[BUG] Fixes #301 and some other issues

gen_imgs.py

@@ -323,7 +323,6 @@ def chicago_tensor():
 
 
 def expectiles():
-
     """Generate expectiles visualization."""
     X, y = mcycle(return_X_y=True)
 

pygam/pygam.py

@@ -406,9 +406,9 @@ def _linear_predictor(self, X=None, modelmat=None, b=None, term=-1):
             contains the spline coefficients
             if None, will use current model coefficients
 
-        term : int, optional
-                  feature for which to compute the linear prediction
-                  if -1, will compute for all features
+        term : int or list of int, default: -1
+            term(s) to use in calculation of linear predictor
+            if -1, all terms are used
 
         Returns
         -------
@@ -485,12 +485,22 @@ def _modelmat(self, X, term=-1):
         modelmat : sparse matrix of len n_samples
             containing model matrix of the spline basis for selected features
         """
+        # take features, dtypes and edge_knots based on supplied term values
+        if term != -1:
+            terms = list(np.atleast_1d(term))
+        else:
+            terms = range(len(self.feature))
+
+        features = [self.feature[i] for i in terms]
+        edge_knots = [self.edge_knots_[i] for i in terms]
+        dtypes = [self.dtype[i] for i in terms]
+
         X = check_X(
             X,
             n_feats=self.statistics_["m_features"],
-            edge_knots=self.edge_knots_,
-            dtypes=self.dtype,
-            features=self.feature,
+            edge_knots=edge_knots,
+            dtypes=dtypes,
+            features=features,
             verbose=self.verbose,
         )
 
@@ -1432,6 +1442,9 @@ def _flatten_mesh(self, Xs, term):
         X = np.zeros((n, self.statistics_["m_features"]))
         for term_, x in zip(terms, Xs):
             X[:, term_.feature] = x.ravel()
+
+        if getattr(self.terms[term], "by", None) is not None:
+            X[:, self.terms[term].by] = 1.0
         return X
 
     def generate_X_grid(self, term, n=100, meshgrid=False):
@@ -1602,14 +1615,6 @@ def partial_dependence(
             shape = X[0].shape
 
             X = self._flatten_mesh(X, term=term)
-            X = check_X(
-                X,
-                n_feats=self.statistics_["m_features"],
-                edge_knots=self.edge_knots_,
-                dtypes=self.dtype,
-                features=self.feature,
-                verbose=self.verbose,
-            )
 
         modelmat = self._modelmat(X, term=term)
         pdep = self._linear_predictor(modelmat=modelmat, term=term)

pygam/terms.py

@@ -938,8 +938,6 @@ def build_columns(self, X, verbose=False):
         -------
         scipy sparse array with n rows
         """
-        X[:, self.feature][:, np.newaxis]
-
         splines = b_spline_basis(
             X[:, self.feature],
             edge_knots=self.edge_knots_,

pygam/tests/test_partial_dependence.py

@@ -1,6 +1,7 @@
+import numpy as np
 import pytest
 
-from pygam import LinearGAM
+from pygam import LinearGAM, f, s
 
 
 class TestPartialDepencence:
@@ -153,3 +154,24 @@ def test_no_X_needed_for_partial_dependence(self, mcycle_gam):
             mcycle_gam.partial_dependence(term=0)
             == mcycle_gam.partial_dependence(term=0, X=XX)
         ).all()
+
+    def test_regression_value_error_in_factor_terms(self):
+        """
+        test https://github.com/dswah/pyGAM/issues/301
+        """
+        X = np.random.standard_normal((100, 3))
+
+        # shift the features away from 0 and 1
+        X[:, 2] = np.random.choice([2, 3], 100, replace=True)
+
+        Y = np.random.standard_normal(100)
+        gam = LinearGAM(s(0) + s(1) + f(2)).fit(X, Y)
+
+        # should be able to evaluate with fixed default values for the factor
+        gam.partial_dependence(0)
+
+        # now do the same, but with a by feature
+        gam = LinearGAM(s(0, by=2) + s(1) + f(2)).fit(X, Y)
+
+        # should be able to evaluate with fixed default values for the factor
+        gam.partial_dependence(0)