np.linalg.multi_dot([row, self._vcov, np.transpose(row)]) def get_nobs(self): """ diff --git a/pyfixest/estimation/fepois_.py b/pyfixest/estimation/fepois_.py index 1dac5feb..040dbcc7 100644 --- a/pyfixest/estimation/fepois_.py +++ b/pyfixest/estimation/fepois_.py @@ -299,7 +299,8 @@ def predict( atol: float = 1e-6, btol: float = 1e-6, type: str = "link", - ) -> np.ndarray: + compute_stdp: bool = False + ) -> pd.DataFrame: """ Return predicted values from regression model. @@ -334,13 +335,13 @@ def predict( btol : Float, default 1e-6 Another stopping tolerance for scipy.sparse.linalg.lsqr(). See https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.linalg.lsqr.html - - + compute_stdp: boolean + Ignored, included to conform with method signature of feols.predict() Returns ------- - np.ndarray - A flat array with the predicted values of the regression model. + pred_results : pd.DataFrame + Dataframe with columns "y_hat" with predicted values from regression model """ _Xbeta = self._Xbeta.flatten() _has_fixef = self._has_fixef @@ -355,10 +356,13 @@ def predict( ) # y_hat = super().predict(newdata=newdata, type=type, atol=atol, btol=btol) + prediction_df = pd.DataFrame() if type == "link": - return np.exp(_Xbeta) + prediction_df["yhat"] = np.exp(_Xbeta) + return prediction_df elif type == "response": - return _Xbeta + prediction_df["yhat"] = _Xbeta + return prediction_df else: raise ValueError("type must be one of 'response' or 'link'.") diff --git a/pyproject.toml b/pyproject.toml index 7d5e4de2..5c6a933c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,6 +37,7 @@ wildboottest = ">=0.2.0" pre-commit = "^3.6.0" doubleml = "^0.7.1" marginaleffects = "^0.0.10" +statsmodels = "^0.14.1" [tool.poetry.group.docs.dependencies] causaldata = "*" diff --git a/tests/.coverage b/tests/.coverage index ef76747f..29f0509c 100644 Binary files a/tests/.coverage and b/tests/.coverage differ diff --git a/tests/test_predict_resid_fixef.py b/tests/test_predict_resid_fixef.py index f95aa65d..54da5e11 100644 --- a/tests/test_predict_resid_fixef.py +++ b/tests/test_predict_resid_fixef.py @@ -37,8 +37,8 @@ def test_internally(data): # predict via feols, without fixed effect fit = feols(fml="Y~csw(X1, X2)", data=data, vcov="iid") mod = fit.fetch_model(0) - original_prediction = mod.predict() - updated_prediction = mod.predict(newdata=mod._data) + original_prediction = mod.predict().yhat + updated_prediction = mod.predict(newdata=mod._data).yhat np.allclose(original_prediction, updated_prediction) assert mod._data.shape[0] == original_prediction.shape[0] assert mod._data.shape[0] == updated_prediction.shape[0] @@ -47,15 +47,15 @@ def test_internally(data): fit = feols(fml="Y~csw(X1, X2) | f1", data=data, vcov="iid") mod = fit.fetch_model(0) mod.fixef() - original_prediction = mod.predict() - updated_prediction = mod.predict(newdata=mod._data) + original_prediction = mod.predict().yhat + updated_prediction = mod.predict(newdata=mod._data).yhat np.allclose(original_prediction, updated_prediction) assert mod._data.shape[0] == original_prediction.shape[0] assert mod._data.shape[0] == updated_prediction.shape[0] # now expect error with updated predicted being a subset of data with pytest.raises(ValueError): - updated_prediction = mod.predict(newdata=data.iloc[0:100, :]) + updated_prediction = mod.predict(newdata=data.iloc[0:100, :]).yhat np.allclose(original_prediction, updated_prediction) # fepois NotImplementedError(s) @@ -123,18 +123,18 @@ def test_vs_fixest(data, fml): # raise ValueError("sumFE for Poisson are not equal") # test predict for OLS - if not np.allclose(feols_mod.predict(), r_fixest_ols.rx2("fitted.values")): + if not np.allclose(feols_mod.predict().yhat, r_fixest_ols.rx2("fitted.values")): raise ValueError("Predictions for OLS are not equal") - if not np.allclose(len(feols_mod.predict()), len(stats.predict(r_fixest_ols))): + if not np.allclose(len(feols_mod.predict().yhat), len(stats.predict(r_fixest_ols))): raise ValueError("Predictions for OLS are not the same length") # test predict for Poisson - # if not np.allclose(fepois_mod.predict(), r_fixest_pois.rx2("fitted.values")): + # if not np.allclose(fepois_mod.predict().yhat, r_fixest_pois.rx2("fitted.values")): # raise ValueError("Predictions for Poisson are not equal") # test on new data - OLS. if not np.allclose( - feols_mod.predict(newdata=data2), stats.predict(r_fixest_ols, newdata=data2) + feols_mod.predict(newdata=data2).yhat, stats.predict(r_fixest_ols, newdata=data2) ): raise ValueError("Predictions for OLS are not equal") @@ -171,7 +171,7 @@ def test_predict_nas(): # test 1 fml = "Y ~ X1 + X2 | f1" fit = feols(fml, data=data) - res = fit.predict(newdata=data) + res = fit.predict(newdata=data).yhat fit_r = fixest.feols(ro.Formula(fml), data=data) res_r = stats.predict(fit_r, newdata=data) np.testing.assert_allclose(res, res_r, atol=1e-05, rtol=1e-05) @@ -184,7 +184,7 @@ def test_predict_nas(): fml = "Y ~ X1 + X2 | f1" fit = feols(fml, data=data) - res = fit.predict(newdata=newdata) + res = fit.predict(newdata=newdata).yhat fit_r = fixest.feols(ro.Formula(fml), data=data) res_r = stats.predict(fit_r, newdata=newdata) np.testing.assert_allclose(res, res_r, atol=1e-05, rtol=1e-05) @@ -192,7 +192,7 @@ def test_predict_nas(): assert len(res) == len(res_r) newdata.loc[198, "Y"] = np.nan - res = fit.predict(newdata=newdata) + res = fit.predict(newdata=newdata).yhat res_r = stats.predict(fit_r, newdata=newdata) np.testing.assert_allclose(res, res_r, atol=1e-05, rtol=1e-05) assert newdata.shape[0] == len(res) @@ -201,7 +201,7 @@ def test_predict_nas(): # test 3 fml = "Y ~ X1 + X2 + f1| f1 " fit = feols(fml, data=data) - res = fit.predict(newdata=data) + res = fit.predict(newdata=data).yhat fit_r = fixest.feols(ro.Formula(fml), data=data) res_r = stats.predict(fit_r, newdata=data) np.testing.assert_allclose(res, res_r, atol=1e-05, rtol=1e-05) @@ -229,7 +229,7 @@ def test_new_fixef_level(data, fml): se="hetero", ) - updated_prediction_py = feols_mod.predict(newdata=data2) + updated_prediction_py = feols_mod.predict(newdata=data2).yhat updated_prediction_r = stats.predict(r_fixest_ols, newdata=data2) if not np.allclose(updated_prediction_py, updated_prediction_r): @@ -249,7 +249,7 @@ def test_categorical_covariate_predict(): df_sub = df.query("x == 1 or x == 2 or x == 3").copy() py_fit = feols("y ~ C(x, contr.treatment(base=1))", df) - py_predict = py_fit.predict(df_sub) + py_predict = py_fit.predict(df_sub).yhat r_predict = np.array( [ diff --git a/tests/test_stdp.py b/tests/test_stdp.py new file mode 100644 index 00000000..8af6b503 --- /dev/null +++ b/tests/test_stdp.py @@ -0,0 +1,22 @@ +import numpy as np +import statsmodels.api as sm + +from pyfixest.estimation.estimation import feols +from pyfixest.utils.utils import get_data + + +def test_stdp(): + """Compare the standard error of the prediction to statsmodels.get_prediction().""" + data = get_data().dropna() + + fit = feols("Y ~ X1 + X2", data=data) + stdp = fit.predict(compute_stdp=True).stdp + + X = data[["X1","X2"]] + Y = data["Y"] + X = sm.add_constant(X) + model = sm.OLS(Y, X).fit() + predictions = model.get_prediction() + stdp_sm = predictions.var_pred_mean + + np.testing.assert_allclose(stdp, stdp_sm)