From c6618d225b5048971a72a93edc0a97081cf9ce20 Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 22:15:19 +0100 Subject: [PATCH 1/6] Handle unseen values in MCA --- prince/mca.py | 6 ++-- pyproject.toml | 2 +- tests/test_mca.py | 92 ++++++++++++++++++++++++++++++++++++----------- 3 files changed, 77 insertions(+), 23 deletions(-) diff --git a/prince/mca.py b/prince/mca.py index 76ca057..ac72be8 100644 --- a/prince/mca.py +++ b/prince/mca.py @@ -37,8 +37,9 @@ def __init__( def _prepare(self, X): if self.one_hot: - # Create the one-hot encoder if it doesn't exist (usually because we're in the fit method) - X = pd.get_dummies(X, columns=X.columns) + X = pd.get_dummies(X, columns=X.columns, prefix_sep="__") + if (one_hot_columns_ := getattr(self, "one_hot_columns_", None)) is not None: + X = X.reindex(columns=one_hot_columns_.union(X.columns), fill_value=False) return X def get_feature_names_out(self, input_features=None): @@ -62,6 +63,7 @@ def fit(self, X, y=None): # One-hot encode the data one_hot = self._prepare(X) + self.one_hot_columns_ = one_hot.columns # We need the number of columns to apply the Greenacre correction self.J_ = one_hot.shape[1] diff --git a/pyproject.toml b/pyproject.toml index cce471e..bd8aa41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "prince" -version = "0.13.1" +version = "0.14.0" description = "Factor analysis in Python: PCA, CA, MCA, MFA, FAMD, GPA" authors = ["Max Halford "] license = "MIT" diff --git a/tests/test_mca.py b/tests/test_mca.py index 3f77dbb..f81fc84 100644 --- a/tests/test_mca.py +++ b/tests/test_mca.py @@ -1,5 +1,6 @@ from __future__ import annotations +import io import tempfile import numpy as np @@ -64,7 +65,10 @@ def test_col_coords(self): if self.sup_cols: F = pd.concat((F, load_df_from_R("ca$quali.sup$coord"))) P = self.ca.column_coordinates(self.dataset) - np.testing.assert_allclose(F.abs(), P.abs()) + # Prince adds a prefix to each column. We need to remove it in order to align the rows + # of the two dataframes + P.index = [idx.split("__", 1)[1] for idx in P.index] + np.testing.assert_allclose(F.abs(), P.abs().loc[F.index]) else: super().test_col_coords() @@ -74,7 +78,10 @@ def test_col_cos2(self): if self.sup_cols: F = pd.concat((F, load_df_from_R("ca$quali.sup$cos2"))) P = self.ca.column_cosine_similarities(self.dataset) - np.testing.assert_allclose(F, P) + # Prince adds a prefix to each column. We need to remove it in order to align the rows + # of the two dataframes + P.index = [idx.split("__", 1)[1] for idx in P.index] + np.testing.assert_allclose(F, P.loc[F.index]) else: super().test_col_cos2() @@ -89,23 +96,23 @@ def test_with_and_without_one_hot(): >>> mca = prince.MCA(n_components=2, one_hot=True, engine="scipy") >>> mca = mca.fit(df) >>> mca.transform(df).round(2).abs().sort_index(axis='columns') - 0 1 - 0 2.0 0.00 - 1 0.5 0.65 - 2 0.5 0.65 - 3 0.5 0.65 - 4 0.5 1.94 + 0 1 + 0 0.00 2.0 + 1 0.65 0.5 + 2 0.65 0.5 + 3 0.65 0.5 + 4 1.94 0.5 >>> mca = prince.MCA(n_components=2, one_hot=False, engine="scipy") >>> one_hot = pd.get_dummies(df, columns=['foo', 'bar']) >>> mca = mca.fit(one_hot) >>> mca.transform(one_hot).round(2).abs().sort_index(axis='columns') - 0 1 - 0 2.0 0.00 - 1 0.5 0.65 - 2 0.5 0.65 - 3 0.5 0.65 - 4 0.5 1.94 + 0 1 + 0 0.00 2.0 + 1 0.65 0.5 + 2 0.65 0.5 + 3 0.65 0.5 + 4 1.94 0.5 """ @@ -122,12 +129,12 @@ def test_issue_131(): >>> mca = prince.MCA(engine="scipy") >>> mca = mca.fit(df) >>> mca.transform(df).round(2).abs().sort_index(axis='columns') - 0 1 - 0 2.0 0.00 - 1 0.5 0.65 - 2 0.5 0.65 - 3 0.5 0.65 - 4 0.5 1.94 + 0 1 + 0 0.00 2.0 + 1 0.65 0.5 + 2 0.65 0.5 + 3 0.65 0.5 + 4 1.94 0.5 >>> mca.K_, mca.J_ (2, 8) @@ -185,3 +192,48 @@ def test_type_doesnt_matter(): for i in range(len(outputs) - 1): np.testing.assert_allclose(outputs[i], outputs[i + 1]) + + +issue_161_data = ''' +,category,userid,location,applicationname,browser\n +0,Portal Login,a@b.com,"San Jose, CA, United States",A,Chrome\n +1,Application Access,b@b.com,"San Jose, CA, United States",B,Other\n +2,Application Access,a@b.com,"San Jose, CA, United States",C,Other\n +3,Portal Login,c@b.com,"San Diego, CA, United States",A,Chrome\n +''' + +def test_issue_161(): + """ + + https://github.com/MaxHalford/prince/issues/161 + + >>> data = pd.read_csv(io.StringIO(issue_161_data), index_col=0) + + >>> mca = prince.MCA( + ... n_components=10, + ... n_iter=3, + ... copy=True, + ... check_input=True, + ... engine='sklearn', + ... random_state=42, + ... handle_unknown='ignore' + ... ) + >>> mca = mca.fit(data[:3]) + + >>> mca.eigenvalues_summary + eigenvalue % of variance % of variance (cumulative) + component + 0 0.673 67.32% 67.32% + 1 0.327 32.68% 100.00% + + >>> mca.row_coordinates(data[:3]) + 0 1 + 0 1.120811 -0.209242 + 1 -0.820491 -0.571660 + 2 -0.300320 0.780902 + + >>> mca.transform(data[3:]) + 0 1 + 3 1.664888 -0.640285 + + """ From 1862019a5472b0784851f02bf7b562e5b84dfaaa Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 22:16:54 +0100 Subject: [PATCH 2/6] Update mca.py --- prince/mca.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/prince/mca.py b/prince/mca.py index ac72be8..6c3b128 100644 --- a/prince/mca.py +++ b/prince/mca.py @@ -22,7 +22,6 @@ def __init__( random_state=None, engine="sklearn", one_hot=True, - handle_unknown="error", ): super().__init__( n_components=n_components, @@ -33,7 +32,6 @@ def __init__( engine=engine, ) self.one_hot = one_hot - self.handle_unknown = handle_unknown def _prepare(self, X): if self.one_hot: From e8af7952018fce87a06a8dcf4112c998dcb20e71 Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 22:24:05 +0100 Subject: [PATCH 3/6] update deps --- poetry.lock | 1946 +++++++++++++++++++++++++-------------------- pyproject.toml | 6 +- tests/test_mca.py | 3 +- 3 files changed, 1091 insertions(+), 864 deletions(-) diff --git a/poetry.lock b/poetry.lock index c688dd0..6a90b5a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,99 +1,94 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "bcd37323cbaf216f6765b8c8baa1a3c55383c07f6bee167fe64437eb3999fa0d" +content-hash = "9db48deb5ea3c336bf4089e2f305057ddf21f60f34a15c1e7a0aa14af5e80169" diff --git a/pyproject.toml b/pyproject.toml index bd8aa41..44de044 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,9 +7,9 @@ license = "MIT" [tool.poetry.dependencies] python = "^3.9" -scikit-learn = "^1.0.2" -pandas = "^1.4.1 || ^2.0.0" -altair = "^4.2.2 || ^5.0.0" +scikit-learn = "^1.5.1" +pandas = "^2.2.0" +altair = "^5.0.0" [tool.poetry.group.dev.dependencies] nbconvert = "^7.2.9" diff --git a/tests/test_mca.py b/tests/test_mca.py index f81fc84..b8987b4 100644 --- a/tests/test_mca.py +++ b/tests/test_mca.py @@ -215,8 +215,7 @@ def test_issue_161(): ... copy=True, ... check_input=True, ... engine='sklearn', - ... random_state=42, - ... handle_unknown='ignore' + ... random_state=42 ... ) >>> mca = mca.fit(data[:3]) From 26eb96232275e68037a44f02590d14bf32b002a4 Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 22:48:29 +0100 Subject: [PATCH 4/6] fix famd on unseen values --- prince/famd.py | 2 +- tests/test_famd.py | 30 ++++++++++++++++++++++++++++++ tests/test_mca.py | 6 +++--- 3 files changed, 34 insertions(+), 4 deletions(-) diff --git a/prince/famd.py b/prince/famd.py index 37f575a..dcdc395 100644 --- a/prince/famd.py +++ b/prince/famd.py @@ -112,7 +112,7 @@ def row_coordinates(self, X): prop = X_cat.sum() / X_cat.sum().sum() * 2 X_cat = X_cat.sub(X_cat.mean(axis="rows")).div(prop**0.5, axis="columns") - Z = pd.concat([X_num, X_cat], axis=1) + Z = pd.concat([X_num, X_cat.sparse.to_dense()], axis=1).fillna(0.0) return super().row_coordinates(Z) diff --git a/tests/test_famd.py b/tests/test_famd.py index 11e152a..367b416 100644 --- a/tests/test_famd.py +++ b/tests/test_famd.py @@ -96,3 +96,33 @@ def test_col_contrib(self): F = load_df_from_R("famd$var$contrib") P = self.famd.column_contributions_ np.testing.assert_allclose(F, P * 100) + + +def test_issue_169(): + """ + + https://github.com/MaxHalford/prince/issues/169 + + >>> import pandas as pd + >>> from prince import FAMD + >>> df = pd.DataFrame({'var1':['c', 'a', 'b','c'], 'var2':['x','y','y','z'],'var2': [0.,10.,30.4,0.]}) + + >>> famd = FAMD(n_components=2, random_state=42) + >>> famd = famd.fit(df[:3]) + + >>> famd.transform(df[0:3]) + component 0 1 + 0 -1.303760 -0.658334 + 1 -0.335621 0.981047 + 2 1.639381 -0.322713 + + >>> famd.transform(df[0:2]) + component 0 1 + 0 -1.000920 -0.669274 + 1 -0.092001 0.669274 + + >>> famd.transform(df[3:]) + component 0 1 + 3 -0.869173 -1.215925e-16 + + """ diff --git a/tests/test_mca.py b/tests/test_mca.py index b8987b4..beecd17 100644 --- a/tests/test_mca.py +++ b/tests/test_mca.py @@ -1,6 +1,5 @@ from __future__ import annotations -import io import tempfile import numpy as np @@ -194,13 +193,14 @@ def test_type_doesnt_matter(): np.testing.assert_allclose(outputs[i], outputs[i + 1]) -issue_161_data = ''' +issue_161_data = """ ,category,userid,location,applicationname,browser\n 0,Portal Login,a@b.com,"San Jose, CA, United States",A,Chrome\n 1,Application Access,b@b.com,"San Jose, CA, United States",B,Other\n 2,Application Access,a@b.com,"San Jose, CA, United States",C,Other\n 3,Portal Login,c@b.com,"San Diego, CA, United States",A,Chrome\n -''' +""" + def test_issue_161(): """ From c82f33b49e932fc9de6eeceb1d70ad1df96a8801 Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 23:05:49 +0100 Subject: [PATCH 5/6] pin python 3.11.4 for testing --- .github/actions/install-env/action.yml | 2 +- tests/test_mca.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/actions/install-env/action.yml b/.github/actions/install-env/action.yml index 86337e6..09069a7 100644 --- a/.github/actions/install-env/action.yml +++ b/.github/actions/install-env/action.yml @@ -9,7 +9,7 @@ runs: id: set-up-python uses: actions/setup-python@v4 with: - python-version: "3.11" + python-version: "3.11.4" - name: Load cached Poetry installation uses: actions/cache@v3 diff --git a/tests/test_mca.py b/tests/test_mca.py index beecd17..2092ffa 100644 --- a/tests/test_mca.py +++ b/tests/test_mca.py @@ -207,6 +207,7 @@ def test_issue_161(): https://github.com/MaxHalford/prince/issues/161 + >>> import io >>> data = pd.read_csv(io.StringIO(issue_161_data), index_col=0) >>> mca = prince.MCA( From cba2c9fcd74be0b5e68b3d9ba61b2a8b217a7b00 Mon Sep 17 00:00:00 2001 From: Max Halford Date: Sun, 17 Nov 2024 23:13:33 +0100 Subject: [PATCH 6/6] Update action.yml --- .github/actions/install-env/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/install-env/action.yml b/.github/actions/install-env/action.yml index 09069a7..86337e6 100644 --- a/.github/actions/install-env/action.yml +++ b/.github/actions/install-env/action.yml @@ -9,7 +9,7 @@ runs: id: set-up-python uses: actions/setup-python@v4 with: - python-version: "3.11.4" + python-version: "3.11" - name: Load cached Poetry installation uses: actions/cache@v3