Add pval_digits argument.

tableone/formatting.py

@@ -35,32 +35,39 @@ def set_display_options(max_rows=None,
             warnings.warn(msg)
 
 
-def format_pvalues(table, pval, pval_adjust, pval_threshold):
+def format_pvalues(table, pval, pval_adjust, pval_threshold, pval_digits):
     """
-    Formats the p value columns, applying rounding rules and adding
-    significance markers based on defined thresholds.
+    Formats p-values to a fixed number of decimal places and optionally adds
+    significance markers based on a threshold.
     """
-    # round pval column and convert to string
-    if pval and pval_adjust:
-        table['P-Value (adjusted)'] = table['P-Value (adjusted)'].apply('{:.3f}'.format).astype(str)
-        table.loc[table['P-Value (adjusted)'] == '0.000',
-                  'P-Value (adjusted)'] = '<0.001'
-
+    def _format(p):
+        if pd.isnull(p):
+            return ""
+        try:
+            fval = float(p)
+        except Exception:
+            return str(p)
+        if fval < 10**(-pval_digits):
+            return f"<{10**(-pval_digits):.{pval_digits}f}"
+        return f"{fval:.{pval_digits}f}"
+
+    if pval_adjust:
+        col = 'P-Value (adjusted)'
         if pval_threshold:
-            asterisk_mask = table['P-Value (adjusted)'] < pval_threshold
-            table.loc[asterisk_mask, 'P-Value (adjusted)'] = (
-                table['P-Value (adjusted)'][asterisk_mask].astype(str)+"*"  # type: ignore
-            )
+            asterisk_mask = table[col] < pval_threshold
+            table[col] = table[col].apply(_format).astype(str)
+            table.loc[asterisk_mask, col] += "*"
+        else:
+            table[col] = table[col].apply(_format).astype(str)
 
     elif pval:
-        table['P-Value'] = table['P-Value'].apply('{:.3f}'.format).astype(str)
-        table.loc[table['P-Value'] == '0.000', 'P-Value'] = '<0.001'
-
+        col = 'P-Value'
         if pval_threshold:
-            asterisk_mask = table['P-Value'] < pval_threshold
-            table.loc[asterisk_mask, 'P-Value'] = (
-                table['P-Value'][asterisk_mask].astype(str)+"*"  # type: ignore
-            )
+            asterisk_mask = table[col] < pval_threshold
+            table[col] = table[col].apply(_format).astype(str)
+            table.loc[asterisk_mask, col] += "*"
+        else:
+            table[col] = table[col].apply(_format).astype(str)
 
     return table
 

tableone/tableone.py

@@ -103,7 +103,12 @@ class TableOne:
         `holm-sidak` : step down method using Sidak adjustments
         `simes-hochberg` : step-up method (independent)
         `hommel` : closed method based on Simes tests (non-negative)
-
+    pval_digits : int, default=3
+        Number of decimal places to display for p-values.
+    pval_threshold : float, optional
+        Threshold below which p-values are marked with an asterisk (*).
+        For example, if set to 0.05, all p-values less than 0.05 will be
+        displayed with a trailing asterisk (e.g., '0.012*').
     htest_name : bool, optional
         Display a column with the names of hypothesis tests (default: False).
     htest : dict, optional
@@ -219,7 +224,8 @@ def __init__(self, data: pd.DataFrame,
                  dip_test: bool = False, normal_test: bool = False,
                  tukey_test: bool = False,
                  pval_threshold: Optional[float] = None,
-                 include_null: Optional[bool] = True) -> None:
+                 include_null: Optional[bool] = True,
+                 pval_digits: int = 3) -> None:
 
         # Warn about deprecated parameters
         handle_deprecated_parameters(labels, isnull, pval_test_name, remarks)
@@ -234,7 +240,7 @@ def __init__(self, data: pd.DataFrame,
                                                htest, missing, ddof, rename, sort, limit, order,
                                                label_suffix, decimals, smd, overall, row_percent,
                                                dip_test, normal_test, tukey_test, pval_threshold,
-                                               include_null)
+                                               include_null, pval_digits)
 
         # Initialize intermediate tables
         self.initialize_intermediate_tables()
@@ -276,7 +282,7 @@ def initialize_core_attributes(self, data, columns, categorical, continuous, gro
                                    htest, missing, ddof, rename, sort, limit, order,
                                    label_suffix, decimals, smd, overall, row_percent, 
                                    dip_test, normal_test, tukey_test, pval_threshold,
-                                   include_null):
+                                   include_null, pval_digits):
         """
         Initialize attributes.
         """
@@ -305,6 +311,7 @@ def initialize_core_attributes(self, data, columns, categorical, continuous, gro
         self._pval_adjust = pval_adjust
         self._pval_test_name = htest_name
         self._pval_threshold = pval_threshold
+        self._pval_digits = pval_digits
         self._reserved_columns = ['Missing', 'P-Value', 'Test', 'P-Value (adjusted)', 'SMD', 'Overall']
         self._row_percent = row_percent
         self._smd = smd
@@ -654,7 +661,7 @@ def _create_tableone(self, data):
         table.columns = table.columns.values.astype(str)
 
         table = sort_and_reindex(table, self._smd, self.smd_table, self._sort, self._columns)
-        table = format_pvalues(table, self._pval, self._pval_adjust, self._pval_threshold)
+        table = format_pvalues(table, self._pval, self._pval_adjust, self._pval_threshold, self._pval_digits)
         table = format_smd_columns(table, self._smd, self.smd_table)
         table = apply_order(table, self._order, self._groupby)
         table = apply_limits(table, data, self._limit, self._categorical, self._order)

tests/unit/test_tableone.py

@@ -1393,3 +1393,26 @@ def test_handle_categorical_nulls_does_not_affect_continuous():
     result = handle_categorical_nulls(df, categorical=['cat'])
     assert result['cont'].dtype == float
     assert result['cat'].iloc[2] == 'None'
+
+
+def test_pval_digits_custom_formatting():
+    df = pd.DataFrame({
+        'group': ['A', 'A', 'B', 'B', 'B'],
+        'x': [1, 5, 1, 2, 2],
+        'y': [1, 2, 5, 5, 6]
+    })
+
+    t1 = TableOne(df, columns=['x'], categorical=['x'], groupby='group', pval=True, pval_digits=5)
+    pval = t1.tableone['Grouped by group']['P-Value'].iloc[1]
+    assert pval == '0.23262'
+
+    t2 = TableOne(df, columns=['x'], categorical=['x'], groupby='group', pval=True, pval_digits=3,
+                pval_threshold=0.3)
+    pval = t2.tableone['Grouped by group']['P-Value'].iloc[1]
+    assert pval == '0.233*'
+
+
+    t3 = TableOne(df, columns=['y'], continuous=['y'], groupby='group', pval=True, pval_digits=1,
+                  pval_threshold=0.3)
+    pval = t3.tableone['Grouped by group']['P-Value'].iloc[1]
+    assert pval == '<0.1*'