From 3580e487802005b37bb221c99d89c3302a2bfac8 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Sun, 16 Aug 2026 14:57:05 +0000
Subject: [PATCH 1/5] bump version to 0.1.32

Bump version in pyproject.toml to 0.1.32 following local Aalen-Johansen and secondary Cox calibration smoothing release.

Co-authored-by: uriahf <11351434+uriahf@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 uv.lock        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e5f1edcd..77e16513 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ dependencies = [
     "great-tables>=0.18.0",
 ]
 name = "rtichoke"
-version = "0.1.31"
+version = "0.1.32"
 description = "interactive visualizations for performance of predictive models"
 readme = "README.md"
 
diff --git a/uv.lock b/uv.lock
index 97a06832..e83f7972 100644
--- a/uv.lock
+++ b/uv.lock
@@ -5119,7 +5119,7 @@ wheels = [
 
 [[package]]
 name = "rtichoke"
-version = "0.1.31"
+version = "0.1.32"
 source = { editable = "." }
 dependencies = [
     { name = "great-tables", version = "0.21.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },

From 4da11750db48a0d4867dbf291fa4f8c7d0da26f6 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Sun, 16 Aug 2026 15:17:16 +0000
Subject: [PATCH 2/5] ci: update docs workflow build and export steps

Ensure demo HTML exports are run in the push-to-main docs action so that Great Docs publishes full interactive examples.

Co-authored-by: uriahf <11351434+uriahf@users.noreply.github.com>
---
 .github/workflows/docs.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 990d6de1..facc9e1c 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -37,6 +37,17 @@ jobs:
       - name: Build Great Docs site
         run: uv run great-docs build
 
+      - name: Export Great Tables performance table demo
+        run: uv run marimo export html --no-include-code examples/performance_table_demo.py -o great-docs/_site/performance-table-demo.html
+
+      - name: Export Reactable performance table demo
+        run: |
+          uv run quarto render examples/performance_table_reactable.qmd --output performance-table-reactable.html
+          grep -q '.Reactable {' performance-table-reactable.html
+          grep -q 'Real Positive' performance-table-reactable.html
+          mv performance-table-reactable.html great-docs/_site/performance-table-reactable.html
+          cp -R examples/performance_table_reactable_files great-docs/_site/performance_table_reactable_files
+
       - name: Publish documentation
         uses: JamesIves/github-pages-deploy-action@v4
         with:

From 4ac23930870c0d40e4899a952a2ae61e5a3db295 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Sun, 16 Aug 2026 15:24:16 +0000
Subject: [PATCH 3/5] docs: add user guide page for calibration curves and
 smooth methods

Added user_guide/05-calibration-curves.qmd detailing standard binary calibration, time-dependent calibration, and the three smooth_method options (local_aj, secondary_cox, pseudo_values).

Co-authored-by: uriahf <11351434+uriahf@users.noreply.github.com>
---
 user_guide/05-calibration-curves.qmd | 86 ++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100644 user_guide/05-calibration-curves.qmd

diff --git a/user_guide/05-calibration-curves.qmd b/user_guide/05-calibration-curves.qmd
new file mode 100644
index 00000000..72fdcd99
--- /dev/null
+++ b/user_guide/05-calibration-curves.qmd
@@ -0,0 +1,86 @@
+---
+title: "Calibration Curves"
+guide-section: "Curves"
+---
+
+Calibration evaluates how well predicted risks from a classification or time-to-event model align with observed outcome rates.
+
+## Standard Calibration (`create_calibration_curve`)
+
+For binary outcomes:
+
+```python
+import rtichoke as rk
+
+fig = rk.create_calibration_curve(
+    probs={"Model A": probs_a},
+    reals=reals_binary,
+    calibration_type="smooth",
+)
+```
+
+`calibration_type` can be set to `"discrete"` (deciles) or `"smooth"` (lowess curve).
+
+## Time-Dependent Calibration (`create_calibration_curve_times`)
+
+When evaluating risk predictions at a specific time horizon $t$:
+
+```python
+heuristics_sets = [
+    {
+        "censoring_heuristic": "adjusted",
+        "competing_heuristic": "adjusted_as_negative",
+    }
+]
+
+fig = rk.create_calibration_curve_times(
+    probs={"Model A": probs_a},
+    reals=reals_time_to_event,
+    times=times,
+    fixed_time_horizons=[3.0, 5.0],
+    heuristics_sets=heuristics_sets,
+    calibration_type="smooth",
+    smooth_method="local_aj",
+)
+```
+
+## Smoothing Methods for Time-Dependent Calibration
+
+When `calibration_type="smooth"`, `create_calibration_curve_times` supports three distinct statistical smoothing methods via the `smooth_method` parameter:
+
+### 1. Local Aalen-Johansen (`smooth_method="local_aj"`, Default)
+
+**Gerds' favoured local neighborhood method** (`riskRegression::plotCalibration(method="nne", cens.method="local")`):
+
+- Computes local Aalen-Johansen / Kaplan-Meier cumulative incidence estimates within nearest-neighborhood risk windows across predicted probabilities.
+- Fully non-parametric and handles both standard survival and competing risks ($0=\text{censored}$, $1=\text{event}$, $2=\text{competing event}$).
+- You can tune the neighborhood window using the optional `bandwidth` parameter (e.g., `bandwidth=0.2`).
+
+### 2. Secondary Cox Model (`smooth_method="secondary_cox"`)
+
+**Austin, Harrell & McLernon original time-to-event method** (Austin et al. 2020 / McLernon et al. 2023):
+
+- Fits a secondary cause-specific Cox proportional hazards model on the complementary log-log transformed predictions ($\log(-\log(1-p))$).
+- Evaluates predicted cumulative incidence at horizon $t$ across the grid of predicted probabilities.
+
+### 3. Pseudo-Values LOWESS (`smooth_method="pseudo_values"`)
+
+**Jackknife pseudo-observations method**:
+
+- Computes leave-one-out Aalen-Johansen pseudo-values for each subject at horizon $t$.
+- Applies LOWESS smoothing against predicted probabilities.
+
+## Discrete (Binned) Calibration
+
+For binned decile plots at time horizons, pass `calibration_type="discrete"`:
+
+```python
+fig = rk.create_calibration_curve_times(
+    probs={"Model A": probs_a},
+    reals=reals_time_to_event,
+    times=times,
+    fixed_time_horizons=[5.0],
+    heuristics_sets=heuristics_sets,
+    calibration_type="discrete",
+)
+```

From 1fc86c115ddd13b7acde953b69365c1253250147 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Sun, 16 Aug 2026 15:29:25 +0000
Subject: [PATCH 4/5] docs: add user guide page and update workflows for
 calibration smooth methods

- Added `user_guide/05-calibration-curves.qmd` documenting standard and time-dependent calibration.
- Detailed the three smoothing methods: `local_aj` (Gerds' local neighborhood method), `secondary_cox` (Austin, Harrell & McLernon method), and `pseudo_values` (jackknife pseudo-values lowess).
- Updated `.github/workflows/docs.yml` to include demo exports when deploying documentation on push to main.
- Bumped package version to `v0.1.32`.

Co-authored-by: uriahf <11351434+uriahf@users.noreply.github.com>

From 5d7f9b822834aff497d096cb9fed9f47252ac0e8 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Sun, 16 Aug 2026 17:31:34 +0000
Subject: [PATCH 5/5] docs: add user guide page and update workflows for
 calibration smooth methods

- Added `user_guide/05-calibration-curves.qmd` documenting standard and time-dependent calibration.
- Detailed the three smoothing methods: `local_aj` (Gerds' local neighborhood method), `secondary_cox` (Austin, Harrell & McLernon method), and `pseudo_values` (jackknife pseudo-values lowess).
- Updated `.github/workflows/docs.yml` to include demo exports when deploying documentation on push to main.
- Bumped package version to `v0.1.32`.

Co-authored-by: uriahf <11351434+uriahf@users.noreply.github.com>