feat(CLR): add closure_target parameter

GispoCoding · Dec 17, 2024 · 3bcfedd · 3bcfedd
1 parent 33f4d78
commit 3bcfedd
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/eis_toolkit/transformations/coda/clr.py b/eis_toolkit/transformations/coda/clr.py
@@ -9,7 +9,7 @@
 from eis_toolkit.exceptions import InvalidColumnException, NumericValueSignException
 from eis_toolkit.utilities.aitchison_geometry import _closure
 from eis_toolkit.utilities.checks.compositional import check_in_simplex_sample_space
-from eis_toolkit.utilities.miscellaneous import rename_columns, rename_columns_by_pattern
+from eis_toolkit.utilities.miscellaneous import perform_closure, rename_columns, rename_columns_by_pattern
 
 
 @beartype
@@ -26,13 +26,18 @@ def _clr_transform(df: pd.DataFrame) -> pd.DataFrame:
 
 
 @beartype
-def clr_transform(df: pd.DataFrame, columns: Optional[Sequence[str]] = None) -> pd.DataFrame:
+def clr_transform(
+    df: pd.DataFrame,
+    columns: Optional[Sequence[str]] = None,
+    closure_target: Optional[int] = None,
+) -> pd.DataFrame:
     """
     Perform a centered logratio transformation on the data.
 
     Args:
         df: A dataframe of compositional data.
         columns: The names of the columns to be transformed.
+        closure_target: Target row sum for closure. If None, no closure is performed.
 
     Returns:
         A new dataframe containing the CLR transformed data.
@@ -52,6 +57,9 @@ def clr_transform(df: pd.DataFrame, columns: Optional[Sequence[str]] = None) ->
     else:
         columns_to_transform = df.columns.to_list()
 
+    if closure_target is not None:
+        df = perform_closure(df, columns_to_transform, closure_target)
+
     check_in_simplex_sample_space(df)
 
     return rename_columns_by_pattern(_clr_transform(df))