nested-recd 0.1.0__tar.gz → 0.2.3__tar.gz

nested_recd-0.2.3/PKG-INFO

@@ -0,0 +1,228 @@
+Metadata-Version: 2.4
+Name: nested-recd
+Version: 0.2.3
+Summary: Nested ordinal RECD: Φ1–Φ3, continuous excess³ (exportable Level-3 proxy), Res_pair (strong residual), and λ-weighted Discrete Extramental Clock
+Author-email: Johel Padilla-Villanueva <joel.padilla2@upr.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/johelpadilla/nested-recd
+Project-URL: Repository, https://github.com/johelpadilla/nested-recd
+Project-URL: Issues, https://github.com/johelpadilla/nested-recd/issues
+Project-URL: Documentation, https://github.com/johelpadilla/nested-recd#readme
+Project-URL: DOI, https://doi.org/10.5281/zenodo.22970079
+Keywords: RECD,ordinal patterns,nested time,Systemic Tau,complexity,early-warning,network physiology,Bandt-Pompe
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+# nested-recd
+
+> **Correction (0.2.3).** Versions ≤ 0.2.2 computed `H_joint` and the pairwise
+> entropies inside `Syn` with `np.unique` on a list of tuples and no `axis=0`.
+> NumPy flattens that input, so `Syn`, `excess3` and binary `phi3` were not the
+> published definition when `N ≥ 3`. `Surp` and `Res_pair` were not affected.
+> For `N = 2`, `Syn` is 0 either way. 0.2.3 counts joint rows.
+> `legacy_pooled_counting=True` reproduces the old numbers and warns.
+> See `CHANGELOG.md`. This version:
+> [10.5281/zenodo.22970079](https://doi.org/10.5281/zenodo.22970079).
+> The 0.2.2 deposit remains
+> [10.5281/zenodo.21937204](https://doi.org/10.5281/zenodo.21937204).
+
+[![PyPI version](https://img.shields.io/pypi/v/nested-recd.svg)](https://pypi.org/project/nested-recd/)
+[![Python](https://img.shields.io/pypi/pyversions/nested-recd.svg)](https://pypi.org/project/nested-recd/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+**Nested ordinal RECD** — pure-NumPy implementation of nested ordinal conjunction levels (Φ₁, Φ₂, Φ₃), the continuous **excess³** Level-3 *proxy* (T-IV; not the strong residual), optional **Res_pair** \(=\mathrm{KL}(P\|P^{(2)})\), Gibbs-α weights, and λ-weighted Discrete Extramental Clock (RECD) accumulation.
+
+This is the **canonical nested-clock software** for the Systemic Tau / RECD stack (foundations paper, excess³ methods preprint, cardiac CCTP/SDDB pilot, Academy Learning Tau).
+
+**Léxico (no negociable):** *strong Level-3* := `Res_pair`. *excess3* := exportable proxy. Report `w` with any Res_pair figure. Abundance (excess3) ≠ aggregation share \(f_3\).
+
+## Install
+
+```bash
+pip install nested-recd
+```
+
+From source (development):
+
+```bash
+pip install -e ".[dev]"
+```
+
+## excess³ contract (methods)
+
+Canonical specification: Padilla-Villanueva (2026), *excess³: A Pre-Specified Continuous Proxy…*  
+DOI: [10.5281/zenodo.21385937](https://doi.org/10.5281/zenodo.21385937) · repo: [github.com/johelpadilla/excess3](https://github.com/johelpadilla/excess3)
+
+| Rule | Software |
+|------|----------|
+| `excess3 = 0.6·Syn + 0.4·Surp` | `ALPHA_SYN`, `ALPHA_SURP` (fixed a priori) |
+| Continuous primary | `out["excess3"]` / `compute_phi3_excess` |
+| Φ₃ secondary | binary ticks of excess3 vs `theta3` |
+| Null on full contrast | `surrogate_pvalue_delta_excess3` (phase-shuffle / permute on `\|Δ\|`) |
+| Proxy ≠ full PID | documented; no complete Williams–Beer atom claimed |
+| Parallel nesting | Φ₁, Φ₂, excess³ computed without hard Boolean ascent |
+
+Defaults: `m=3`, delay `1`, window `13`, `theta3=0.10` (software); cardio-like reference `DEFAULT_THETA3_CARDIO=0.08`.
+
+## Quick start
+
+```python
+import numpy as np
+from nested_recd import compute_recd_from_conjunctions, ALPHA_SYN, ALPHA_SURP
+
+rng = np.random.default_rng(0)
+X = rng.normal(size=(800, 3)).cumsum(axis=0)
+
+out = compute_recd_from_conjunctions(X, m=3, d=4, theta3=0.10)
+
+print("mean excess³ (primary):", float(np.nanmean(out["excess3"])))
+print("Φ3 active fraction:", float(np.nanmean(out["phi3"] > 0)))
+print("weights:", out["params"]["alpha_syn"], out["params"]["alpha_surp"])
+print("final T_recd:", float(out["T_recd"][-1]))
+```
+
+### Strong residual Res_pair (optional)
+
+```python
+out = compute_recd_from_conjunctions(X, compute_res=True)
+# or, on a symbol window:
+from nested_recd import compute_res_pair_window
+# Always report window length with Res_pair (Nota 4: w=13 can bias chaos).
+```
+
+### Continuous excess³ only
+
+```python
+from nested_recd import generate_multivariate_symbols, compute_phi3_excess
+
+S = generate_multivariate_symbols(X, m=3)
+phi3, excess3 = compute_phi3_excess(S, window=13, theta=0.10, stride=1)
+```
+
+### Surrogate p-value on |Δ excess3|
+
+```python
+from nested_recd import surrogate_pvalue_delta_excess3
+
+res = surrogate_pvalue_delta_excess3(X, split=400, n_surr=99, method="phase", seed=0)
+print(res["delta_obs"], res["p_value"])
+```
+
+### Optional τ_s for λ regime weights
+
+```python
+out = compute_recd_from_conjunctions(X, tau_s=tau_s)
+# or
+out = compute_recd_from_conjunctions(X, lam_override=0.5)
+```
+
+**Note:** `delta_recd` / `T_recd` use **binary Φ₃** in the α-weighted clock (legacy Discrete Extramental Clock). For **exportable / scalable** Level-3 reporting, use continuous **excess³** and nulls on `|Δ excess3|`. For **strong** Level-3 claims, report **`res_pair`** (enable `compute_res=True`) **and the window `w`**. Do not identify the two.
+
+## What it computes
+
+| Symbol | Meaning |
+|--------|---------|
+| **Φ₁** | Co-occurrence of identical ordinal symbols across variable pairs |
+| **Φ₂** | Persistence of pairwise ordinal relations over lag `d` |
+| **excess³** | Continuous hybrid: `0.6·Syn + 0.4·Surp` (**exportable Level-3 proxy**; T-IV) |
+| **Φ₃** | Binary ticks of excess³ above `theta3` (**secondary**) |
+| **Res_pair** | Strong Level-3 residual `KL(P ‖ P^(2))` (optional; always report `w`) |
+| **λ** | Chaos / reorganization intensity (from `τ_s` or `lam_override`) |
+| **α(λ)** | Design-engine weights (template or Gibbs-α); **not** a joint observable |
+| **ΔRECD** | `α₁Φ₁ + α₂Φ₂ + α₃Φ₃` (legacy clock; binary Φ₃) |
+| **T_recd** | Cumulative sum of ΔRECD |
+
+Ordinal symbols use Bandt–Pompe patterns (`m=3` by default).
+
+## Surrogates
+
+```python
+from nested_recd import phase_shuffle_independent, random_permutation_independent
+
+X_null = phase_shuffle_independent(X, seed=42)
+X_perm = random_permutation_independent(X, seed=42)
+```
+
+## API surface
+
+```python
+from nested_recd import (
+    ALPHA_SYN, ALPHA_SURP,
+    DEFAULT_THETA3, DEFAULT_THETA3_CARDIO,
+    compute_recd_from_conjunctions,
+    compute_phi1, compute_phi2, compute_phi3,
+    compute_phi3_excess, compute_excess3_window,
+    mean_excess_pre_post, surrogate_pvalue_delta_excess3,
+    compute_lambda, alpha_weights, alpha_weights_gibbs, regime_lambda_proxy,
+    compute_res_pair, compute_res_pair_window,
+    compute_weighted_contributions, high_level3_rate,
+    generate_multivariate_symbols,
+    phase_shuffle_independent, generate_surrogate_ensemble,
+)
+```
+
+## Relation to other projects
+
+| Project | Role |
+|---------|------|
+| [`systemictau`](https://pypi.org/project/systemictau/) | Full Systemic Tau library (τ_s, gate RECD, studio) — optional `[nested]` extra |
+| [`systemictau-web`](https://github.com/johelpadilla/systemictau-web) | Streamlit app; depends on this package |
+| [`excess3`](https://github.com/johelpadilla/excess3) | Methods + intro ES + primer (specification) |
+| [`cctp-sddb-systemic-tau`](https://github.com/johelpadilla/cctp-sddb-systemic-tau) | Cardiac VF pilot |
+| This package | Lightweight, installable nested-time / excess³ core |
+
+## Citation
+
+If you use excess³ / Level-3 from this package, cite the **methods** preprint (canonical specification):
+
+> Padilla-Villanueva, J. (2026). *excess³: A Pre-Specified Continuous Proxy for Order-3 Synergistic Surplus* (methods). Zenodo. https://doi.org/10.5281/zenodo.21385937
+
+This software (0.2.3):
+
+> Padilla-Villanueva, J. (2026). *nested-recd 0.2.3: Nested ordinal RECD, excess³ proxy, and Res_pair*. Zenodo. https://doi.org/10.5281/zenodo.22970079
+
+The previous release (0.2.2), which pooled symbols inside Syn, remains citable as https://doi.org/10.5281/zenodo.21937204.
+
+Software / related stack:
+
+> Padilla-Villanueva, J. (2026). Systemic Tau software archive. Zenodo. https://doi.org/10.5281/zenodo.20576241
+
+CCTP/SDDB pilot:
+
+> Padilla-Villanueva, J. (2026). *CCTP/SDDB: Systemic Tau and ordinal RECD before spontaneous ventricular fibrillation* (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.21270699
+
+```bibtex
+@software{padilla_nested_recd_2026,
+  author  = {Padilla-Villanueva, Johel},
+  title   = {nested-recd: Nested ordinal RECD levels and continuous excess³},
+  year    = {2026},
+  url     = {https://github.com/johelpadilla/nested-recd},
+  version = {0.2.3},
+  doi     = {10.5281/zenodo.22970079}
+}
+```
+
+## License
+
+MIT © 2026 Johel Padilla-Villanueva  
+ORCID: [0000-0002-5797-6931](https://orcid.org/0000-0002-5797-6931)

nested_recd-0.2.3/README.md

@@ -0,0 +1,193 @@
+# nested-recd
+
+> **Correction (0.2.3).** Versions ≤ 0.2.2 computed `H_joint` and the pairwise
+> entropies inside `Syn` with `np.unique` on a list of tuples and no `axis=0`.
+> NumPy flattens that input, so `Syn`, `excess3` and binary `phi3` were not the
+> published definition when `N ≥ 3`. `Surp` and `Res_pair` were not affected.
+> For `N = 2`, `Syn` is 0 either way. 0.2.3 counts joint rows.
+> `legacy_pooled_counting=True` reproduces the old numbers and warns.
+> See `CHANGELOG.md`. This version:
+> [10.5281/zenodo.22970079](https://doi.org/10.5281/zenodo.22970079).
+> The 0.2.2 deposit remains
+> [10.5281/zenodo.21937204](https://doi.org/10.5281/zenodo.21937204).
+
+[![PyPI version](https://img.shields.io/pypi/v/nested-recd.svg)](https://pypi.org/project/nested-recd/)
+[![Python](https://img.shields.io/pypi/pyversions/nested-recd.svg)](https://pypi.org/project/nested-recd/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+**Nested ordinal RECD** — pure-NumPy implementation of nested ordinal conjunction levels (Φ₁, Φ₂, Φ₃), the continuous **excess³** Level-3 *proxy* (T-IV; not the strong residual), optional **Res_pair** \(=\mathrm{KL}(P\|P^{(2)})\), Gibbs-α weights, and λ-weighted Discrete Extramental Clock (RECD) accumulation.
+
+This is the **canonical nested-clock software** for the Systemic Tau / RECD stack (foundations paper, excess³ methods preprint, cardiac CCTP/SDDB pilot, Academy Learning Tau).
+
+**Léxico (no negociable):** *strong Level-3* := `Res_pair`. *excess3* := exportable proxy. Report `w` with any Res_pair figure. Abundance (excess3) ≠ aggregation share \(f_3\).
+
+## Install
+
+```bash
+pip install nested-recd
+```
+
+From source (development):
+
+```bash
+pip install -e ".[dev]"
+```
+
+## excess³ contract (methods)
+
+Canonical specification: Padilla-Villanueva (2026), *excess³: A Pre-Specified Continuous Proxy…*  
+DOI: [10.5281/zenodo.21385937](https://doi.org/10.5281/zenodo.21385937) · repo: [github.com/johelpadilla/excess3](https://github.com/johelpadilla/excess3)
+
+| Rule | Software |
+|------|----------|
+| `excess3 = 0.6·Syn + 0.4·Surp` | `ALPHA_SYN`, `ALPHA_SURP` (fixed a priori) |
+| Continuous primary | `out["excess3"]` / `compute_phi3_excess` |
+| Φ₃ secondary | binary ticks of excess3 vs `theta3` |
+| Null on full contrast | `surrogate_pvalue_delta_excess3` (phase-shuffle / permute on `\|Δ\|`) |
+| Proxy ≠ full PID | documented; no complete Williams–Beer atom claimed |
+| Parallel nesting | Φ₁, Φ₂, excess³ computed without hard Boolean ascent |
+
+Defaults: `m=3`, delay `1`, window `13`, `theta3=0.10` (software); cardio-like reference `DEFAULT_THETA3_CARDIO=0.08`.
+
+## Quick start
+
+```python
+import numpy as np
+from nested_recd import compute_recd_from_conjunctions, ALPHA_SYN, ALPHA_SURP
+
+rng = np.random.default_rng(0)
+X = rng.normal(size=(800, 3)).cumsum(axis=0)
+
+out = compute_recd_from_conjunctions(X, m=3, d=4, theta3=0.10)
+
+print("mean excess³ (primary):", float(np.nanmean(out["excess3"])))
+print("Φ3 active fraction:", float(np.nanmean(out["phi3"] > 0)))
+print("weights:", out["params"]["alpha_syn"], out["params"]["alpha_surp"])
+print("final T_recd:", float(out["T_recd"][-1]))
+```
+
+### Strong residual Res_pair (optional)
+
+```python
+out = compute_recd_from_conjunctions(X, compute_res=True)
+# or, on a symbol window:
+from nested_recd import compute_res_pair_window
+# Always report window length with Res_pair (Nota 4: w=13 can bias chaos).
+```
+
+### Continuous excess³ only
+
+```python
+from nested_recd import generate_multivariate_symbols, compute_phi3_excess
+
+S = generate_multivariate_symbols(X, m=3)
+phi3, excess3 = compute_phi3_excess(S, window=13, theta=0.10, stride=1)
+```
+
+### Surrogate p-value on |Δ excess3|
+
+```python
+from nested_recd import surrogate_pvalue_delta_excess3
+
+res = surrogate_pvalue_delta_excess3(X, split=400, n_surr=99, method="phase", seed=0)
+print(res["delta_obs"], res["p_value"])
+```
+
+### Optional τ_s for λ regime weights
+
+```python
+out = compute_recd_from_conjunctions(X, tau_s=tau_s)
+# or
+out = compute_recd_from_conjunctions(X, lam_override=0.5)
+```
+
+**Note:** `delta_recd` / `T_recd` use **binary Φ₃** in the α-weighted clock (legacy Discrete Extramental Clock). For **exportable / scalable** Level-3 reporting, use continuous **excess³** and nulls on `|Δ excess3|`. For **strong** Level-3 claims, report **`res_pair`** (enable `compute_res=True`) **and the window `w`**. Do not identify the two.
+
+## What it computes
+
+| Symbol | Meaning |
+|--------|---------|
+| **Φ₁** | Co-occurrence of identical ordinal symbols across variable pairs |
+| **Φ₂** | Persistence of pairwise ordinal relations over lag `d` |
+| **excess³** | Continuous hybrid: `0.6·Syn + 0.4·Surp` (**exportable Level-3 proxy**; T-IV) |
+| **Φ₃** | Binary ticks of excess³ above `theta3` (**secondary**) |
+| **Res_pair** | Strong Level-3 residual `KL(P ‖ P^(2))` (optional; always report `w`) |
+| **λ** | Chaos / reorganization intensity (from `τ_s` or `lam_override`) |
+| **α(λ)** | Design-engine weights (template or Gibbs-α); **not** a joint observable |
+| **ΔRECD** | `α₁Φ₁ + α₂Φ₂ + α₃Φ₃` (legacy clock; binary Φ₃) |
+| **T_recd** | Cumulative sum of ΔRECD |
+
+Ordinal symbols use Bandt–Pompe patterns (`m=3` by default).
+
+## Surrogates
+
+```python
+from nested_recd import phase_shuffle_independent, random_permutation_independent
+
+X_null = phase_shuffle_independent(X, seed=42)
+X_perm = random_permutation_independent(X, seed=42)
+```
+
+## API surface
+
+```python
+from nested_recd import (
+    ALPHA_SYN, ALPHA_SURP,
+    DEFAULT_THETA3, DEFAULT_THETA3_CARDIO,
+    compute_recd_from_conjunctions,
+    compute_phi1, compute_phi2, compute_phi3,
+    compute_phi3_excess, compute_excess3_window,
+    mean_excess_pre_post, surrogate_pvalue_delta_excess3,
+    compute_lambda, alpha_weights, alpha_weights_gibbs, regime_lambda_proxy,
+    compute_res_pair, compute_res_pair_window,
+    compute_weighted_contributions, high_level3_rate,
+    generate_multivariate_symbols,
+    phase_shuffle_independent, generate_surrogate_ensemble,
+)
+```
+
+## Relation to other projects
+
+| Project | Role |
+|---------|------|
+| [`systemictau`](https://pypi.org/project/systemictau/) | Full Systemic Tau library (τ_s, gate RECD, studio) — optional `[nested]` extra |
+| [`systemictau-web`](https://github.com/johelpadilla/systemictau-web) | Streamlit app; depends on this package |
+| [`excess3`](https://github.com/johelpadilla/excess3) | Methods + intro ES + primer (specification) |
+| [`cctp-sddb-systemic-tau`](https://github.com/johelpadilla/cctp-sddb-systemic-tau) | Cardiac VF pilot |
+| This package | Lightweight, installable nested-time / excess³ core |
+
+## Citation
+
+If you use excess³ / Level-3 from this package, cite the **methods** preprint (canonical specification):
+
+> Padilla-Villanueva, J. (2026). *excess³: A Pre-Specified Continuous Proxy for Order-3 Synergistic Surplus* (methods). Zenodo. https://doi.org/10.5281/zenodo.21385937
+
+This software (0.2.3):
+
+> Padilla-Villanueva, J. (2026). *nested-recd 0.2.3: Nested ordinal RECD, excess³ proxy, and Res_pair*. Zenodo. https://doi.org/10.5281/zenodo.22970079
+
+The previous release (0.2.2), which pooled symbols inside Syn, remains citable as https://doi.org/10.5281/zenodo.21937204.
+
+Software / related stack:
+
+> Padilla-Villanueva, J. (2026). Systemic Tau software archive. Zenodo. https://doi.org/10.5281/zenodo.20576241
+
+CCTP/SDDB pilot:
+
+> Padilla-Villanueva, J. (2026). *CCTP/SDDB: Systemic Tau and ordinal RECD before spontaneous ventricular fibrillation* (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.21270699
+
+```bibtex
+@software{padilla_nested_recd_2026,
+  author  = {Padilla-Villanueva, Johel},
+  title   = {nested-recd: Nested ordinal RECD levels and continuous excess³},
+  year    = {2026},
+  url     = {https://github.com/johelpadilla/nested-recd},
+  version = {0.2.3},
+  doi     = {10.5281/zenodo.22970079}
+}
+```
+
+## License
+
+MIT © 2026 Johel Padilla-Villanueva  
+ORCID: [0000-0002-5797-6931](https://orcid.org/0000-0002-5797-6931)

{nested_recd-0.1.0 → nested_recd-0.2.3}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nested-recd"
-version = "0.1.0"
-description = "Nested ordinal RECD: Φ1–Φ3 conjunction levels and λ-weighted Discrete Extramental Clock"
+version = "0.2.3"
+description = "Nested ordinal RECD: Φ1–Φ3, continuous excess³ (exportable Level-3 proxy), Res_pair (strong residual), and λ-weighted Discrete Extramental Clock"
 readme = "README.md"
 requires-python = ">=3.9"
 license = "MIT"
@@ -49,7 +49,7 @@ Homepage = "https://github.com/johelpadilla/nested-recd"
 Repository = "https://github.com/johelpadilla/nested-recd"
 Issues = "https://github.com/johelpadilla/nested-recd/issues"
 Documentation = "https://github.com/johelpadilla/nested-recd#readme"
-DOI = "https://doi.org/10.5281/zenodo.21270699"
+DOI = "https://doi.org/10.5281/zenodo.22970079"
 
 [tool.setuptools.packages.find]
 where = ["src"]

{nested_recd-0.1.0 → nested_recd-0.2.3}/src/nested_recd/__init__.py

@@ -2,8 +2,9 @@
 nested-recd
 ===========
 
-Nested ordinal RECD: Φ₁ / Φ₂ / Φ₃ conjunction levels and λ-weighted
-Discrete Extramental Clock accumulation.
+Nested ordinal RECD: Φ₁ / Φ₂ / Φ₃ conjunction levels, continuous excess³
+(exportable Level-3 proxy; not the strong residual), optional Res_pair,
+and λ-weighted Discrete Extramental Clock.
 
 Quick start
 -----------
@@ -11,7 +12,7 @@ Quick start
 >>> from nested_recd import compute_recd_from_conjunctions
 >>> X = np.random.randn(500, 3).cumsum(axis=0)
 >>> out = compute_recd_from_conjunctions(X)
->>> out["T_recd"][-1]
+>>> float(np.nanmean(out["excess3"]))  # continuous Level-3 *proxy* (T-IV)
 """
 
 from nested_recd.ordinal_levels import (
@@ -19,15 +20,29 @@ from nested_recd.ordinal_levels import (
     DEFAULT_DELAY,
     DEFAULT_D_PERSIST,
     DEFAULT_WINDOW_TAU,
+    DEFAULT_WINDOW,
     DEFAULT_THETA_CHAOS,
     DEFAULT_THETA3,
+    DEFAULT_THETA3_CARDIO,
     DELTA_FEIGENBAUM,
+    ALPHA_SYN,
+    ALPHA_SURP,
     generate_multivariate_symbols,
     compute_phi1,
     compute_phi2,
     compute_phi3,
+    compute_phi3_excess,
+    compute_excess3_window,
+    compute_res_pair_window,
+    compute_res_pair,
+    pairwise_maxent_ipf,
+    kl_divergence,
+    mean_excess_pre_post,
+    surrogate_pvalue_delta_excess3,
     compute_lambda,
     alpha_weights,
+    alpha_weights_gibbs,
+    alpha_compare_template_gibbs,
     regime_lambda_proxy,
     compute_recd_from_conjunctions,
     simple_level_classification,
@@ -43,7 +58,7 @@ from nested_recd.surrogates import (
     compute_null_distribution,
 )
 
-__version__ = "0.1.0"
+__version__ = "0.2.3"
 
 __all__ = [
     "__version__",
@@ -51,15 +66,29 @@ __all__ = [
     "DEFAULT_DELAY",
     "DEFAULT_D_PERSIST",
     "DEFAULT_WINDOW_TAU",
+    "DEFAULT_WINDOW",
     "DEFAULT_THETA_CHAOS",
     "DEFAULT_THETA3",
+    "DEFAULT_THETA3_CARDIO",
     "DELTA_FEIGENBAUM",
+    "ALPHA_SYN",
+    "ALPHA_SURP",
     "generate_multivariate_symbols",
     "compute_phi1",
     "compute_phi2",
     "compute_phi3",
+    "compute_phi3_excess",
+    "compute_excess3_window",
+    "compute_res_pair_window",
+    "compute_res_pair",
+    "pairwise_maxent_ipf",
+    "kl_divergence",
+    "mean_excess_pre_post",
+    "surrogate_pvalue_delta_excess3",
     "compute_lambda",
     "alpha_weights",
+    "alpha_weights_gibbs",
+    "alpha_compare_template_gibbs",
     "regime_lambda_proxy",
     "compute_recd_from_conjunctions",
     "simple_level_classification",