Merge pull request #141 from PythonPredictions/#135-Remove-mandatory-id-column

Defaults id_column to None for PIGs & tests

Author: patrickleonardy

cobra/evaluation/pigs_tables.py

@@ -8,9 +8,9 @@
 import cobra.utils as utils
 
 def generate_pig_tables(basetable: pd.DataFrame,
-                        id_column_name: str,
                         target_column_name: str,
-                        preprocessed_predictors: list) -> pd.DataFrame:
+                        preprocessed_predictors: list,
+                        id_column_name: str = None) -> pd.DataFrame:
     """Compute PIG tables for all predictors in preprocessed_predictors.
 
     The output is a DataFrame with columns ``variable``, ``label``,
@@ -20,35 +20,41 @@ def generate_pig_tables(basetable: pd.DataFrame,
     ----------
     basetable : pd.DataFrame
         Basetable to compute PIG tables from.
-    id_column_name : str
-        Name of the basetable column containing the IDs of the basetable rows
-        (e.g. customernumber).
     target_column_name : str
         Name of the basetable column containing the target values to predict.
     preprocessed_predictors: list
         List of basetable column names containing preprocessed predictors.
-
+    id_column_name : str, default=None
+        Name of the basetable column containing the IDs of the basetable rows
+        (e.g. customernumber). 
     Returns
     -------
     pd.DataFrame
         DataFrame containing a PIG table for all predictors.
     """
+
+    #check if there is a id-column and define no_predictor accordingly
+    if id_column_name == None:
+        no_predictor = [target_column_name]
+    else:
+        no_predictor = [id_column_name, target_column_name]
+    
+
     pigs = [
         compute_pig_table(basetable,
                           column_name,
                           target_column_name,
-                          id_column_name)
+                          )
         for column_name in sorted(preprocessed_predictors)
-        if column_name not in [id_column_name, target_column_name]
+        if column_name not in no_predictor
     ]
-    output = pd.concat(pigs)
+    output = pd.concat(pigs, ignore_index=True)
     return output
 
 
 def compute_pig_table(basetable: pd.DataFrame,
                       predictor_column_name: str,
-                      target_column_name: str,
-                      id_column_name: str) -> pd.DataFrame:
+                      target_column_name: str) -> pd.DataFrame:
     """Compute the PIG table of a given predictor for a given target.
 
     Parameters
@@ -59,8 +65,6 @@ def compute_pig_table(basetable: pd.DataFrame,
         Predictor name of which to compute the pig table.
     target_column_name : str
         Name of the target variable.
-    id_column_name : str
-        Name of the id column (used to count population size).
 
     Returns
     -------
@@ -72,12 +76,18 @@ def compute_pig_table(basetable: pd.DataFrame,
     # group by the binned variable, compute the incidence
     # (= mean of the target for the given bin) and compute the bin size
     # (e.g. COUNT(id_column_name)). After that, rename the columns
+
     res = (basetable.groupby(predictor_column_name)
-           .agg({target_column_name: "mean", id_column_name: "size"})
+           .agg(
+                avg_target = (target_column_name, "mean"),
+                pop_size = (target_column_name, "size")
+           )
            .reset_index()
-           .rename(columns={predictor_column_name: "label",
-                            target_column_name: "avg_target",
-                            id_column_name: "pop_size"}))
+           .rename(
+                columns={predictor_column_name: "label"}
+           )
+    )
+
 
     # add the column name to a variable column
     # add the average incidence

tests/preprocessing/test_pig_tables.py

@@ -0,0 +1,56 @@
+import pytest
+
+import pandas as pd
+from cobra.evaluation.pigs_tables import generate_pig_tables
+
+from typing import Optional
+
+
+class TestPigTablesGeneration:
+    @pytest.mark.parametrize(
+        "id_col_name", [None, "col_id"]
+    )  # test None as this is the default value in generate pig tabels
+    def test_col_id(self, id_col_name: Optional[str]):
+
+        # input
+        data = pd.DataFrame(
+            {
+                "col_id": [0, 1, 3, 4, 6],
+                "survived": [0, 1, 1, 0, 0],
+                "pclass": [3, 1, 1, 3, 1],
+                "sex": ["male", "female", "female", "male", "male"],
+                "age": [22.0, 38.0, 35.0, 35.0, 54.0],
+            }
+        )
+        target = "survived"
+        prep_col = ["pclass", "sex", "age"]
+
+        # output
+        out = generate_pig_tables(
+            basetable=data,
+            target_column_name=target,
+            preprocessed_predictors=prep_col,
+            id_column_name=id_col_name,
+        )
+
+        # expected
+        expected = pd.DataFrame(
+            {
+                "variable": [
+                    "age",
+                    "age",
+                    "age",
+                    "age",
+                    "pclass",
+                    "pclass",
+                    "sex",
+                    "sex",
+                ],
+                "label": [22.0, 35.0, 38.0, 54.0, 1, 3, "female", "male"],
+                "pop_size": [0.2, 0.4, 0.2, 0.2, 0.6, 0.4, 0.4, 0.6],
+                "global_avg_target": [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4],
+                "avg_target": [0.0, 0.5, 1.0, 0.0, 0.6666666666666666, 0.0, 1.0, 0.0],
+            }
+        )
+
+        pd.testing.assert_frame_equal(out, expected)