Fix merge_visits

Author: svittoz

changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Unreleased
+
+### Fixed
+- Fix merge_visits sort_values.groupby.first
+
 ## v0.1.8 (2024-06-13)
 
 ### Fixed

eds_scikit/period/stays.py

@@ -6,6 +6,7 @@
 from eds_scikit.utils.checks import MissingConceptError, algo_checker, concept_checker
 from eds_scikit.utils.datetime_helpers import substract_datetime
 from eds_scikit.utils.framework import get_framework
+from eds_scikit.utils.sort_values_first import sort_values_first
 from eds_scikit.utils.typing import DataFrame
 
 
@@ -73,10 +74,10 @@ def cleaning(
 @concept_checker(concepts=["STAY_ID", "CONTIGUOUS_STAY_ID"])
 def merge_visits(
     vo: DataFrame,
+    open_stay_end_datetime: Optional[datetime],
     remove_deleted_visits: bool = True,
     long_stay_threshold: timedelta = timedelta(days=365),
     long_stay_filtering: Optional[str] = "all",
-    open_stay_end_datetime: Optional[datetime] = None,
     max_timedelta: timedelta = timedelta(days=2),
     merge_different_hospitals: bool = False,
     merge_different_source_values: Union[bool, List[str]] = ["hospitalisés", "urgence"],
@@ -108,6 +109,11 @@ def merge_visits(
         - care_site_id (if ``merge_different_hospitals == True``)
         - visit_source_value (if ``merge_different_source_values != False``)
         - row_status_source_value (if ``remove_deleted_visits= True``)
+    open_stay_end_datetime: Optional[datetime]
+        Datetime to use in order to fill the `visit_end_datetime` of open visits. This is necessary in
+        order to compute stay duration and to filter long stays.
+        You might provide the extraction date of your data or datetime.now()
+        (be aware it will produce undeterministic outputs).
     remove_deleted_visits: bool
         Wether to remove deleted visits from the merging procedure.
         Deleted visits are extracted via the `row_status_source_value` column
@@ -126,10 +132,6 @@ def merge_visits(
         Long stays are determined by the ``long_stay_threshold`` value.
     long_stay_threshold : timedelta
         Minimum visit duration value to consider a visit as candidate for "long visits filtering"
-    open_stay_end_datetime: Optional[datetime]
-        Datetime to use in order to fill the `visit_end_datetime` of open visits. This is necessary in
-        order to compute stay duration and to filter long stays. If not provided `datetime.now()` will be used.
-        You might provide the extraction date of your data here.
     max_timedelta : timedelta
         Maximum time difference between the end of a visit and the start of another to consider
         them as belonging to the same stay. This duration is internally converted in seconds before
@@ -291,21 +293,18 @@ def get_first(
             how="inner",
         )
 
-        # Getting the corresponding first visit
-        first_visit = (
-            merged.sort_values(
-                by=[flag_name, "visit_start_datetime_1"], ascending=[False, False]
-            )
-            .groupby("visit_occurrence_id_2")
-            .first()["visit_occurrence_id_1"]
-            .reset_index()
-            .rename(
-                columns={
-                    "visit_occurrence_id_1": f"{concept_prefix}STAY_ID",
-                    "visit_occurrence_id_2": "visit_occurrence_id",
-                }
-            )
+        first_visit = sort_values_first(
+            merged,
+            by_cols=["visit_occurrence_id_2"],
+            cols=[flag_name, "visit_start_datetime_1", "visit_occurrence_id_1"],
+        )
+        first_visit = first_visit.rename(
+            columns={
+                "visit_occurrence_id_1": f"{concept_prefix}STAY_ID",
+                "visit_occurrence_id_2": "visit_occurrence_id",
+            }
         )
+        first_visit = first_visit[["visit_occurrence_id", f"{concept_prefix}STAY_ID"]]
 
         return merged, first_visit
 

eds_scikit/utils/sort_values_first.py

@@ -0,0 +1,30 @@
+from typing import List
+
+from eds_scikit.utils.typing import DataFrame
+
+
+def sort_values_first(
+    df: DataFrame, by_cols: List[str], cols: List[str], ascending: bool = False
+):
+    """
+    Replace dataframe.sort_value(cols).groupby(by_cols).first()
+
+    Parameters
+    ----------
+    df : DataFrame
+    by_cols : List[str]
+        columns to groupby
+    cols : List[str]
+        columns to sort
+    ascending : bool
+    """
+
+    return (
+        df.groupby(by_cols)
+        .apply(
+            lambda group: group.sort_values(
+                by=cols, ascending=[ascending for i in cols]
+            ).head(1)
+        )
+        .reset_index(drop=True)
+    )

tests/test_sort_values_first.py

@@ -0,0 +1,51 @@
+import numpy as np
+import pandas as pd
+import pytest
+
+from eds_scikit.utils import framework
+from eds_scikit.utils.sort_values_first import sort_values_first
+from eds_scikit.utils.test_utils import assert_equal_no_order
+
+# Create a DataFrame
+np.random.seed(0)
+size = 10000
+data = {
+    "A": np.random.choice(["X", "Y", "Z"], size),
+    "B": np.random.randint(1, 5, size),
+    "C": np.random.randint(1, 5, size),
+    "D": np.random.randint(1, 5, size),
+    "E": np.random.randint(1, 5, size),
+}
+
+inputs = pd.DataFrame(data)
+inputs.loc[0, "B"] = 0
+inputs.loc[0, "C"] = 4
+
+
+@pytest.mark.parametrize(
+    "module",
+    ["pandas", "koalas"],
+)
+def test_sort_values_first(module):
+
+    inputs_fr = framework.to(module, inputs)
+
+    computed = framework.pandas(
+        sort_values_first(inputs_fr, ["A"], ["B", "C"], ascending=True)
+    )
+    expected = (
+        inputs.sort_values(["B", "C"], ascending=True)
+        .groupby("A", as_index=False)
+        .first()
+    )
+    assert_equal_no_order(computed, expected)
+
+    computed = framework.pandas(
+        sort_values_first(inputs_fr, ["A"], ["B", "C"], ascending=False)
+    )
+    expected = (
+        inputs.sort_values(["B", "C"], ascending=False)
+        .groupby("A", as_index=False)
+        .first()
+    )
+    assert_equal_no_order(computed, expected)

tests/test_visit_merging.py

@@ -1,3 +1,5 @@
+from datetime import datetime
+
 import pandas as pd
 import pytest
 
@@ -43,7 +45,10 @@
 ]
 
 
-@pytest.mark.parametrize("module", ["pandas", "koalas"])
+@pytest.mark.parametrize(
+    "module",
+    ["pandas", "koalas"],
+)
 @pytest.mark.parametrize(
     "params, results",
     [(params, results) for params, results in zip(all_params, all_results)],
@@ -53,9 +58,7 @@ def test_visit_merging(module, params, results):
     results = framework.to(module, results)
 
     vo = framework.to(module, ds.visit_occurrence)
-    merged = merge_visits(vo, **params)
+    merged = merge_visits(vo, datetime(2023, 1, 1), **params)
     merged = framework.pandas(merged)
-
-    assert_equal_no_order(
-        merged[["visit_occurrence_id", "STAY_ID", "CONTIGUOUS_STAY_ID"]], results
-    )
+    merged = merged[results.columns]
+    assert_equal_no_order(merged, results, check_dtype=False)