pySEQTarget 0.13.0__tar.gz → 0.13.2__tar.gz

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: pySEQTarget
-Version: 0.13.0
+Version: 0.13.2
 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>
+Maintainer-email: Ryan O'Dea <ryan.odea@psi.ch>, Tom Palmer <remlapmot@hotmail.com>
 License: MIT
 Project-URL: Homepage, https://github.com/CausalInference/pySEQTarget
 Project-URL: Repository, https://github.com/CausalInference/pySEQTarget

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/pySEQTarget/SEQopts.py

@@ -36,6 +36,9 @@ class SEQopts:
     :type excused: bool
     :param excused_colnames: Column names (at the same length of treatment_level) specifying excused conditions, default ``[]``
     :type excused_colnames: List[str]
+    :param expand_only: If True, ``SEQuential.expand()`` returns the expanded dataset and skips weighting,
+        modelling, and survival steps
+    :type expand_only: bool
     :param followup_class: Boolean to force followup values to be treated as classes
     :type followup_class: bool
     :param followup_include: Boolean to force regular followup values into model covariates
@@ -121,6 +124,7 @@ class SEQopts:
     denominator: Optional[str] = None
     excused: bool = False
     excused_colnames: List[str] = field(default_factory=lambda: [])
+    expand_only: bool = False
     followup_class: bool = False
     followup_include: bool = True
     followup_max: int = None
@@ -161,6 +165,7 @@ class SEQopts:
     def _validate_bools(self):
         bools = [
             "excused",
+            "expand_only",
             "followup_class",
             "followup_include",
             "followup_spline",

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/pySEQTarget/SEQuential.py

@@ -107,9 +107,11 @@ class SEQuential:
         _param_checker(self)
         _data_checker(self)
 
-    def expand(self) -> None:
+    def expand(self):
         """
-        Creates the sequentially nested, emulated target trial structure
+        Creates the sequentially nested, emulated target trial structure.
+        If ``expand_only`` is set in parameters, returns the expanded dataset as a
+        :class:`polars.DataFrame` and skips all subsequent analysis steps.
         """
         start = time.perf_counter()
         kept = [
@@ -160,7 +162,9 @@ class SEQuential:
             pl.col(self.id_col).cast(pl.Utf8).alias(self.id_col)
         )
 
-        if self.method != "ITT":
+        if self.method == "dose-response" or (
+            self.method == "censoring" and not self.expand_only
+        ):
             _dynamic(self)
         if self.selection_random:
             _random_selection(self)
@@ -169,6 +173,9 @@ class SEQuential:
         end = time.perf_counter()
         self._expansion_time = _format_time(start, end)
 
+        if self.expand_only:
+            return self.DT
+
     def bootstrap(self, **kwargs) -> None:
         """
         Internally sets up bootstrapping - creating a list of IDs to use per iteration

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/pySEQTarget.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: pySEQTarget
-Version: 0.13.0
+Version: 0.13.2
 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>
+Maintainer-email: Ryan O'Dea <ryan.odea@psi.ch>, Tom Palmer <remlapmot@hotmail.com>
 License: MIT
 Project-URL: Homepage, https://github.com/CausalInference/pySEQTarget
 Project-URL: Repository, https://github.com/CausalInference/pySEQTarget

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pySEQTarget"
-version = "0.13.0"
+version = "0.13.2"
 description = "Sequentially Nested Target Trial Emulation"
 readme = "README.md"
 license = {text = "MIT"}
@@ -30,6 +30,7 @@ authors = [
 
 maintainers = [
     {name = "Ryan O'Dea", email = "ryan.odea@psi.ch"},
+    {name = "Tom Palmer", email = "remlapmot@hotmail.com"},
 ]
 
 dependencies = [

{pyseqtarget-0.13.0 → pyseqtarget-0.13.2}/tests/test_expansion.py

@@ -1,6 +1,7 @@
 import polars as pl
+from polars.testing import assert_frame_equal
 
-from pySEQTarget import SEQuential
+from pySEQTarget import SEQopts, SEQuential
 
 
 def _make_model(data):
@@ -90,3 +91,38 @@ def test_expansion_truncates_each_trial_independently():
 
     # Trial 1 starts at time=1, outcome at time=3 → followup 0,1,2
     assert sorted(trial_1["followup"].to_list()) == [0, 1, 2]
+
+
+def test_expand_only_returns_expanded_dataframe():
+    """expand_only=True should return the expanded DataFrame directly and the
+    return value should equal self.DT from a standard expand() call."""
+    data = pl.DataFrame(
+        {
+            "ID": [1, 1, 1, 1, 1],
+            "time": [0, 1, 2, 3, 4],
+            "eligible": [1, 0, 0, 0, 0],
+            "treatment": [0, 1, 0, 1, 0],
+            "outcome": [0, 0, 0, 0, 0],
+        }
+    )
+
+    model_only = SEQuential(
+        data,
+        id_col="ID",
+        time_col="time",
+        eligible_col="eligible",
+        treatment_col="treatment",
+        outcome_col="outcome",
+        time_varying_cols=[],
+        fixed_cols=[],
+        parameters=SEQopts(expand_only=True),
+    )
+    result = model_only.expand()
+
+    assert isinstance(result, pl.DataFrame)
+    assert_frame_equal(result, model_only.DT)
+
+    model_full = _make_model(data)
+    model_full.expand()
+
+    assert_frame_equal(result, model_full.DT)