pycomorb 0.4__tar.gz → 0.4.2__tar.gz

{pycomorb-0.4/src/pycomorb.egg-info → pycomorb-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycomorb
-Version: 0.4
+Version: 0.4.2
 Summary: Comorbidity and frailty score calculation utilities (Charlson, Elixhauser, Gagne, HFRS) using polars
 Author-email: Finn Fassbender <finn.fassbender@charite.de>
 License-Expression: MIT
@@ -32,7 +32,7 @@ It is inspired by the R package [`comorbidity`](https://github.com/ellessenne/co
 
 ## Supported Variants
 
-See [common/README.md](src/pycomorb/common/README.md) for more details and references.
+See [common/README.md](https://github.com/CUB-CORR/pycomorb/blob/main/src/pycomorb/common/README.md) for more details and references.
 
 ### Charlson Comorbidity Index
 

{pycomorb-0.4 → pycomorb-0.4.2}/README.md

@@ -17,7 +17,7 @@ It is inspired by the R package [`comorbidity`](https://github.com/ellessenne/co
 
 ## Supported Variants
 
-See [common/README.md](src/pycomorb/common/README.md) for more details and references.
+See [common/README.md](https://github.com/CUB-CORR/pycomorb/blob/main/src/pycomorb/common/README.md) for more details and references.
 
 ### Charlson Comorbidity Index
 

{pycomorb-0.4 → pycomorb-0.4.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pycomorb"
-version = "0.4"
+version = "0.4.2"
 authors = [
   { name="Finn Fassbender", email="finn.fassbender@charite.de" },
 ]

{pycomorb-0.4 → pycomorb-0.4.2}/src/pycomorb/CustomComorbidityIndex.py

@@ -132,31 +132,6 @@ def CustomComorbidityIndex(
             .drop_nulls("best_prefix")
         )
 
-        (
-            unique_codes.with_columns(
-                pl.col(code_col).str.slice(0, n).alias(f"prefix_{n}")
-                for n in range(1, len(longest_code) + 1)
-            )
-            .with_columns(
-                pl.when(pl.col(f"prefix_{n}").is_in(code_prefixes))
-                .then(pl.col(f"prefix_{n}"))
-                .otherwise(None)
-                .alias(f"prefix_{n}")
-                for n in range(1, len(longest_code) + 1)
-            )
-            .with_columns(
-                pl.concat_list(
-                    pl.col(f"prefix_{n}")
-                    for n in range(1, len(longest_code) + 1)
-                )
-                .list.drop_nulls()
-                .list.unique()
-                .list.join(", ")
-                .alias("best_prefixes")
-            )
-            .write_csv("best_prefix.csv")
-        )
-
         code_to_category = (
             best_prefix.join(
                 code_map, left_on="best_prefix", right_on="prefix", how="left"
@@ -195,7 +170,9 @@ def CustomComorbidityIndex(
 
         # Combine: outer join on id_col, take max for each category
         all_categories = sorted(set(cats9) | set(cats10))
-        df_combined = df9.join(df10, on=id_col, how="outer", suffix="_right")
+        df_combined = df9.join(
+            df10, on=id_col, how="outer", suffix="_right", coalesce=True
+        )
         for cat in all_categories:
             left = cat
             right = f"{cat}_right"

{pycomorb-0.4 → pycomorb-0.4.2}/src/pycomorb/GagneComorbidityIndex.py

@@ -36,6 +36,7 @@ def GagneComorbidityIndex(
     icd_version: str = "icd9",
     icd_version_col: str = None,
     return_categories=False,
+    gagne_name: bool = False,
 ):
     """
     Calculate the Gagne Comorbidity Index using ICD codes.
@@ -49,7 +50,7 @@ def GagneComorbidityIndex(
         return_categories (bool): If True, also return presence indicators for each Gagne category.
 
     Returns:
-        - DataFrame with [id_col, "Gagne Score"].
+        - DataFrame with [id_col, "Combined Comorbidity Score"].
         - DataFrame with category indicators if return_categories is True, else None.
     """
 
@@ -68,9 +69,9 @@ def GagneComorbidityIndex(
     definition_file = "GAGNE.csv"
     definition_file_path = Path(__file__).parent / f"common/{definition_file}"
     weight_col_name = "weights"
-    score_col_name = "Gagne Score"
+    score_col_name = "Gagne Score" if gagne_name else "Combined Comorbidity Score"
 
-    # Define mutual exclusion rules for Gagne
+    # Define mutual exclusion rules for combined score
     mutual_exclusion_rules = [
         ("Complicated diabetes", "Uncomplicated diabetes")
     ]

{pycomorb-0.4 → pycomorb-0.4.2}/src/pycomorb/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Finn Fassbender"""
 __email__ = "finn.fassbender@charite.de"
-__version__ = "0.4"
+__version__ = "0.4.2"
 
 from .CharlsonComorbidityIndex import CharlsonComorbidityIndex
 from .ElixhauserComorbidityIndex import ElixhauserComorbidityIndex
@@ -94,6 +94,7 @@ def comorbidity(
             icd_version=icd_version,
             icd_version_col=icd_version_col,
             return_categories=return_categories,
+            gagne_name="gagne" in score,
         )
     elif score in (
         "hfrs",

{pycomorb-0.4 → pycomorb-0.4.2/src/pycomorb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycomorb
-Version: 0.4
+Version: 0.4.2
 Summary: Comorbidity and frailty score calculation utilities (Charlson, Elixhauser, Gagne, HFRS) using polars
 Author-email: Finn Fassbender <finn.fassbender@charite.de>
 License-Expression: MIT
@@ -32,7 +32,7 @@ It is inspired by the R package [`comorbidity`](https://github.com/ellessenne/co
 
 ## Supported Variants
 
-See [common/README.md](src/pycomorb/common/README.md) for more details and references.
+See [common/README.md](https://github.com/CUB-CORR/pycomorb/blob/main/src/pycomorb/common/README.md) for more details and references.
 
 ### Charlson Comorbidity Index