pySEQTarget 0.13.2__tar.gz → 0.13.3__tar.gz

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pySEQTarget
-Version: 0.13.2
+Version: 0.13.3
 Summary: Sequentially Nested Target Trial Emulation
 Author-email: Ryan O'Dea <ryan.odea@psi.ch>, Alejandro Szmulewicz <aszmulewicz@hsph.harvard.edu>, Tom Palmer <tom.palmer@bristol.ac.uk>, Miguel Hernán <mhernan@hsph.harvard.edu>
 Maintainer-email: Ryan O'Dea <ryan.odea@psi.ch>, Tom Palmer <remlapmot@hotmail.com>

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/pySEQTarget/SEQopts.py

@@ -45,6 +45,8 @@ class SEQopts:
     :type followup_include: bool
     :param followup_spline: Boolean to force followup values to be fit to cubic spline
     :type followup_spline: bool
+    :param followup_spline_df: Degrees of freedom for the followup cubic spline, default ``4``
+    :type followup_spline_df: int
     :param followup_max: Maximum allowed followup in analysis
     :type followup_max: int or None
     :param followup_min: Minimum allowed followup in analysis
@@ -130,6 +132,7 @@ class SEQopts:
     followup_max: int = None
     followup_min: int = 0
     followup_spline: bool = False
+    followup_spline_df: int = 4
     hazard_estimate: bool = False
     indicator_baseline: str = "_bas"
     indicator_squared: str = "_sq"

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/pySEQTarget/analysis/_outcome_fit.py

@@ -1,12 +1,30 @@
 import re
 
+import numpy as np
 import polars as pl
 import statsmodels.api as sm
 import statsmodels.formula.api as smf
 
 
-def _apply_spline_formula(formula, indicator_squared):
-    spline = "cr(followup, df=3)"
+def _compute_spline_knots(followup_arr, df=3):
+    lower = float(np.min(followup_arr))
+    upper = float(np.max(followup_arr))
+    n_inner = df - 2
+    if n_inner == 0:
+        inner_knots = []
+    else:
+        # Replicate patsy's knot placement: percentiles of unique values in [lower, upper]
+        x = np.unique(followup_arr[(lower <= followup_arr) & (followup_arr <= upper)])
+        q = np.linspace(0, 100, n_inner + 2)[1:-1]
+        inner_knots = np.percentile(x, q.tolist()).tolist()
+    return inner_knots, lower, upper
+
+
+def _apply_spline_formula(formula, indicator_squared, spline_knots):
+    inner_knots, lower, upper = spline_knots
+    spline = (
+        f"cr(followup, knots={inner_knots}, lower_bound={lower}, upper_bound={upper})"
+    )
 
     formula = re.sub(r"(\w+)\s*\*\s*followup\b", rf"\1*{spline}", formula)
     formula = re.sub(r"\bfollowup\s*\*\s*(\w+)", rf"{spline}*\1", formula)
@@ -18,8 +36,8 @@ def _apply_spline_formula(formula, indicator_squared):
     formula = re.sub(r"^\s*\+\s*|\s*\+\s*$", "", formula).strip()
 
     if formula:
-        return f"{formula} + I({spline}**2)"
-    return f"I({spline}**2)"
+        return f"{formula} + {spline}"
+    return spline
 
 
 def _cast_categories(self, df_pd):
@@ -64,7 +82,13 @@ def _outcome_fit(
     df_pd = _cast_categories(self, df.to_pandas())
 
     if self.followup_spline:
-        formula = _apply_spline_formula(formula, self.indicator_squared)
+        if getattr(self, "_current_boot_idx", None) is None:
+            self._followup_spline_knots = _compute_spline_knots(
+                self.DT["followup"].to_numpy(), df=self.followup_spline_df
+            )
+        formula = _apply_spline_formula(
+            formula, self.indicator_squared, self._followup_spline_knots
+        )
 
     full_formula = f"{outcome} ~ {formula}"
 

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/pySEQTarget/error/_param_checker.py

@@ -44,6 +44,9 @@ def _param_checker(self):
             "Only one of followup_class or followup_include can be set to True."
         )
 
+    if self.followup_spline_df < 2:
+        raise ValueError("followup_spline_df must be at least 2.")
+
     if (
         self.weighted
         and self.method == "ITT"

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/pySEQTarget.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pySEQTarget
-Version: 0.13.2
+Version: 0.13.3
 Summary: Sequentially Nested Target Trial Emulation
 Author-email: Ryan O'Dea <ryan.odea@psi.ch>, Alejandro Szmulewicz <aszmulewicz@hsph.harvard.edu>, Tom Palmer <tom.palmer@bristol.ac.uk>, Miguel Hernán <mhernan@hsph.harvard.edu>
 Maintainer-email: Ryan O'Dea <ryan.odea@psi.ch>, Tom Palmer <remlapmot@hotmail.com>

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pySEQTarget"
-version = "0.13.2"
+version = "0.13.3"
 description = "Sequentially Nested Target Trial Emulation"
 readme = "README.md"
 license = {text = "MIT"}

{pyseqtarget-0.13.2 → pyseqtarget-0.13.3}/tests/test_followup_options.py

@@ -57,17 +57,18 @@ def test_followup_spline():
     s.fit()
     matrix = s.outcome_model[0]["outcome"].summary2().tables[1]["Coef."].to_list()
     expected = [
-        -6.264817962084417,
-        0.20125056343026881,
-        0.12568743032952776,
-        0.03823426390103046,
-        0.0006607691746414019,
-        0.003343365539743267,
-        -0.01319460158923785,
-        0.19601796921732118,
-        -0.5186462478511427,
-        0.37598656666756103,
-        1.6553848469346044,
+        -4.804282252748607,
+        0.19115933860001255,
+        0.12717121164606823,
+        0.044310717515918724,
+        0.0005814999431447507,
+        0.0032948355025455216,
+        -0.013371824500839971,
+        0.19972467861548412,
+        -2.027245615586753,
+        -1.395729861856384,
+        -0.9397731941281695,
+        -0.4415335811772879,
     ]
     assert [round(x, 3) for x in matrix] == [round(x, 3) for x in expected]