nested-recd 0.1.0__tar.gz

nested_recd-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Johel Padilla-Villanueva
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nested_recd-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nested-recd
+Version: 0.1.0
+Summary: Nested ordinal RECD: Φ1–Φ3 conjunction levels 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.21270699
+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
+
+[![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) and λ-weighted Discrete Extramental Clock (RECD) accumulation.
+
+This is the standalone library behind the nested-time structure used in the CCTP/SDDB cardiac pilot and the experimental design in *Conversación de la naturaleza del tiempo*.
+
+## Install
+
+```bash
+pip install nested-recd
+```
+
+From source:
+
+```bash
+pip install git+https://github.com/johelpadilla/nested-recd.git
+```
+
+## Quick start
+
+```python
+import numpy as np
+from nested_recd import compute_recd_from_conjunctions, compute_weighted_contributions
+
+# Multivariate series: shape (T, N)
+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 Φ1:", float(np.nanmean(out["phi1"])))
+print("mean Φ2:", float(np.nanmean(out["phi2"])))
+print("Φ3 active fraction:", float(np.nanmean(out["phi3"] > 0)))
+print("final T_recd:", float(out["T_recd"][-1]))
+
+w = compute_weighted_contributions(out)
+print("frac level-3 contribution:", w["frac_contrib3"])
+```
+
+Optional: supply a Systemic Tau series `tau_s` (aligned in time) so that λ is derived empirically:
+
+```python
+out = compute_recd_from_conjunctions(X, tau_s=tau_s)
+```
+
+Or fix the regime weight with a scalar / array override:
+
+```python
+out = compute_recd_from_conjunctions(X, lam_override=0.5)
+```
+
+## What it computes
+
+| Symbol | Meaning |
+|--------|---------|
+| **Φ₁** | Co-occurrence of identical ordinal symbols across variable pairs |
+| **Φ₂** | Persistence of pairwise ordinal relations over lag `d` |
+| **Φ₃** | Higher-order synergy proxy (total-correlation excess + joint surprise) |
+| **λ** | Chaos / reorganization intensity (from `τ_s` or `lam_override`) |
+| **α(λ)** | Level weights: α₁ decays with λ; α₂, α₃ grow with λ |
+| **ΔRECD** | `α₁Φ₁ + α₂Φ₂ + α₃Φ₃` |
+| **T_recd** | Cumulative sum of ΔRECD (nested-time clock) |
+
+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)   # IAAFT per column
+X_perm = random_permutation_independent(X, seed=42)
+```
+
+## API surface
+
+```python
+from nested_recd import (
+    compute_recd_from_conjunctions,
+    compute_phi1, compute_phi2, compute_phi3,
+    compute_lambda, alpha_weights, regime_lambda_proxy,
+    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, platform, studio) |
+| [`cctp-sddb-systemic-tau`](https://github.com/johelpadilla/cctp-sddb-systemic-tau) | Cardiac VF pilot using this nested RECD pipeline |
+| This package | Lightweight, installable nested-time / ordinal RECD core |
+
+## Citation
+
+If you use this software, please cite the CCTP/SDDB pilot archive:
+
+> 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
+
+And the theoretical nested-time / RECD framework as appropriate for your venue.
+
+```bibtex
+@software{padilla_nested_recd_2026,
+  author  = {Padilla-Villanueva, Johel},
+  title   = {nested-recd: Nested ordinal RECD levels},
+  year    = {2026},
+  url     = {https://github.com/johelpadilla/nested-recd},
+  version = {0.1.0}
+}
+```
+
+## License
+
+MIT © 2026 Johel Padilla-Villanueva  
+ORCID: [0000-0002-5797-6931](https://orcid.org/0000-0002-5797-6931)

nested_recd-0.1.0/README.md

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+# nested-recd
+
+[![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) and λ-weighted Discrete Extramental Clock (RECD) accumulation.
+
+This is the standalone library behind the nested-time structure used in the CCTP/SDDB cardiac pilot and the experimental design in *Conversación de la naturaleza del tiempo*.
+
+## Install
+
+```bash
+pip install nested-recd
+```
+
+From source:
+
+```bash
+pip install git+https://github.com/johelpadilla/nested-recd.git
+```
+
+## Quick start
+
+```python
+import numpy as np
+from nested_recd import compute_recd_from_conjunctions, compute_weighted_contributions
+
+# Multivariate series: shape (T, N)
+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 Φ1:", float(np.nanmean(out["phi1"])))
+print("mean Φ2:", float(np.nanmean(out["phi2"])))
+print("Φ3 active fraction:", float(np.nanmean(out["phi3"] > 0)))
+print("final T_recd:", float(out["T_recd"][-1]))
+
+w = compute_weighted_contributions(out)
+print("frac level-3 contribution:", w["frac_contrib3"])
+```
+
+Optional: supply a Systemic Tau series `tau_s` (aligned in time) so that λ is derived empirically:
+
+```python
+out = compute_recd_from_conjunctions(X, tau_s=tau_s)
+```
+
+Or fix the regime weight with a scalar / array override:
+
+```python
+out = compute_recd_from_conjunctions(X, lam_override=0.5)
+```
+
+## What it computes
+
+| Symbol | Meaning |
+|--------|---------|
+| **Φ₁** | Co-occurrence of identical ordinal symbols across variable pairs |
+| **Φ₂** | Persistence of pairwise ordinal relations over lag `d` |
+| **Φ₃** | Higher-order synergy proxy (total-correlation excess + joint surprise) |
+| **λ** | Chaos / reorganization intensity (from `τ_s` or `lam_override`) |
+| **α(λ)** | Level weights: α₁ decays with λ; α₂, α₃ grow with λ |
+| **ΔRECD** | `α₁Φ₁ + α₂Φ₂ + α₃Φ₃` |
+| **T_recd** | Cumulative sum of ΔRECD (nested-time clock) |
+
+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)   # IAAFT per column
+X_perm = random_permutation_independent(X, seed=42)
+```
+
+## API surface
+
+```python
+from nested_recd import (
+    compute_recd_from_conjunctions,
+    compute_phi1, compute_phi2, compute_phi3,
+    compute_lambda, alpha_weights, regime_lambda_proxy,
+    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, platform, studio) |
+| [`cctp-sddb-systemic-tau`](https://github.com/johelpadilla/cctp-sddb-systemic-tau) | Cardiac VF pilot using this nested RECD pipeline |
+| This package | Lightweight, installable nested-time / ordinal RECD core |
+
+## Citation
+
+If you use this software, please cite the CCTP/SDDB pilot archive:
+
+> 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
+
+And the theoretical nested-time / RECD framework as appropriate for your venue.
+
+```bibtex
+@software{padilla_nested_recd_2026,
+  author  = {Padilla-Villanueva, Johel},
+  title   = {nested-recd: Nested ordinal RECD levels},
+  year    = {2026},
+  url     = {https://github.com/johelpadilla/nested-recd},
+  version = {0.1.0}
+}
+```
+
+## License
+
+MIT © 2026 Johel Padilla-Villanueva  
+ORCID: [0000-0002-5797-6931](https://orcid.org/0000-0002-5797-6931)

nested_recd-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+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"
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Johel Padilla-Villanueva", email = "joel.padilla2@upr.edu" },
+]
+keywords = [
+    "RECD",
+    "ordinal patterns",
+    "nested time",
+    "Systemic Tau",
+    "complexity",
+    "early-warning",
+    "network physiology",
+    "Bandt-Pompe",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "numpy>=1.22",
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=7.0", "pytest-cov>=4.0", "build", "twine"]
+
+[project.urls]
+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"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+nested_recd = ["py.typed"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["src"]

nested_recd-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

nested_recd-0.1.0/src/nested_recd/__init__.py

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+"""
+nested-recd
+===========
+
+Nested ordinal RECD: Φ₁ / Φ₂ / Φ₃ conjunction levels and λ-weighted
+Discrete Extramental Clock accumulation.
+
+Quick start
+-----------
+>>> import numpy as np
+>>> 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]
+"""
+
+from nested_recd.ordinal_levels import (
+    DEFAULT_M,
+    DEFAULT_DELAY,
+    DEFAULT_D_PERSIST,
+    DEFAULT_WINDOW_TAU,
+    DEFAULT_THETA_CHAOS,
+    DEFAULT_THETA3,
+    DELTA_FEIGENBAUM,
+    generate_multivariate_symbols,
+    compute_phi1,
+    compute_phi2,
+    compute_phi3,
+    compute_lambda,
+    alpha_weights,
+    regime_lambda_proxy,
+    compute_recd_from_conjunctions,
+    simple_level_classification,
+    compute_weighted_contributions,
+    high_level3_rate,
+    run_logical_demonstrations,
+)
+from nested_recd.surrogates import (
+    iaaft_surrogate_1d,
+    phase_shuffle_independent,
+    random_permutation_independent,
+    generate_surrogate_ensemble,
+    compute_null_distribution,
+)
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "__version__",
+    "DEFAULT_M",
+    "DEFAULT_DELAY",
+    "DEFAULT_D_PERSIST",
+    "DEFAULT_WINDOW_TAU",
+    "DEFAULT_THETA_CHAOS",
+    "DEFAULT_THETA3",
+    "DELTA_FEIGENBAUM",
+    "generate_multivariate_symbols",
+    "compute_phi1",
+    "compute_phi2",
+    "compute_phi3",
+    "compute_lambda",
+    "alpha_weights",
+    "regime_lambda_proxy",
+    "compute_recd_from_conjunctions",
+    "simple_level_classification",
+    "compute_weighted_contributions",
+    "high_level3_rate",
+    "run_logical_demonstrations",
+    "iaaft_surrogate_1d",
+    "phase_shuffle_independent",
+    "random_permutation_independent",
+    "generate_surrogate_ensemble",
+    "compute_null_distribution",
+]