pystaar 1.0.0__tar.gz

pystaar-1.0.0/LICENSE

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+Copyright (c) 2026 pySTAAR contributors.
+All rights reserved.
+
+This software is proprietary and confidential. No permission is granted to use,
+copy, modify, merge, publish, distribute, sublicense, or sell this software
+without prior written authorization from the copyright holder.

pystaar-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pystaar
+Version: 1.0.0
+Summary: Python migration of the STAAR R package
+Author: STAAR migration
+License-Expression: LicenseRef-Proprietary
+Project-URL: Homepage, https://github.com/xiaozhouwang/pySTAAR
+Project-URL: Repository, https://github.com/xiaozhouwang/pySTAAR
+Project-URL: Documentation, https://github.com/xiaozhouwang/pySTAAR/tree/main/docs
+Project-URL: Issues, https://github.com/xiaozhouwang/pySTAAR/issues
+Keywords: staar,genomics,genetics,rare-variant,association-testing
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+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 :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyyaml>=6.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# pySTAAR
+
+Python 版 STAAR（R 包）迁移项目，面向中文统计遗传/基因组分析用户。
+
+For English docs, see [`docs/README.md`](docs/README.md).
+
+## 项目定位
+
+- 已完成计划内功能迁移（到 `STAAR-56`）。
+- 默认 workflow 入口覆盖：STAAR、条件分析、Binary SPA、单变异得分检验、AI-STAAR。
+- 当前 parity 基线为 pure-Python 路径（related workflows 不依赖预计算 R 协方差文件）。
+
+## 快速安装
+
+普通用户（发布版）：
+
+```bash
+pip install pystaar
+```
+
+本仓库开发模式：
+
+```bash
+pip install -e '.[dev]'
+```
+
+## 快速运行
+
+```python
+from pystaar import staar_unrelated_glm
+
+res = staar_unrelated_glm(
+    dataset="example",
+    seed=600,
+    rare_maf_cutoff=0.05,
+)
+print("STAAR-O:", res["results_STAAR_O"])
+```
+
+## R 用户迁移入口
+
+- 完整迁移说明：[`docs/migration_from_r.md`](docs/migration_from_r.md)
+- 15 分钟迁移清单：[`docs/migration_r_quickstart_cn.md`](docs/migration_r_quickstart_cn.md)
+- 数据目录模板：[`docs/data_directory_template_cn.md`](docs/data_directory_template_cn.md)
+
+## 文档导航
+
+- 中文快速入门：[`docs/README_CN.md`](docs/README_CN.md)
+- 英文快速入门：[`docs/README.md`](docs/README.md)
+- 安装与环境：[`docs/installation.md`](docs/installation.md)
+- 性能对比总览（Python vs R）：[`docs/performance_comparison.md`](docs/performance_comparison.md)
+- 性能口径说明：官方跨平台结论以 OpenBLAS backend 为准；macOS Accelerate 本地参考见 `examples/1kg_parity/README.md`。
+- 本地 1KG 对比示例（数据级 + 模拟完整 workflow）：[`examples/1kg_parity/README.md`](examples/1kg_parity/README.md)
+- 教程：
+  - [`docs/tutorials/01_basic_staar.md`](docs/tutorials/01_basic_staar.md)
+  - [`docs/tutorials/02_binary_spa.md`](docs/tutorials/02_binary_spa.md)
+  - [`docs/tutorials/03_related_samples.md`](docs/tutorials/03_related_samples.md)
+  - [`docs/tutorials/04_conditional.md`](docs/tutorials/04_conditional.md)
+  - [`docs/tutorials/05_ai_staar.md`](docs/tutorials/05_ai_staar.md)
+- API 文档：
+  - [`docs/api/null_models.md`](docs/api/null_models.md)
+  - [`docs/api/staar_functions.md`](docs/api/staar_functions.md)
+  - [`docs/api/output_fields.md`](docs/api/output_fields.md)
+  - [`docs/api/utilities.md`](docs/api/utilities.md)
+  - [`docs/api/stability.md`](docs/api/stability.md)
+- 变更记录：[`CHANGELOG.md`](CHANGELOG.md)
+
+## 一致性说明
+
+- 历史偏差记录 `DEV-001` 已关闭，仅保留历史背景。
+- 当前状态与 release 口径以 [`reports/summary.md`](reports/summary.md) 和 [`reports/deviations.md`](reports/deviations.md) 为准。

pystaar-1.0.0/README.md

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+# pySTAAR
+
+Python 版 STAAR（R 包）迁移项目，面向中文统计遗传/基因组分析用户。
+
+For English docs, see [`docs/README.md`](docs/README.md).
+
+## 项目定位
+
+- 已完成计划内功能迁移（到 `STAAR-56`）。
+- 默认 workflow 入口覆盖：STAAR、条件分析、Binary SPA、单变异得分检验、AI-STAAR。
+- 当前 parity 基线为 pure-Python 路径（related workflows 不依赖预计算 R 协方差文件）。
+
+## 快速安装
+
+普通用户（发布版）：
+
+```bash
+pip install pystaar
+```
+
+本仓库开发模式：
+
+```bash
+pip install -e '.[dev]'
+```
+
+## 快速运行
+
+```python
+from pystaar import staar_unrelated_glm
+
+res = staar_unrelated_glm(
+    dataset="example",
+    seed=600,
+    rare_maf_cutoff=0.05,
+)
+print("STAAR-O:", res["results_STAAR_O"])
+```
+
+## R 用户迁移入口
+
+- 完整迁移说明：[`docs/migration_from_r.md`](docs/migration_from_r.md)
+- 15 分钟迁移清单：[`docs/migration_r_quickstart_cn.md`](docs/migration_r_quickstart_cn.md)
+- 数据目录模板：[`docs/data_directory_template_cn.md`](docs/data_directory_template_cn.md)
+
+## 文档导航
+
+- 中文快速入门：[`docs/README_CN.md`](docs/README_CN.md)
+- 英文快速入门：[`docs/README.md`](docs/README.md)
+- 安装与环境：[`docs/installation.md`](docs/installation.md)
+- 性能对比总览（Python vs R）：[`docs/performance_comparison.md`](docs/performance_comparison.md)
+- 性能口径说明：官方跨平台结论以 OpenBLAS backend 为准；macOS Accelerate 本地参考见 `examples/1kg_parity/README.md`。
+- 本地 1KG 对比示例（数据级 + 模拟完整 workflow）：[`examples/1kg_parity/README.md`](examples/1kg_parity/README.md)
+- 教程：
+  - [`docs/tutorials/01_basic_staar.md`](docs/tutorials/01_basic_staar.md)
+  - [`docs/tutorials/02_binary_spa.md`](docs/tutorials/02_binary_spa.md)
+  - [`docs/tutorials/03_related_samples.md`](docs/tutorials/03_related_samples.md)
+  - [`docs/tutorials/04_conditional.md`](docs/tutorials/04_conditional.md)
+  - [`docs/tutorials/05_ai_staar.md`](docs/tutorials/05_ai_staar.md)
+- API 文档：
+  - [`docs/api/null_models.md`](docs/api/null_models.md)
+  - [`docs/api/staar_functions.md`](docs/api/staar_functions.md)
+  - [`docs/api/output_fields.md`](docs/api/output_fields.md)
+  - [`docs/api/utilities.md`](docs/api/utilities.md)
+  - [`docs/api/stability.md`](docs/api/stability.md)
+- 变更记录：[`CHANGELOG.md`](CHANGELOG.md)
+
+## 一致性说明
+
+- 历史偏差记录 `DEV-001` 已关闭，仅保留历史背景。
+- 当前状态与 release 口径以 [`reports/summary.md`](reports/summary.md) 和 [`reports/deviations.md`](reports/deviations.md) 为准。

pystaar-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pystaar"
+version = "1.0.0"
+description = "Python migration of the STAAR R package"
+readme = "README.md"
+requires-python = ">=3.9"
+license = "LicenseRef-Proprietary"
+license-files = ["LICENSE"]
+authors = [
+  { name = "STAAR migration" }
+]
+keywords = [
+  "staar",
+  "genomics",
+  "genetics",
+  "rare-variant",
+  "association-testing",
+]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "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 :: Bio-Informatics",
+]
+dependencies = [
+  "numpy>=1.24",
+  "scipy>=1.10",
+  "pandas>=2.0",
+  "pyyaml>=6.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/xiaozhouwang/pySTAAR"
+Repository = "https://github.com/xiaozhouwang/pySTAAR"
+Documentation = "https://github.com/xiaozhouwang/pySTAAR/tree/main/docs"
+Issues = "https://github.com/xiaozhouwang/pySTAAR/issues"
+
+[project.optional-dependencies]
+dev = [
+  "pytest>=7.0",
+]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+pystaar = ["_data/*"]

pystaar-1.0.0/setup.cfg

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

pystaar-1.0.0/src/pystaar/__init__.py

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+"""Python migration of the STAAR R package.
+
+Public API includes:
+- R-compatible names (e.g., ``STAAR`` / ``AI_STAAR`` / ``CCT``).
+- Python workflow entry points used by parity scenarios.
+"""
+
+from .models import (
+    fit_null_glm,
+    fit_null_glm_binary_spa,
+    fit_null_glmmkin,
+    fit_null_glmmkin_binary_spa,
+)
+from .staar_core import (
+    _get_eigensolver_runtime_info,
+    ai_staar,
+    indiv_score_test_region,
+    indiv_score_test_region_cond,
+    matrix_flip,
+    staar,
+    staar_binary_spa,
+    staar_cond,
+)
+from .staar_stats import cct
+from .workflows import (
+    ai_staar_related_dense_glmmkin,
+    ai_staar_related_dense_glmmkin_find_weight,
+    ai_staar_related_sparse_glmmkin,
+    ai_staar_related_sparse_glmmkin_find_weight,
+    ai_staar_unrelated_glm,
+    ai_staar_unrelated_glm_find_weight,
+    clear_runtime_caches,
+    get_runtime_cache_info,
+    indiv_score_related_dense_glmmkin,
+    indiv_score_related_dense_glmmkin_cond,
+    indiv_score_related_sparse_glmmkin,
+    indiv_score_related_sparse_glmmkin_cond,
+    indiv_score_unrelated_glm,
+    indiv_score_unrelated_glm_cond,
+    staar_related_dense_binary_spa,
+    staar_related_dense_glmmkin,
+    staar_related_dense_glmmkin_cond,
+    staar_related_sparse_binary_spa,
+    staar_related_sparse_glmmkin,
+    staar_related_sparse_glmmkin_cond,
+    staar_unrelated_binary_spa,
+    staar_unrelated_glm,
+    staar_unrelated_glm_cond,
+)
+
+# R-compatible aliases from STAAR NAMESPACE exports.
+CCT = cct
+fit_null_glm_Binary_SPA = fit_null_glm_binary_spa
+fit_null_glmmkin_Binary_SPA = fit_null_glmmkin_binary_spa
+STAAR = staar
+STAAR_cond = staar_cond
+Indiv_Score_Test_Region = indiv_score_test_region
+Indiv_Score_Test_Region_cond = indiv_score_test_region_cond
+STAAR_Binary_SPA = staar_binary_spa
+AI_STAAR = ai_staar
+
+__all__ = [
+    "CCT",
+    "fit_null_glm",
+    "fit_null_glmmkin",
+    "fit_null_glm_Binary_SPA",
+    "fit_null_glmmkin_Binary_SPA",
+    "matrix_flip",
+    "STAAR",
+    "STAAR_cond",
+    "STAAR_Binary_SPA",
+    "Indiv_Score_Test_Region",
+    "Indiv_Score_Test_Region_cond",
+    "AI_STAAR",
+    "staar_unrelated_glm",
+    "staar_related_sparse_glmmkin",
+    "staar_related_dense_glmmkin",
+    "staar_unrelated_glm_cond",
+    "staar_related_sparse_glmmkin_cond",
+    "staar_related_dense_glmmkin_cond",
+    "staar_unrelated_binary_spa",
+    "staar_related_sparse_binary_spa",
+    "staar_related_dense_binary_spa",
+    "indiv_score_unrelated_glm",
+    "indiv_score_related_sparse_glmmkin",
+    "indiv_score_related_dense_glmmkin",
+    "indiv_score_unrelated_glm_cond",
+    "indiv_score_related_sparse_glmmkin_cond",
+    "indiv_score_related_dense_glmmkin_cond",
+    "ai_staar_unrelated_glm",
+    "ai_staar_related_sparse_glmmkin",
+    "ai_staar_related_dense_glmmkin",
+    "ai_staar_unrelated_glm_find_weight",
+    "ai_staar_related_sparse_glmmkin_find_weight",
+    "ai_staar_related_dense_glmmkin_find_weight",
+    "get_runtime_cache_info",
+    "clear_runtime_caches",
+    "get_eigensolver_runtime_info",
+]
+
+
+def get_eigensolver_runtime_info():
+    """Return backend-aware eigensolver runtime selection metadata."""
+    return _get_eigensolver_runtime_info()

pystaar-1.0.0/src/pystaar/_data/DATA_SOURCE.md

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+# Data Source and Fingerprints
+
+- Document date: 2026-02-07
+- Scope: files under `data/` used by Python parity workflows.
+
+## Source
+
+- Upstream project: `https://github.com/xihaoli/STAAR`
+- Upstream commit for baseline extraction: `9db9dd504905b9f469146f670e5f6dbe3e08d01a`
+- Baseline source record: `baselines/SOURCE.md`
+- Raw input used to generate `data/`: `baselines/example_sim_data.rds`
+- Dataset type: simulated example dataset generated by baseline extraction scripts
+- License context:
+  - Upstream package license: `GPL-3` (`../STAAR/DESCRIPTION`)
+  - License text available at `../STAAR/LICENSE.md`
+
+## Raw Input Checksum
+
+| file | size_bytes | sha256 |
+|---|---:|---|
+| `baselines/example_sim_data.rds` | 1312814 | `89498efaa1140720d512e92b4fb80d5141dfbec174dca54df29d553ef7b92fe6` |
+| `baselines/nonexample601_sim_data.rds` | 1307967 | `3104c42d8fff5cd75f824bb10e282366b593c6f22ad924885263bdee63513241` |
+| `baselines/nonexample602_sim_data.rds` | 1304535 | `97f2757233fd25d4fcdb3171cdcb8f341aa330f65078ad4753137bf1de2d77fb` |
+
+## Exported Runtime Files
+
+| file | size_bytes | sha256 |
+|---|---:|---|
+| `data/example_geno.mtx` | 76674 | `c7fe50fdb539ff71601b4542c78d5d829d67ec5f9932f1dde5830b6ad3692569` |
+| `data/example_kins_sparse.mtx` | 300091 | `e6dbc9c0597345876e29317b22404d69f4b64915ecce9a02299439c399cd56c2` |
+| `data/example_kins_dense.mtx` | 300091 | `e6dbc9c0597345876e29317b22404d69f4b64915ecce9a02299439c399cd56c2` |
+| `data/example_phred.csv` | 27924 | `272e43cfe806a2a980de6293fb353ee4cbb5d66722d8ef765b59c4eecad6d0bb` |
+| `data/example_pheno_unrelated.csv` | 381409 | `e0f4caf7398060761040d4f709b546e6531a6808b713ea5681e8921b5becd8f3` |
+| `data/example_pheno_related.csv` | 429554 | `3f0a8ba32fe7bcf1c8eafc6666b64b3bbbf0b9a145f58b5a065442ff2f3c6396` |
+| `data/nonexample601_geno.mtx` | 77624 | `2b9de0a4d95f22a9b7d7912e3189ccfbc170efd80566aac34b53f09a6182ec5d` |
+| `data/nonexample601_kins_sparse.mtx` | 300091 | `5783413a57c288fac6964946e1c4bd5d9453ca3c87a24847fd4619da5e037243` |
+| `data/nonexample601_kins_dense.mtx` | 300091 | `5783413a57c288fac6964946e1c4bd5d9453ca3c87a24847fd4619da5e037243` |
+| `data/nonexample601_phred.csv` | 24686 | `576e4f60f5d42653c18eb157e2c3847710f97538cf81e5fa44320adbabb16741` |
+| `data/nonexample601_pheno_unrelated.csv` | 381071 | `c0fb8111ed7128fddc2b13e2ed6986d4566a4732e43960a82f925942d72f0358` |
+| `data/nonexample601_pheno_related.csv` | 429309 | `26a2cc47bfb5f902a37495bad541be760a81cf8972ed306f4c82f8c67b6665c4` |
+| `data/nonexample602_geno.mtx` | 62711 | `1ca6579addfa90c0cca6cbd77b4d272f2bf1b9ed36a4c881111e191783f3af15` |
+| `data/nonexample602_kins_sparse.mtx` | 300091 | `5783413a57c288fac6964946e1c4bd5d9453ca3c87a24847fd4619da5e037243` |
+| `data/nonexample602_kins_dense.mtx` | 300091 | `5783413a57c288fac6964946e1c4bd5d9453ca3c87a24847fd4619da5e037243` |
+| `data/nonexample602_phred.csv` | 25214 | `808a8ddd4780b409ed32cd62f5a1dafb6452db83494e96e3358d8953fc6675a1` |
+| `data/nonexample602_pheno_unrelated.csv` | 381102 | `4a6a588cabee87e60064354b9811cdf9181a0f5c47e27418edb49b284091c965` |
+| `data/nonexample602_pheno_related.csv` | 429283 | `8692f9b8051d11dbc4d6b7173fe890c395705c2e637fc22b0fb549ff0edad750` |
+| `data/example_glmmkin_cov.csv` | 555749 | `f6893ba9f034143c0b8eab7fda2fe020e8e43ac0280fbd1bd3824fa20c3311e6` |
+| `data/example_glmmkin_cov_rare_maf_0_01.csv` | 495166 | `c08479c923d9207da12c4e4d8faa64cf80390291223700b423eb15a1cf649ebc` |
+| `data/example_glmmkin_scaled_residuals.csv` | 182493 | `55ebe906e9c63fb25e8bbc4bf4f4ac05966401af8a66bbba972cd48a4a3c29ca` |
+| `data/example_glmmkin_cov_cond_sparse.csv` | 554222 | `a816f345142065cd3a95c3616f9c00e64f433e26ea57704b9dd1670b604130b2` |
+| `data/example_glmmkin_cov_cond_dense.csv` | 555130 | `05ad3b8d587404a850182310edac55fdc11e48c3092ddb954653145250c43a55` |
+| `data/example_glmmkin_binary_spa_sparse_fitted.csv` | 188525 | `8c827840b987e39d853de2ef505f5d730c6085e52339d8d2f549a136e12ffa93` |
+| `data/example_glmmkin_binary_spa_sparse_scaled_residuals.csv` | 197780 | `5613078915493f8152ba5b10e0bd1b66aaa218166d912122500d867e008144cd` |
+| `data/example_glmmkin_binary_spa_sparse_XW.csv` | 643616 | `d89f82fa11888f012abf4806651a2f4df1f0f2fccc5cb397e3879e39945c3ea6` |
+| `data/example_glmmkin_binary_spa_sparse_XXWX_inv.csv` | 614222 | `cdf1b7cf565f5ce68f00f8b77bfc37d8151a5689dc233eee1957d09656e95ae1` |
+| `data/example_glmmkin_binary_spa_dense_fitted.csv` | 188469 | `82e3baef157b2d90d14aa042f117e4d2871a9041079a0eb6390951f160f5429f` |
+| `data/example_glmmkin_binary_spa_dense_scaled_residuals.csv` | 197716 | `084a4bbfa11a8827af81d2625d6e8eedfbee53654a843543679992bb662b56c5` |
+| `data/example_glmmkin_binary_spa_dense_XW.csv` | 557284 | `846283deb00c944da332684ccddf38c36598fe21cddce5929cce908cfd2a2f3d` |
+| `data/example_glmmkin_binary_spa_dense_XXWX_inv.csv` | 614480 | `3bb01dabd6258d4c56e75b275f4ca95faa4503e89d2c258e6e68a460c5e5a36e` |
+| `data/example_glm_binary_spa_cov_filter.csv` | 571828 | `5ec312432b33f86ce4774053d70e40dea641a012699298c9411b4fe541909711` |
+| `data/example_glmmkin_binary_spa_sparse_cov_filter.csv` | 571750 | `30d089be8804cedb8789e51bf4572ccbfcaf36dd4734d1bbc50ad71b9232271a` |
+| `data/example_glmmkin_binary_spa_dense_cov_filter.csv` | 571635 | `2349ab58cab8516b45612d09fc46554e29f33d46f6550ba798051b136f4164d1` |
+| `data/example_ai_pop_groups.csv` | 60012 | `8563a26d5075f4664322997f703b40e6314666744fd3051ea94a3354d17de17c` |
+| `data/example_ai_pop_weights_1_1.csv` | 148 | `e710f254e379c81ec26bcb543d4c88048ae12df46855cfcac8ebbe4192dca2a0` |
+| `data/example_ai_pop_weights_1_25.csv` | 148 | `454abfff9449d29ecd6ee26a9b18c66fa1da8c698c5e94ca6481497e1b92ec51` |
+| `data/example_ai_cov_sparse_s1_b1.csv` | 567327 | `518a448dbf542b663161482a2bcfc1d583651ef59d53ac4088cce7b4357529e8` |
+| `data/example_ai_cov_sparse_s1_b2.csv` | 567952 | `193b1d6d8e3947c30128878d1a7f624bd30e793fc18d2bb581bcc851f5c477dd` |
+| `data/example_ai_cov_sparse_s2_b1.csv` | 515145 | `1a1b0f072cbfc51d172b50b0ecf402d67ac8f9663b27e872b6eed83a24a23c62` |
+| `data/example_ai_cov_sparse_s2_b2.csv` | 517885 | `0a76a6891c6e911bfa4be1ce1d6165d5f306f5ff35fbd1d4b2ec14dddafe9895` |
+| `data/example_ai_cov_dense_s1_b1.csv` | 567248 | `9db30d895f8cf289eb32b8ffe7fea715fb1fea7cb8574c139add0b3c29b7e470` |
+| `data/example_ai_cov_dense_s1_b2.csv` | 568040 | `2801f7b4be47f16875ba5eb5175ab84f01dc728c99b0fc9d56bfd5fa5d2242fd` |
+| `data/example_ai_cov_dense_s2_b1.csv` | 515109 | `5efca5a228e054ec6c887301c545e5e832098ab3c3e42cac75e156f52c3cc9ae` |
+| `data/example_ai_cov_dense_s2_b2.csv` | 517701 | `d9ccdd07c0d7a7278f45bffa96f4d15f879a676da44d806247b6d33e708504df` |
+
+## Structured Fingerprints
+
+- `data/example_pheno_unrelated.csv`: rows=10000, cols=3, columns=`Y,X1,X2`
+- `data/example_pheno_related.csv`: rows=10000, cols=4, columns=`Y,X1,X2,id`
+- `data/example_phred.csv`: rows=163, cols=10, columns=`Z1,Z2,Z3,Z4,Z5,Z6,Z7,Z8,Z9,Z10`
+- `data/example_geno.mtx`: shape=`10000x163`, nnz=7486
+- `data/example_kins_sparse.mtx`: shape=`10000x10000`, nnz=35000
+- `data/example_kins_dense.mtx`: shape=`10000x10000`, nnz=35000
+- `data/nonexample601_pheno_unrelated.csv`: rows=10000, cols=3, columns=`Y,X1,X2`
+- `data/nonexample601_pheno_related.csv`: rows=10000, cols=4, columns=`Y,X1,X2,id`
+- `data/nonexample601_phred.csv`: rows=144, cols=10, columns=`Z1,Z2,Z3,Z4,Z5,Z6,Z7,Z8,Z9,Z10`
+- `data/nonexample601_geno.mtx`: shape=`10000x144`, nnz=7636
+- `data/nonexample601_kins_sparse.mtx`: shape=`10000x10000`, nnz=35000
+- `data/nonexample601_kins_dense.mtx`: shape=`10000x10000`, nnz=35000
+- `data/nonexample602_pheno_unrelated.csv`: rows=10000, cols=3, columns=`Y,X1,X2`
+- `data/nonexample602_pheno_related.csv`: rows=10000, cols=4, columns=`Y,X1,X2,id`
+- `data/nonexample602_phred.csv`: rows=147, cols=10, columns=`Z1,Z2,Z3,Z4,Z5,Z6,Z7,Z8,Z9,Z10`
+- `data/nonexample602_geno.mtx`: shape=`10000x147`, nnz=6174
+- `data/nonexample602_kins_sparse.mtx`: shape=`10000x10000`, nnz=35000
+- `data/nonexample602_kins_dense.mtx`: shape=`10000x10000`, nnz=35000
+- `data/example_glmmkin_cov.csv`: shape=`163x163`
+- `data/example_glmmkin_cov_rare_maf_0_01.csv`: shape=`153x153`
+- `data/example_glmmkin_cov_cond_sparse.csv`: shape=`163x163`
+- `data/example_glmmkin_cov_cond_dense.csv`: shape=`163x163`
+- `data/example_glmmkin_binary_spa_sparse_fitted.csv`: shape=`10000x1`
+- `data/example_glmmkin_binary_spa_sparse_scaled_residuals.csv`: shape=`10000x1`
+- `data/example_glmmkin_binary_spa_sparse_XW.csv`: shape=`3x10000`
+- `data/example_glmmkin_binary_spa_sparse_XXWX_inv.csv`: shape=`10000x3`
+- `data/example_glmmkin_binary_spa_dense_fitted.csv`: shape=`10000x1`
+- `data/example_glmmkin_binary_spa_dense_scaled_residuals.csv`: shape=`10000x1`
+- `data/example_glmmkin_binary_spa_dense_XW.csv`: shape=`3x10000`
+- `data/example_glmmkin_binary_spa_dense_XXWX_inv.csv`: shape=`10000x3`
+- `data/example_glm_binary_spa_cov_filter.csv`: shape=`163x163`
+- `data/example_glmmkin_binary_spa_sparse_cov_filter.csv`: shape=`163x163`
+- `data/example_glmmkin_binary_spa_dense_cov_filter.csv`: shape=`163x163`
+- `data/example_ai_pop_groups.csv`: rows=10000, cols=1, columns=`pop_group`
+- `data/example_ai_pop_weights_1_1.csv`: rows=3, cols=3, columns=`population,B1,B2`
+- `data/example_ai_pop_weights_1_25.csv`: rows=3, cols=3, columns=`population,B1,B2`
+- `data/example_ai_cov_sparse_s1_b1.csv`: shape=`163x163`
+- `data/example_ai_cov_sparse_s1_b2.csv`: shape=`163x163`
+- `data/example_ai_cov_sparse_s2_b1.csv`: shape=`163x163`
+- `data/example_ai_cov_sparse_s2_b2.csv`: shape=`163x163`
+- `data/example_ai_cov_dense_s1_b1.csv`: shape=`163x163`
+- `data/example_ai_cov_dense_s1_b2.csv`: shape=`163x163`
+- `data/example_ai_cov_dense_s2_b1.csv`: shape=`163x163`
+- `data/example_ai_cov_dense_s2_b2.csv`: shape=`163x163`
+
+## Generation Path
+
+`data/` exports are generated by:
+
+- `scripts/export_example_data.R`
+- `baselines/scripts/extract_related_sparse_glmmkin_cond.R` (conditional covariance export)
+- `baselines/scripts/extract_related_dense_glmmkin_cond.R` (conditional covariance export)
+- `baselines/scripts/extract_related_sparse_binary_spa.R` (related binary SPA null-model components)
+- `baselines/scripts/extract_related_dense_binary_spa.R` (related binary SPA null-model components)
+- `baselines/scripts/extract_unrelated_binary_spa_filter.R` (unrelated binary SPA prefilter covariance export)
+- `baselines/scripts/extract_related_sparse_binary_spa_filter.R` (related sparse binary SPA prefilter covariance export)
+- `baselines/scripts/extract_related_dense_binary_spa_filter.R` (related dense binary SPA prefilter covariance export)
+- `baselines/scripts/extract_ai_staar_unrelated.R` (AI-STAAR ancestry metadata export)
+- `baselines/scripts/extract_ai_staar_related_sparse.R` (AI-STAAR sparse related covariance export)
+- `baselines/scripts/extract_ai_staar_related_dense.R` (AI-STAAR dense related covariance export)
+- `../STAAR` one-shot extraction script (`/tmp/extract_nonexample601.R`) for non-clone `nonexample601` dataset + sentinels (`STAAR-47`)
+- `../STAAR` one-shot extraction script (`/tmp/extract_nonexample602.R`) for second-seed `nonexample602` dataset (`STAAR-54`)
+
+Command:
+
+- `Rscript scripts/export_example_data.R`
+- `Rscript /tmp/extract_nonexample601.R` (executed in `../STAAR`, then copied `nonexample601_*` outputs)
+- `Rscript /tmp/extract_nonexample602.R` (executed in `../STAAR`, then copied `nonexample602_*` outputs)