Skip to content

Preserve formulas in follow-up hazard-ratio refits #1703

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dnncha wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Preserve formulas in follow-up hazard-ratio refits #1703

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4f29f0d
Preserve fitted formula in follow-up hazard ratios
dnncha Sep 27, 2026
1e0f781
Test formula preservation in follow-up hazard ratios
dnncha Sep 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions lifelines/fitters/coxph_fitter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -287,6 +287,7 @@ def fit(

"""
self.strata = utils._to_list_or_singleton(utils.coalesce(strata, self.strata))
self.formula = formula
self._model = self._fit_model(
df,
duration_col,
Expand Down Expand Up @@ -858,6 +859,7 @@ def compute_followup_hazard_ratios(self, training_df: DataFrame, followup_times:
weights_col=self.weights_col,
cluster_col=self.cluster_col,
entry_col=self.entry_col,
formula=self.formula,
)
results[t] = model.hazard_ratios_
return DataFrame(results).T
Expand Down
8 changes: 8 additions & 0 deletions lifelines/tests/test_estimation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3248,6 +3248,14 @@ def test_compute_followup_hazard_ratios(self, cph, cph_spline, rossi):
cph_spline.fit(rossi, "week", "arrest")
cph_spline.compute_followup_hazard_ratios(rossi, [15, 25, 35, 45])

def test_compute_followup_hazard_ratios_preserves_formula(self, cph, rossi):
cph.fit(rossi, "week", "arrest", formula="fin + age + race")

result = cph.compute_followup_hazard_ratios(rossi, [rossi["week"].max()])

assert_index_equal(result.columns, cph.hazard_ratios_.index)
assert_series_equal(result.iloc[0], cph.hazard_ratios_, check_names=False)

def test_model_can_accept_null_covariates(self, cph, rossi):
cph.fit(rossi[["week", "arrest"]], "week", "arrest")
assert True
Expand Down