From f0a453824270780c269ffec0f89c638a36875e35 Mon Sep 17 00:00:00 2001 From: Jinotech Date: Sun, 20 Sep 2026 08:35:13 +1200 Subject: [PATCH] feat(stage1): audit GSHS outcome components --- .learnings/ERRORS.md | 89 + Progression.md | 28 +- .../audit_gshs_primary_outcome_components.py | 399 + .../stage1/build_primary_outcome_registry.py | 109 +- .../gshs_primary_outcome_component_audit.json | 9119 +++++++++++++++++ .../gshs_primary_outcome_component_audit.md | 43 + research/stage1/primary_outcome_registry.json | 210 +- research/stage1/primary_outcome_registry.md | 8 +- 8 files changed, 9856 insertions(+), 149 deletions(-) create mode 100644 research/stage1/audit_gshs_primary_outcome_components.py create mode 100644 research/stage1/gshs_primary_outcome_component_audit.json create mode 100644 research/stage1/gshs_primary_outcome_component_audit.md diff --git a/.learnings/ERRORS.md b/.learnings/ERRORS.md index 0ecb023..82bb2f9 100644 --- a/.learnings/ERRORS.md +++ b/.learnings/ERRORS.md @@ -2,6 +2,95 @@ Command failures and integration errors. +--- +## [ERR-20260920-035] gshs-questionnaire-directory-assumption + +**Logged**: 2026-09-20 +**Priority**: low +**Status**: resolved +**Area**: docs + +### Summary +The first questionnaire inventory command assumed a non-existent `03_questionnaires_and_codebooks` directory. + +### Error +`rg` returned an OS error because that path does not exist. + +### Context +The dataset uses `GSHS/Questionnaire`, while `03_examples` is a separate directory. No files were changed. + +### Suggested Fix +Enumerate the GSHS root before applying a documentation-path convention. + +### Metadata +- Reproducible: yes +- Related Files: `Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire` +- Pattern-Key: docs.path-assumption + +### Resolution +- **Resolved**: 2026-09-20 +- **Notes**: Enumerating the root located the actual questionnaire directory and the audit continued there. + +--- +## [ERR-20260920-034] project-python-document-parser-missing + +**Logged**: 2026-09-20 +**Priority**: low +**Status**: resolved +**Area**: dependencies + +### Summary +The project research environment does not include `python-docx`, `pypdf`, or `pdfplumber`, so an exploratory source-extraction import failed. + +### Error +`ModuleNotFoundError: No module named 'docx'`. + +### Context +These packages are available in the Codex bundled document runtime. The final component audit uses only the project standard library and records verified source paths, pages/sections, and hashes, so it does not introduce an undeclared runtime dependency. + +### Suggested Fix +Use the bundled read-only document runtime for source inspection unless document parsing becomes a reproducible project pipeline dependency; only then add and lock the packages in the project environment. + +### Metadata +- Reproducible: yes +- Related Files: `research/stage1/gshs_primary_outcome_component_audit.json` +- Pattern-Key: dependency.optional-document-parser + +### Resolution +- **Resolved**: 2026-09-20 +- **Notes**: Source text was extracted with the bundled runtime and key PDF pages were rendered with Poppler for visual verification. + +--- +## [ERR-20260920-033] repeated-gshs-pandas-memory-exhaustion + +**Logged**: 2026-09-20 +**Priority**: medium +**Status**: resolved +**Area**: runtime + +### Summary +An exploratory pandas cross-tab scan again exhausted memory while parsing the 637-column GSHS CSV. + +### Error +`pandas.errors.ParserError: Error tokenizing data. C error: out of memory`. + +### Context +This is a recurrence of `ERR-20260920-029` during a new component-level relation check. The source file was not changed. + +### Suggested Fix +Use a streaming `csv.reader` scan with fixed column indices for all full-file GSHS audits. + +### Metadata +- Reproducible: yes +- Related Files: `research/stage1/audit_gshs_primary_outcome_components.py` +- Pattern-Key: runtime.memory-exhaustion +- Related Error: `ERR-20260920-029` +- Recurrence Count: 2 + +### Resolution +- **Resolved**: 2026-09-20 +- **Notes**: The streaming audit completed all 673,499 rows, all 191 components, and all three raw/binary relationship checks without a dense pandas load. + --- ## [ERR-20260920-032] samhsa-pdf-direct-fetch-forbidden diff --git a/Progression.md b/Progression.md index 3844a73..5a8bc29 100644 --- a/Progression.md +++ b/Progression.md @@ -1,9 +1,9 @@ # 项目进度档案 -版本：1.9 +版本：1.10 建立日期：2026-09-20 当前总状态：`in_progress` -当前阶段：阶段 1 `in_progress`；NSDUH 青少年尝试题的施测与公开数据可用性已核清，GSHS 组件来源和双人审核尚未完成 +当前阶段：阶段 1 `in_progress`；NSDUH 青少年尝试题及 GSHS 191 组件覆盖/原始与二元表示关系已核清，YRBS 直接来源、缺失规则和双人审核尚未完成 ## 1. 管理规则 @@ -28,7 +28,7 @@ | 阶段 | 名称 | 状态 | 当前判定 | |---|---|---|---| | 0 | 冻结研究问题、范围与版本 | `passed` | 四项交付物齐备，Gate 0 已通过；研究工具链补强与锁定完成 | -| 1 | 有来源证据的题库和回答层 | `in_progress` | 数据契约、入口审计、主要结局登记和 NSDUH 尝试题来源核验已完成；GSHS/YRBS 直接来源、编码规则与人工双重审核尚未完成 | +| 1 | 有来源证据的题库和回答层 | `in_progress` | 数据契约、入口审计、主要结局登记、NSDUH 尝试题来源核验及 GSHS 191 组件审计已完成；YRBS 直接来源、编码/缺失规则与人工双重审核尚未完成 | | 2 | 可行性、可识别性和连接审计 | `not_started` | 等待 Gate 1 | | 3 | 冻结验证协议与已知真值模拟 | `not_started` | 等待 Gate 2 | | 4 | 直接协调和传统基线 | `not_started` | 等待 Gate 3 | @@ -87,7 +87,7 @@ Gate 0 当前判定：`passed`。四项交付物齐备；目标总体政策、 | P1 | R、PyMC/ArviZ、心理测量包与 CUDA Toolkit 曾缺失 | 已解决：项目 Python/R 环境和 CUDA 端到端验收通过 | 后续仅按锁定文件维护；任何升级必须重跑三套烟雾测试 | | P1 | 文献初筛尚未形成可审计矩阵 | 研究定位和“贡献”表述仍不稳定 | 建立 literature matrix，记录 DOI、来源、证据层级和项目关系 | | P0 | NSDUH 的 `YSUI03/YUSUICTRY` 已确认施测，但尝试及严重度字段不在当前本地公开使用数据中；2024 指南明确记录派生尝试变量因披露风险排除 | 当前微数据只能外部验证意念/计划，不能验证尝试 | 不从其他题推导尝试；如核心设计必须使用尝试，评估受限数据申请或预先设计的聚合结果方案 | -| P1 | GSHS `_b_` 与无前缀题目版本、YRBS 年度题目文本仍缺直接官方文档复核 | 不能批准题目家族或跨调查锚定 | 按组件/年度建立直接来源证据和冲突清单 | +| P1 | GSHS 已证明 `_b_` 为派生/重复表示，但 Solomon Islands 2023 缺本地直接来源；YRBS 年度题目文本仍缺直接官方文档复核 | 不能批准全部题目家族或跨调查锚定 | 获取 Solomon Islands 来源；按年度复核 YRBS 并建立冲突清单 | ## 8. 行动日志 @@ -707,6 +707,20 @@ Gate 0 当前判定：`passed`。四项交付物齐备；目标总体政策、 - 推送状态：`pushed`；研究增量提交 `7d50ae6` 已推送至 `origin/main`，本地与远端 HEAD 核对一致。 - 下一步：建立 GSHS 191 个组件中的主要结局题目版本与来源映射，保持 `_b_`、无前缀、二分类和频数型版本分离。 +### A-20260920-056：完成 GSHS 191 组件主要结局与表示关系审计 + +- 时间：2026-09-20 +- 阶段：1（有来源证据的题库和回答层） +- 动作：行动前完整读取 `Document/research-workflow.md`、本进度档案并核对干净 Git 状态；流式扫描 GSHS 673,499 行；将 191 个已选组件与组件登记逐一核对；读取六个国家/地区的本地问卷、常规代码本和 Binary Codebook，并对 Ghana 关键 PDF 页做视觉复核。 +- 输入：`GSHS.csv`、`调查组件筛选明细.csv`、GSHS 数据字典；Ghana、India、Jamaica、Mongolia、Morocco、Wallis and Futuna 的国家/地区问卷与代码本。 +- 输出：新增 `audit_gshs_primary_outcome_components.py`、`gshs_primary_outcome_component_audit.json`、`gshs_primary_outcome_component_audit.md`；主要结局登记升级至 v1.2；更新 `.learnings/ERRORS.md`。 +- 检查：脚本通过 `py_compile`；JSON 可解析；191 个组件与登记完全一致，673,499 行全部覆盖，组件行数不一致为 0；仅 7 个组件有主要结局值，184 个没有；六个有结局组件具备本地直接来源，Solomon Islands 2023 尚缺；三组原始/`_b_` 关系均无异常组合。 +- 新证据：常规代码本中的 `MH_CONSIDERSUI`、`MH_PLANSUI`、`MH_ATTEMPTSUI` 是三项实际施测题；Binary Codebook 把 `MH_B_*` 定义为比例指标。逐行数据进一步确认意念和计划的 `_b_` 与原始二元编码完全相同，尝试的 `_b_` 精确按“0 次=否、1 次及以上=是”派生。因此 `_b_` 不再作为独立施测题计数；登记候选由 69 条降为 66 条，另有 11 条派生/非独立记录。 +- 质量边界：六个组件的文件语言只证明可用来源语言，不自动证明每名受访者的实际施测语言；Solomon Islands 直接来源、确切年龄/年级总体、规范缺失原因和两名实际审核者仍未完成。所有记录保持 `provisional`，Gate 1 仍为 `in_progress`。 +- 工程记录：重复的 pandas 全表内存耗尽改为固定列索引的流式扫描，记为已解决 `ERR-20260920-033`；项目环境未安装可选文档解析器和错误目录假设分别记为已解决 `ERR-20260920-034`、`ERR-20260920-035`，未把可选解析器无必要地加入正式建模环境。 +- 推送状态：`push_pending`；待本行动校验、提交并推送后回写提交号。 +- 下一步：直接复核 YRBS 年度主要结局问卷/代码本，继续隔离 2021/2023 数据，并形成三套调查的回答编码与缺失规则草案。 + ## 9. 剩余工作量估算（2026-09-20 基线） | 阶段 | 主要工作 | 预计人周 | 主要波动来源 | @@ -729,6 +743,6 @@ Gate 0 当前判定：`passed`。四项交付物齐备；目标总体政策、 阶段 1 下一行动： -1. 建立 GSHS 191 个组件中的主要结局题目版本与官方来源映射，保持 `_b_`、无前缀、二分类和频数型版本分离； -2. 直接复核 YRBS 年度主要结局题目，并继续隔离 2021/2023 数据； -3. 随后形成回答编码/缺失规则草案，并把需要两名实际审核者处理的记录导出为审核队列。 +1. 直接复核 YRBS 年度主要结局题目，并继续隔离 2021/2023 数据； +2. 获取或定位 Solomon Islands 2023 GSHS 的国家问卷/代码本； +3. 随后形成三套调查的回答编码/缺失规则草案，并把需要两名实际审核者处理的记录导出为审核队列。 diff --git a/research/stage1/audit_gshs_primary_outcome_components.py b/research/stage1/audit_gshs_primary_outcome_components.py new file mode 100644 index 0000000..8a23d11 --- /dev/null +++ b/research/stage1/audit_gshs_primary_outcome_components.py @@ -0,0 +1,399 @@ +"""Audit GSHS primary-outcome coverage across all selected components. + +The audit is deliberately conservative. It verifies observed column relations and +records local questionnaire/codebook provenance, but it does not approve item +equivalence, missing-value recodes, population scope, or human review. +""" + +from __future__ import annotations + +import csv +import hashlib +import json +from collections import Counter, defaultdict +from pathlib import Path + + +ROOT = Path(__file__).resolve().parents[2] +STAGE_DIR = ROOT / "research" / "stage1" +GSHS_ROOT = ROOT / "Dataset" / "GSHS-全球学生健康调查数据" / "GSHS" +DATA = GSHS_ROOT / "01_data" / "GSHS.csv" +COMPONENTS = GSHS_ROOT / "02_documentation" / "调查组件筛选明细.csv" +QUESTIONNAIRES = GSHS_ROOT / "Questionnaire" / "GSHS Per Country" +OUT_JSON = STAGE_DIR / "gshs_primary_outcome_component_audit.json" +OUT_MD = STAGE_DIR / "gshs_primary_outcome_component_audit.md" + +RAW_VARIABLES = { + "raw_mh_considersui": { + "construct": "suicide_ideation", + "question_text": "During the past 12 months, did you seriously consider attempting suicide?", + "response_type": "binary", + "codes": {"1": "Yes", "2": "No"}, + }, + "raw_mh_plansui": { + "construct": "suicide_plan", + "question_text": "During the past 12 months, did you make a plan about how you would attempt suicide?", + "response_type": "binary", + "codes": {"1": "Yes", "2": "No"}, + }, + "raw_mh_attemptsui": { + "construct": "suicide_attempt", + "question_text": "During the past 12 months, how many times did you attempt suicide?", + "response_type": "ordinal_frequency", + "codes": { + "1": "0 times", + "2": "1 time", + "3": "2 or 3 times", + "4": "4 or 5 times", + "5": "6 or more times", + }, + }, +} + +DERIVED_VARIABLES = { + "raw_mh_b_considersui": { + "construct": "suicide_ideation", + "source_variable": "raw_mh_considersui", + "response_type": "binary_derived_or_duplicate", + "codes": {"1": "Yes", "2": "No"}, + "expected_rule": {"1": "1", "2": "2"}, + }, + "raw_mh_b_plansui": { + "construct": "suicide_plan", + "source_variable": "raw_mh_plansui", + "response_type": "binary_derived_or_duplicate", + "codes": {"1": "Yes", "2": "No"}, + "expected_rule": {"1": "1", "2": "2"}, + }, + "raw_mh_b_attemptsui": { + "construct": "suicide_attempt", + "source_variable": "raw_mh_attemptsui", + "response_type": "binary_derived", + "codes": {"1": "Yes", "2": "No"}, + "expected_rule": {"1": "2", "2": "1", "3": "1", "4": "1", "5": "1"}, + }, +} + +ALL_VARIABLES = list(RAW_VARIABLES) + list(DERIVED_VARIABLES) + +SOURCE_PACKAGES = { + "GHA_2022_GSHS_v01::gha_sek_tak2022": { + "question_numbers": {"ideation": "Q33", "plan": "Q34", "attempt": "Q35"}, + "documents": [ + ("Ghana 2022/Sekondi-Takoradi-2022_GSHS_Questionnaire-Final.pdf", "questionnaire", "page 6"), + ("Ghana 2022/2022_Ghana_(Sekondi-Takoradi)_Codebook.pdf", "raw codebook", "pages 7-8"), + ("Ghana 2022/2022_Ghana_(Sekondi-Takoradi)_Binary_Codebook.pdf", "binary codebook", "pages 7-8"), + ], + "source_language_evidence": ["English"], + }, + "IND_2022_GSHS_v01::ind_jaipur_2022": { + "question_numbers": {"ideation": "Q34", "plan": "Q35", "attempt": "Q36"}, + "documents": [ + ("India 2022/Jaipur-2022_GSHS_Questionnaire-Final.docx", "questionnaire", "Q34-Q36"), + ("India 2022/2022_India_(Jaipur)_Codebook.docx", "raw codebook", "MH_CONSIDERSUI through MH_ATTEMPTSUI"), + ("India 2022/2022_India_(Jaipur)_Binary_Codebook.docx", "binary codebook", "MH_B_CONSIDERSUI through MH_B_ATTEMPTSUI"), + ], + "source_language_evidence": ["English"], + }, + "JAM_2023_GSHS_v01::jam_st_cath_2023": { + "question_numbers": {"ideation": "Q28", "plan": "Q29", "attempt": "Q30"}, + "documents": [ + ("Jamaica 2023/FINAL_St. Catherine-2023-GSHS-Questionnaire.docx", "questionnaire", "Q28-Q30"), + ("Jamaica 2023/2023_Jamaica_(St_Catherine)_Codebook.docx", "raw codebook", "MH_CONSIDERSUI through MH_ATTEMPTSUI"), + ("Jamaica 2023/2023_Jamaica_(St_Catherine)_Binary_Codebook.docx", "binary codebook", "MH_B_CONSIDERSUI through MH_B_ATTEMPTSUI"), + ], + "source_language_evidence": ["English"], + }, + "MNG_2023_GSHS_v01::mng2023": { + "question_numbers": {"ideation": "Q36", "plan": "Q37", "attempt": "Q38"}, + "documents": [ + ("Mongolia 2023/Mongolia-GSHS-Questionnaire-ENGLISH.docx", "English questionnaire", "Q36-Q38"), + ("Mongolia 2023/Mongolia-GSHS-Questionnaire-MONGOLIAN.docx", "Mongolian questionnaire", "Q36-Q38"), + ("Mongolia 2023/2023 Mongolia Codebook.docx", "raw codebook", "MH_CONSIDERSUI through MH_ATTEMPTSUI"), + ("Mongolia 2023/2023 Mongolia Binary_Codebook.docx", "binary codebook", "MH_B_CONSIDERSUI through MH_B_ATTEMPTSUI"), + ], + "source_language_evidence": ["English", "Mongolian"], + }, + "2023_MAR_GSHS_v01::mar_fez2023": { + "question_numbers": {"ideation": "Q32", "plan": "Q33", "attempt": "Q34"}, + "documents": [ + ("Morocco 2023/Fez_2022_GSHS_Questionnaire_Final_FRENCH.pdf", "French questionnaire", "page 6"), + ("Morocco 2023/Fez_2022_GSHS_Questionnaire_Final_ENGLISH.pdf", "English questionnaire", "page 6"), + ("Morocco 2023/2023_Maroc_(Fes)_Codebook.pdf", "raw codebook", "pages 7-8"), + ("Morocco 2023/2023_Maroc_(Fes)_Binary_Codebook.pdf", "binary codebook", "pages 7-8"), + ], + "source_language_evidence": ["French", "English reference"], + }, + "WLF_2023_GSHS_v01::wlf_2023": { + "question_numbers": {"ideation": "Q29", "plan": "Q30", "attempt": "Q31"}, + "documents": [ + ("Wallis and Futuna 2023/Wallis and Futuna - GSHS Questionnaire - Final - French.docx", "French questionnaire", "Q29-Q31"), + ("Wallis and Futuna 2023/Wallis and Futuna - GSHS Questionnaire - Final - English.docx", "English questionnaire", "Q29-Q31"), + ("Wallis and Futuna 2023/2023 Wallis and Futuna Codebook.docx", "raw codebook", "MH_CONSIDERSUI through MH_ATTEMPTSUI"), + ("Wallis and Futuna 2023/2023 Wallis and Futuna Binary_Codebook.docx", "binary codebook", "MH_B_CONSIDERSUI through MH_B_ATTEMPTSUI"), + ], + "source_language_evidence": ["French", "English reference"], + }, +} + + +def sha256(path: Path) -> str: + digest = hashlib.sha256() + with path.open("rb") as handle: + for chunk in iter(lambda: handle.read(1024 * 1024), b""): + digest.update(chunk) + return digest.hexdigest() + + +def read_component_metadata() -> dict[str, dict]: + with COMPONENTS.open(encoding="utf-8-sig", newline="") as handle: + rows = list(csv.DictReader(handle)) + selected = {row["dataset_id"]: row for row in rows if row["include_in_master"] == "1"} + if len(selected) != 191: + raise AssertionError(f"Expected 191 selected components, found {len(selected)}") + return selected + + +def scan_data() -> dict: + row_counts: Counter[str] = Counter() + nonmissing: dict[str, Counter[str]] = defaultdict(Counter) + values: dict[str, dict[str, Counter[str]]] = defaultdict(lambda: defaultdict(Counter)) + pairs: dict[str, Counter[tuple[str, str]]] = defaultdict(Counter) + + with DATA.open(encoding="utf-8-sig", newline="") as handle: + reader = csv.reader(handle) + header = next(reader) + indices = {name: header.index(name) for name in ["dataset_id", *ALL_VARIABLES]} + for row in reader: + component = row[indices["dataset_id"]] + row_counts[component] += 1 + observed = {name: row[indices[name]].strip() for name in ALL_VARIABLES} + for name, value in observed.items(): + if value: + nonmissing[component][name] += 1 + values[component][name][value] += 1 + for derived, spec in DERIVED_VARIABLES.items(): + source = spec["source_variable"] + pairs[derived][(observed[source], observed[derived])] += 1 + + return { + "row_counts": row_counts, + "nonmissing": nonmissing, + "values": values, + "pairs": pairs, + } + + +def source_package(component_id: str) -> dict: + package = SOURCE_PACKAGES.get(component_id) + if package is None: + return { + "status": "pending_local_direct_source", + "documents": [], + "question_numbers": None, + "source_language_evidence": [], + "note": "No country questionnaire or codebook for this component was found in the local source package.", + } + documents = [] + for relative, role, section in package["documents"]: + path = QUESTIONNAIRES / relative + if not path.exists(): + raise FileNotFoundError(path) + documents.append( + { + "source_file": str(path.relative_to(ROOT)).replace("\\", "/"), + "role": role, + "page_or_section": section, + "sha256": sha256(path), + } + ) + return { + "status": "local_questionnaire_and_codebooks_located", + "documents": documents, + "question_numbers": package["question_numbers"], + "source_language_evidence": package["source_language_evidence"], + "note": "Available-language documents do not by themselves prove the language actually administered to every respondent.", + } + + +def serial_counter(counter: Counter) -> dict: + return {str(key): value for key, value in sorted(counter.items(), key=lambda item: str(item[0]))} + + +def build_audit() -> dict: + metadata = read_component_metadata() + scan = scan_data() + data_components = set(scan["row_counts"]) + if data_components != set(metadata): + raise AssertionError("GSHS.csv component IDs do not match the 191 selected metadata rows") + + components = [] + row_count_mismatches = [] + for component_id, meta in sorted(metadata.items()): + expected_rows = int(meta["row_count"]) + observed_rows = scan["row_counts"][component_id] + if expected_rows != observed_rows: + row_count_mismatches.append( + {"component_id": component_id, "metadata_rows": expected_rows, "observed_rows": observed_rows} + ) + variable_counts = { + name: { + "nonmissing": scan["nonmissing"][component_id][name], + "value_counts": serial_counter(scan["values"][component_id][name]), + } + for name in ALL_VARIABLES + } + has_primary = any(item["nonmissing"] for item in variable_counts.values()) + components.append( + { + "component_id": component_id, + "reference_id": meta["reference_id"], + "catalog_id": meta["catalog_id"], + "country": meta["country"], + "iso3": meta["iso3"] or None, + "collection_start": meta["collection_start"], + "survey_component": meta["survey_component"], + "survey_scope": meta["survey_scope"], + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": observed_rows, + "canonical_relative_path": meta["canonical_relative_path"], + "catalog_url": meta["catalog_url"], + "primary_outcomes_observed": has_primary, + "variables": variable_counts, + "source_package": source_package(component_id) if has_primary else None, + "review_status": "provisional", + "reviewer_1": None, + "reviewer_2": None, + } + ) + + relation_checks = [] + for derived, spec in DERIVED_VARIABLES.items(): + observed_pairs = scan["pairs"][derived] + unexpected = [] + for (raw, binary), count in observed_pairs.items(): + expected = "" if raw == "" else spec["expected_rule"].get(raw) + if binary != expected: + unexpected.append({"raw": raw or None, "derived": binary or None, "count": count}) + relation_checks.append( + { + "source_variable": spec["source_variable"], + "derived_variable": derived, + "expected_rule": spec["expected_rule"], + "observed_pair_counts": { + f"{raw or ''}->{binary or ''}": count + for (raw, binary), count in sorted(observed_pairs.items()) + }, + "unexpected_pairs": unexpected, + "check_status": "passed" if not unexpected else "failed", + } + ) + + available = [component for component in components if component["primary_outcomes_observed"]] + direct_sources = [ + component for component in available if component["source_package"]["status"] == "local_questionnaire_and_codebooks_located" + ] + return { + "schema_version": "1.0", + "generated_on": "2026-09-20", + "status": "provisional", + "purpose": "Gate 1 component-level coverage and provenance audit for GSHS suicide ideation, plan, and attempt.", + "inputs": { + "data_file": str(DATA.relative_to(ROOT)).replace("\\", "/"), + "data_sha256": sha256(DATA), + "component_registry": str(COMPONENTS.relative_to(ROOT)).replace("\\", "/"), + "component_registry_sha256": sha256(COMPONENTS), + }, + "summary": { + "selected_components": len(components), + "components_with_primary_outcomes": len(available), + "components_without_primary_outcomes": len(components) - len(available), + "components_with_local_direct_sources": len(direct_sources), + "components_pending_local_direct_source": len(available) - len(direct_sources), + "observed_rows": sum(scan["row_counts"].values()), + "row_count_mismatches": len(row_count_mismatches), + }, + "item_definitions": { + "administered_raw_items": RAW_VARIABLES, + "derived_or_duplicate_representations": DERIVED_VARIABLES, + "missing_rule_status": "unresolved; blank values are retained as missing and are not yet assigned a canonical missing type", + }, + "relation_checks": relation_checks, + "row_count_mismatches": row_count_mismatches, + "components": components, + "review_boundary": { + "human_reviewers_required": 2, + "ai_review_is_human_review": False, + "population_scope_approved": False, + "missing_rules_approved": False, + "cross_component_equivalence_approved": False, + "confirmatory_analysis_allowed": False, + }, + } + + +def render_markdown(audit: dict) -> str: + available = [c for c in audit["components"] if c["primary_outcomes_observed"]] + lines = [ + "# GSHS primary-outcome component audit", + "", + "Version: 1.0 | Status: provisional | Generated: 2026-09-20", + "", + "## Result", + "", + f"The selected GSHS master table contains {audit['summary']['selected_components']} components and {audit['summary']['observed_rows']:,} rows. Exactly {audit['summary']['components_with_primary_outcomes']} components contain the three primary suicide outcomes; the remaining {audit['summary']['components_without_primary_outcomes']} contain no observed values in those six columns. Metadata row counts match the consolidated table for all components.", + "", + "The country questionnaires and ordinary codebooks identify three administered items: past-12-month suicide ideation, plan, and attempt frequency. The Binary Codebooks identify the `_b_` columns as binary indicators derived from those items. Row-level checks are exact: ideation and plan binary columns duplicate the raw yes/no coding, while attempt maps 0 times to No and one or more times to Yes. Therefore the `_b_` columns must not be counted as independent administered items.", + "", + "## Components with observed primary outcomes", + "", + "| Component | Country | Rows | Ideation nonmissing | Plan nonmissing | Attempt nonmissing | Direct local sources |", + "|---|---|---:|---:|---:|---:|---|", + ] + for component in available: + variables = component["variables"] + source = component["source_package"]["status"] + lines.append( + f"| `{component['component_id']}` | {component['country']} | {component['observed_rows']:,} | {variables['raw_mh_considersui']['nonmissing']:,} | {variables['raw_mh_plansui']['nonmissing']:,} | {variables['raw_mh_attemptsui']['nonmissing']:,} | {source} |" + ) + lines += [ + "", + "## Representation checks", + "", + "| Raw item | Binary representation | Result | Observed mapping |", + "|---|---|---|---|", + ] + for check in audit["relation_checks"]: + mapping = "; ".join(f"{key}: {value:,}" for key, value in check["observed_pair_counts"].items()) + lines.append( + f"| `{check['source_variable']}` | `{check['derived_variable']}` | {check['check_status']} | {mapping} |" + ) + lines += [ + "", + "## Source boundary", + "", + f"Local questionnaires plus raw and binary codebooks were located for {audit['summary']['components_with_local_direct_sources']} of the 7 components: Ghana, India, Jamaica, Mongolia, Morocco, and Wallis and Futuna. No country-specific Solomon Islands 2023 questionnaire/codebook was found locally, so that component remains pending direct-source acquisition.", + "", + "Available English/French/Mongolian files establish wording evidence but do not by themselves prove the language administered to every respondent. Exact sampled ages/grades, component-specific eligibility, and canonical missing reasons also remain unresolved.", + "", + "## Gate 1 decision", + "", + "Gate 1 remains **in progress**. This audit resolves the 191-component coverage question and the raw-versus-`_b_` representation issue, but it does not satisfy the population/missing-rule or two-human-reviewer requirements. All records remain provisional and are not approved for confirmatory analysis or anchor construction.", + "", + "## Reproduction", + "", + "Run `research/stage1/audit_gshs_primary_outcome_components.py` in the project Python environment. The implementation streams the consolidated CSV and does not load it into pandas memory.", + "", + ] + return "\n".join(lines) + + +def main() -> None: + audit = build_audit() + OUT_JSON.write_text(json.dumps(audit, ensure_ascii=False, indent=2) + "\n", encoding="utf-8") + OUT_MD.write_text(render_markdown(audit), encoding="utf-8") + print(json.dumps(audit["summary"], ensure_ascii=False)) + + +if __name__ == "__main__": + main() diff --git a/research/stage1/build_primary_outcome_registry.py b/research/stage1/build_primary_outcome_registry.py index 91b10a2..bc8c827 100644 --- a/research/stage1/build_primary_outcome_registry.py +++ b/research/stage1/build_primary_outcome_registry.py @@ -26,11 +26,22 @@ OUT_MD = STAGE_DIR / "primary_outcome_registry.md" PRIMARY_CONSTRUCTS = {"suicide_ideation", "suicide_plan", "suicide_attempt"} GSHS_CONSTRUCT = { "raw_mh_considersui": "suicide_ideation", - "raw_mh_b_considersui": "suicide_ideation", "raw_mh_plansui": "suicide_plan", - "raw_mh_b_plansui": "suicide_plan", "raw_mh_attemptsui": "suicide_attempt", - "raw_mh_b_attemptsui": "suicide_attempt", +} +GSHS_DERIVED = { + "raw_mh_b_considersui": ("suicide_ideation", "raw_mh_considersui", "identity binary representation"), + "raw_mh_b_plansui": ("suicide_plan", "raw_mh_plansui", "identity binary representation"), + "raw_mh_b_attemptsui": ( + "suicide_attempt", + "raw_mh_attemptsui", + "1=Yes when attempt frequency is one or more; 2=No when frequency is zero", + ), +} +GSHS_QUESTION = { + "raw_mh_considersui": "During the past 12 months, did you seriously consider attempting suicide?", + "raw_mh_plansui": "During the past 12 months, did you make a plan about how you would attempt suicide?", + "raw_mh_attemptsui": "During the past 12 months, how many times did you attempt suicide?", } NSDUH_YOUTH_RAW = {"YUSUITHK": "suicide_ideation", "YUSUIPLN": "suicide_plan"} NSDUH_YOUTH_DERIVED = {"YUSUITHKYR": "suicide_ideation", "YUSUIPLNYR": "suicide_plan"} @@ -60,36 +71,56 @@ def parquet_columns(path: Path) -> set[str]: return set(pq.ParquetFile(path).schema_arrow.names) -def build_gshs() -> list[dict]: +def build_gshs() -> tuple[list[dict], list[dict]]: frame = pd.read_excel(GSHS_BOOK, sheet_name="Master_Columns", dtype=str, keep_default_na=False) - frame = frame[frame["column_name"].isin(GSHS_CONSTRUCT)].copy() - records = [] + frame = frame[frame["column_name"].isin(set(GSHS_CONSTRUCT) | set(GSHS_DERIVED))].copy() + records: list[dict] = [] + derived_records: list[dict] = [] for row in frame.sort_values("ordinal").to_dict("records"): - records.append( - { - "survey": "GSHS", - "year": None, - "source_variable": row["column_name"], - "construct": GSHS_CONSTRUCT[row["column_name"]], - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": None, - "source_label": clean_text(row["label_variants"]), - "answer_options": parse_json_object(row["value_labels_example"]), - "source_file": str(GSHS_BOOK.relative_to(ROOT)).replace("\\", "/"), - "source_url": None, - "page_or_section": "Master_Columns", - "present_in_local_data": True, - "source_verification_status": "pending_questionnaire_review", - "review_status": "provisional", - "reviewer_1": None, - "reviewer_2": None, - "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence.", - } - ) - return records + variable = row["column_name"] + common = { + "survey": "GSHS", + "year": None, + "source_variable": variable, + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", + "source_label": clean_text(row["label_variants"]), + "answer_options": parse_json_object(row["value_labels_example"]), + "source_file": str(GSHS_BOOK.relative_to(ROOT)).replace("\\", "/"), + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", + "source_url": None, + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", + "present_in_local_data": True, + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", + "review_status": "provisional", + "reviewer_1": None, + "reviewer_2": None, + "link_status": "not_evaluated", + } + if variable in GSHS_CONSTRUCT: + common.update( + { + "construct": GSHS_CONSTRUCT[variable], + "record_type": "administered_raw_candidate", + "question_text": GSHS_QUESTION[variable], + "notes": "Country questionnaires and ordinary codebooks identify this as an administered item. Solomon Islands 2023 direct local source remains pending; population and missing rules are not approved.", + } + ) + records.append(common) + else: + construct, source_variable, derivation_rule = GSHS_DERIVED[variable] + common.update( + { + "construct": construct, + "record_type": "derived_or_duplicate_binary_indicator", + "question_text": None, + "derived_from": source_variable, + "derivation_rule": derivation_rule, + "notes": "Binary Codebooks and exact row-level mapping show this is not an independent administered item.", + } + ) + derived_records.append(common) + return records, derived_records def build_yrbs() -> list[dict]: @@ -235,7 +266,7 @@ def render_markdown(registry: dict) -> str: lines = [ "# Primary outcome source registry", "", - "Version: 1.1 | Status: provisional | Generated: 2026-09-20", + "Version: 1.2 | Status: provisional | Generated: 2026-09-20", "", "## Scope and decision boundary", "", @@ -248,7 +279,7 @@ def render_markdown(registry: dict) -> str: ] for survey in ["GSHS", "YRBS", "NSDUH"]: boundary = { - "GSHS": "Workbook labels/options only; component questionnaires still require direct review.", + "GSHS": "Three administered items occur in 7/191 components; local direct sources cover 6/7, with Solomon Islands pending.", "YRBS": "51 annual candidates; 2021/2023 data remain quarantined; annual PDFs require direct review.", "NSDUH": "Attempt is administered as YSUI03/YUSUICTRY, but the raw and recoded attempt fields are absent from the local public-use package.", }[survey] @@ -261,7 +292,7 @@ def render_markdown(registry: dict) -> str: "", "## Material conflicts and exclusions", "", - "- GSHS exposes both `_b_` and unprefixed variants. They differ in naming and, for attempt, response form (binary versus frequency). They remain separate until questionnaire/component provenance is verified.", + "- GSHS ordinary codebooks identify the three unprefixed variables as administered items. Binary Codebooks plus exact row-level relations identify the three `_b_` columns as derived or duplicate representations, not independent items.", "- GSHS self-harm variables are not included as suicide-attempt items.", "- YRBS metadata contains stale absolute paths from another machine and some automatically extracted neighboring-text contamination. Only exact primary-construct rows were retained, and their direct PDF review is still pending.", "- YRBS 2021 and 2023 item metadata are retained for future migration checks, but their respondent data are quarantined pending layout/import validation.", @@ -271,7 +302,7 @@ def render_markdown(registry: dict) -> str: "", "## Gate 1 status", "", - "Gate 1 remains **in progress**. Before any candidate can enter confirmatory analysis, the project still needs direct official questionnaire/codebook review, exact population and skip-logic verification, canonical response/missing rules, component-specific GSHS provenance, and two actual human reviewers for primary outcomes.", + "Gate 1 remains **in progress**. Before any candidate can enter confirmatory analysis, the project still needs direct YRBS and Solomon Islands GSHS source review, exact population and skip-logic verification, canonical response/missing rules, and two actual human reviewers for primary outcomes.", "", "## Reproduction", "", @@ -282,17 +313,17 @@ def render_markdown(registry: dict) -> str: def main() -> None: - gshs = build_gshs() + gshs, gshs_derived = build_gshs() yrbs = build_yrbs() nsduh_raw, nsduh_derived, nsduh_excluded = build_nsduh() registry = { - "schema_version": "1.1", + "schema_version": "1.2", "generated_on": "2026-09-20", "status": "provisional", "allowed_uses": ["pipeline_development", "source_review_queue"], "prohibited_uses": ["confirmatory_analysis", "approved_anchor_links", "claim_of_human_double_review"], "candidate_records": gshs + yrbs + nsduh_raw, - "derived_records_not_independent_items": nsduh_derived, + "derived_records_not_independent_items": gshs_derived + nsduh_derived, "excluded_nsduh_records": nsduh_excluded, "availability_constraints": [ { @@ -314,7 +345,7 @@ def main() -> None: OUT_MD.write_text(render_markdown(registry), encoding="utf-8") print(json.dumps({ "candidate_records": len(registry["candidate_records"]), - "derived_records": len(nsduh_derived), + "derived_records": len(registry["derived_records_not_independent_items"]), "excluded_nsduh_records": len(nsduh_excluded), "json": str(OUT_JSON.relative_to(ROOT)), "report": str(OUT_MD.relative_to(ROOT)), diff --git a/research/stage1/gshs_primary_outcome_component_audit.json b/research/stage1/gshs_primary_outcome_component_audit.json new file mode 100644 index 0000000..04ebcd4 --- /dev/null +++ b/research/stage1/gshs_primary_outcome_component_audit.json @@ -0,0 +1,9119 @@ +{ + "schema_version": "1.0", + "generated_on": "2026-09-20", + "status": "provisional", + "purpose": "Gate 1 component-level coverage and provenance audit for GSHS suicide ideation, plan, and attempt.", + "inputs": { + "data_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/01_data/GSHS.csv", + "data_sha256": "e5661e3377c5e3bbe19d86cb6db2c78e2bb557eea110116ec5f2d3483158cc52", + "component_registry": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/调查组件筛选明细.csv", + "component_registry_sha256": "ddf387e84a46a2505bcdb244472a288eb84a638a8b8b6cbe3d52e307660826b5" + }, + "summary": { + "selected_components": 191, + "components_with_primary_outcomes": 7, + "components_without_primary_outcomes": 184, + "components_with_local_direct_sources": 6, + "components_pending_local_direct_source": 1, + "observed_rows": 673499, + "row_count_mismatches": 0 + }, + "item_definitions": { + "administered_raw_items": { + "raw_mh_considersui": { + "construct": "suicide_ideation", + "question_text": "During the past 12 months, did you seriously consider attempting suicide?", + "response_type": "binary", + "codes": { + "1": "Yes", + "2": "No" + } + }, + "raw_mh_plansui": { + "construct": "suicide_plan", + "question_text": "During the past 12 months, did you make a plan about how you would attempt suicide?", + "response_type": "binary", + "codes": { + "1": "Yes", + "2": "No" + } + }, + "raw_mh_attemptsui": { + "construct": "suicide_attempt", + "question_text": "During the past 12 months, how many times did you attempt suicide?", + "response_type": "ordinal_frequency", + "codes": { + "1": "0 times", + "2": "1 time", + "3": "2 or 3 times", + "4": "4 or 5 times", + "5": "6 or more times" + } + } + }, + "derived_or_duplicate_representations": { + "raw_mh_b_considersui": { + "construct": "suicide_ideation", + "source_variable": "raw_mh_considersui", + "response_type": "binary_derived_or_duplicate", + "codes": { + "1": "Yes", + "2": "No" + }, + "expected_rule": { + "1": "1", + "2": "2" + } + }, + "raw_mh_b_plansui": { + "construct": "suicide_plan", + "source_variable": "raw_mh_plansui", + "response_type": "binary_derived_or_duplicate", + "codes": { + "1": "Yes", + "2": "No" + }, + "expected_rule": { + "1": "1", + "2": "2" + } + }, + "raw_mh_b_attemptsui": { + "construct": "suicide_attempt", + "source_variable": "raw_mh_attemptsui", + "response_type": "binary_derived", + "codes": { + "1": "Yes", + "2": "No" + }, + "expected_rule": { + "1": "2", + "2": "1", + "3": "1", + "4": "1", + "5": "1" + } + } + }, + "missing_rule_status": "unresolved; blank values are retained as missing and are not yet assigned a canonical missing type" + }, + "relation_checks": [ + { + "source_variable": "raw_mh_considersui", + "derived_variable": "raw_mh_b_considersui", + "expected_rule": { + "1": "1", + "2": "2" + }, + "observed_pair_counts": { + "->": 652749, + "1->1": 4854, + "2->2": 15896 + }, + "unexpected_pairs": [], + "check_status": "passed" + }, + { + "source_variable": "raw_mh_plansui", + "derived_variable": "raw_mh_b_plansui", + "expected_rule": { + "1": "1", + "2": "2" + }, + "observed_pair_counts": { + "->": 652761, + "1->1": 4363, + "2->2": 16375 + }, + "unexpected_pairs": [], + "check_status": "passed" + }, + { + "source_variable": "raw_mh_attemptsui", + "derived_variable": "raw_mh_b_attemptsui", + "expected_rule": { + "1": "2", + "2": "1", + "3": "1", + "4": "1", + "5": "1" + }, + "observed_pair_counts": { + "->": 652461, + "1->2": 16732, + "2->1": 2457, + "3->1": 1139, + "4->1": 325, + "5->1": 385 + }, + "unexpected_pairs": [], + "check_status": "passed" + } + ], + "row_count_mismatches": [], + "components": [ + { + "component_id": "2023_MAR_GSHS_v01::mar_fez2023", + "reference_id": "2023_MAR_GSHS_v01", + "catalog_id": "982", + "country": "Morocco", + "iso3": null, + "collection_start": "2023-05", + "survey_component": "Subnational dataset", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 4172, + "canonical_relative_path": "raw/microdata/2023_MAR_GSHS_v01/MAR-Fez2023.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/982", + "primary_outcomes_observed": true, + "variables": { + "raw_mh_considersui": { + "nonmissing": 3994, + "value_counts": { + "1": 824, + "2": 3170 + } + }, + "raw_mh_plansui": { + "nonmissing": 4019, + "value_counts": { + "1": 626, + "2": 3393 + } + }, + "raw_mh_attemptsui": { + "nonmissing": 4086, + "value_counts": { + "1": 3297, + "2": 463, + "3": 197, + "4": 53, + "5": 76 + } + }, + "raw_mh_b_considersui": { + "nonmissing": 3994, + "value_counts": { + "1": 824, + "2": 3170 + } + }, + "raw_mh_b_plansui": { + "nonmissing": 4019, + "value_counts": { + "1": 626, + "2": 3393 + } + }, + "raw_mh_b_attemptsui": { + "nonmissing": 4086, + "value_counts": { + "1": 789, + "2": 3297 + } + } + }, + "source_package": { + "status": "local_questionnaire_and_codebooks_located", + "documents": [ + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Morocco 2023/Fez_2022_GSHS_Questionnaire_Final_FRENCH.pdf", + "role": "French questionnaire", + "page_or_section": "page 6", + "sha256": "974995b8e4ab2501d9378eb78a76fb5b56d9641b732c702496c84aabe7a3e6b3" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Morocco 2023/Fez_2022_GSHS_Questionnaire_Final_ENGLISH.pdf", + "role": "English questionnaire", + "page_or_section": "page 6", + "sha256": "1e61a93c1ad6335252669d575a13abc32d6896c5f94976ad8af0bfd6ec0fb1c8" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Morocco 2023/2023_Maroc_(Fes)_Codebook.pdf", + "role": "raw codebook", + "page_or_section": "pages 7-8", + "sha256": "421674738047d4c5b42bf78ec9cd8db3b1612c1288bc4dfa8cee91544b581b32" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Morocco 2023/2023_Maroc_(Fes)_Binary_Codebook.pdf", + "role": "binary codebook", + "page_or_section": "pages 7-8", + "sha256": "d676ed96cb4f20330657e7b8fe95291b986c55b766568b054c0cae3f16fc0367" + } + ], + "question_numbers": { + "ideation": "Q32", + "plan": "Q33", + "attempt": "Q34" + }, + "source_language_evidence": [ + "French", + "English reference" + ], + "note": "Available-language documents do not by themselves prove the language actually administered to every respondent." + }, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "AFG_2014_GSHS_v01::afg2014_public_use", + "reference_id": "AFG_2014_GSHS_v01", + "catalog_id": "484", + "country": "Afghanistan", + "iso3": "AFG", + "collection_start": "2014", + "survey_component": "Afghanistan public-use dataset", + "survey_scope": "component", + "population": "school-attending students; 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exact sampled ages/grades remain pending component source review", + "observed_rows": 919, + "canonical_relative_path": "raw/microdata/WLF_2023_GSHS_v01/WLF-2023.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/994", + "primary_outcomes_observed": true, + "variables": { + "raw_mh_considersui": { + "nonmissing": 894, + "value_counts": { + "1": 224, + "2": 670 + } + }, + "raw_mh_plansui": { + "nonmissing": 907, + "value_counts": { + "1": 257, + "2": 650 + } + }, + "raw_mh_attemptsui": { + "nonmissing": 905, + "value_counts": { + "1": 707, + "2": 109, + "3": 57, + "4": 15, + "5": 17 + } + }, + "raw_mh_b_considersui": { + "nonmissing": 894, + "value_counts": { + "1": 224, + "2": 670 + } + }, + "raw_mh_b_plansui": { + "nonmissing": 907, + "value_counts": { + "1": 257, + "2": 650 + } + }, + "raw_mh_b_attemptsui": { + "nonmissing": 905, + "value_counts": { + "1": 198, + "2": 707 + } + } + }, + "source_package": { + "status": "local_questionnaire_and_codebooks_located", + "documents": [ + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Wallis and Futuna 2023/Wallis and Futuna - GSHS Questionnaire - Final - French.docx", + "role": "French questionnaire", + "page_or_section": "Q29-Q31", + "sha256": "9dd9f6bbb798cda611ea7c91a04b39dd4cc68dadeaadfb7322e3582e0acf3d33" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Wallis and Futuna 2023/Wallis and Futuna - GSHS Questionnaire - Final - English.docx", + "role": "English questionnaire", + "page_or_section": "Q29-Q31", + "sha256": "655adba3230750c21b7de7dfbebceb93e1d776ec7bcfd0568a487d1dd65fb18f" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Wallis and Futuna 2023/2023 Wallis and Futuna Codebook.docx", + "role": "raw codebook", + "page_or_section": "MH_CONSIDERSUI through MH_ATTEMPTSUI", + "sha256": "c61028983ec57ed6618a2d23ec6dc2dd370b85a50b7f2e0aa283b0ea8201d259" + }, + { + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire/GSHS Per Country/Wallis and Futuna 2023/2023 Wallis and Futuna Binary_Codebook.docx", + "role": "binary codebook", + "page_or_section": "MH_B_CONSIDERSUI through MH_B_ATTEMPTSUI", + "sha256": "fa38d372dfa50912b4178e46e7f8ea680cdbc0447b20fcc9d3f6258fb941dde4" + } + ], + "question_numbers": { + "ideation": "Q29", + "plan": "Q30", + "attempt": "Q31" + }, + "source_language_evidence": [ + "French", + "English reference" + ], + "note": "Available-language documents do not by themselves prove the language actually administered to every respondent." + }, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "WSM_2011_GSHS_v01::wsm2011_public_use", + "reference_id": "WSM_2011_GSHS_v01", + "catalog_id": "205", + "country": "Samoa", + "iso3": "WSM", + "collection_start": "2011-03", + "survey_component": "National public-use dataset", + "survey_scope": "national", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 2418, + "canonical_relative_path": "raw/microdata/WSM_2011_GSHS_v01/WSM2011_Public_Use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/205", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "WSM_2017_GSHS_v01::wsh2017_gshs_data_public_use", + "reference_id": "WSM_2017_GSHS_v01", + "catalog_id": "773", + "country": "Samoa", + "iso3": "WSM", + "collection_start": "2017", + "survey_component": "", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 1955, + "canonical_relative_path": "raw/microdata/WSM_2017_GSHS_v01/WSH2017_GSHS_Data_Public_Use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/773", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "YEM_2008_GSHS_v01::yem2008_public_use", + "reference_id": "YEM_2008_GSHS_v01", + "catalog_id": "77", + "country": "Yemen", + "iso3": "YEM", + "collection_start": "2008-02", + "survey_component": "Yemen public-use dataset", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 1175, + "canonical_relative_path": "raw/microdata/YEM_2008_GSHS_v01/YEM2008_public_use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/77", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "YEM_2014_GSHS_v01::yeh2014_public_use", + "reference_id": "YEM_2014_GSHS_v01", + "catalog_id": "658", + "country": "Yemen", + "iso3": "YEM", + "collection_start": "2014", + "survey_component": "", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 2655, + "canonical_relative_path": "raw/microdata/YEM_2014_GSHS_v01/YEH2014_Public_Use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/658", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "ZMB_2004_GSHS_v01::zmh2004_public_use", + "reference_id": "ZMB_2004_GSHS_v01", + "catalog_id": "8", + "country": "Zambia", + "iso3": "ZMB", + "collection_start": "2004-06", + "survey_component": "National public-use dataset", + "survey_scope": "national", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 2257, + "canonical_relative_path": "raw/microdata/ZMB_2004_GSHS_v01/ZMH2004_public_use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/8", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "ZWE_2003_GSHS_v01::zwah2003_public_use", + "reference_id": "ZWE_2003_GSHS_v01", + "catalog_id": "9", + "country": "Zimbabwe", + "iso3": "ZWE", + "collection_start": "2003-10", + "survey_component": "Bulawayo public-use dataset", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 1804, + "canonical_relative_path": "raw/microdata/ZWE_2003_GSHS_v01/ZWAH2003_public_use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/9", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "ZWE_2003_GSHS_v01::zwbh2003_public_use", + "reference_id": "ZWE_2003_GSHS_v01", + "catalog_id": "9", + "country": "Zimbabwe", + "iso3": "ZWE", + "collection_start": "2003-10", + "survey_component": "Harare public-use dataset", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 1997, + "canonical_relative_path": "raw/microdata/ZWE_2003_GSHS_v01/ZWBH2003_public_use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/9", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + }, + { + "component_id": "ZWE_2003_GSHS_v01::zwch2003_public_use", + "reference_id": "ZWE_2003_GSHS_v01", + "catalog_id": "9", + "country": "Zimbabwe", + "iso3": "ZWE", + "collection_start": "2003-10", + "survey_component": "Manicaland public-use dataset", + "survey_scope": "component", + "population": "school-attending students; exact sampled ages/grades remain pending component source review", + "observed_rows": 1864, + "canonical_relative_path": "raw/microdata/ZWE_2003_GSHS_v01/ZWCH2003_public_use.dta", + "catalog_url": "https://extranet.who.int/ncdsmicrodata/index.php/catalog/9", + "primary_outcomes_observed": false, + "variables": { + "raw_mh_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_attemptsui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_considersui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_plansui": { + "nonmissing": 0, + "value_counts": {} + }, + "raw_mh_b_attemptsui": { + "nonmissing": 0, + "value_counts": {} + } + }, + "source_package": null, + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null + } + ], + "review_boundary": { + "human_reviewers_required": 2, + "ai_review_is_human_review": false, + "population_scope_approved": false, + "missing_rules_approved": false, + "cross_component_equivalence_approved": false, + "confirmatory_analysis_allowed": false + } +} diff --git a/research/stage1/gshs_primary_outcome_component_audit.md b/research/stage1/gshs_primary_outcome_component_audit.md new file mode 100644 index 0000000..92bbc9f --- /dev/null +++ b/research/stage1/gshs_primary_outcome_component_audit.md @@ -0,0 +1,43 @@ +# GSHS primary-outcome component audit + +Version: 1.0 | Status: provisional | Generated: 2026-09-20 + +## Result + +The selected GSHS master table contains 191 components and 673,499 rows. Exactly 7 components contain the three primary suicide outcomes; the remaining 184 contain no observed values in those six columns. Metadata row counts match the consolidated table for all components. + +The country questionnaires and ordinary codebooks identify three administered items: past-12-month suicide ideation, plan, and attempt frequency. The Binary Codebooks identify the `_b_` columns as binary indicators derived from those items. Row-level checks are exact: ideation and plan binary columns duplicate the raw yes/no coding, while attempt maps 0 times to No and one or more times to Yes. Therefore the `_b_` columns must not be counted as independent administered items. + +## Components with observed primary outcomes + +| Component | Country | Rows | Ideation nonmissing | Plan nonmissing | Attempt nonmissing | Direct local sources | +|---|---|---:|---:|---:|---:|---| +| `2023_MAR_GSHS_v01::mar_fez2023` | Morocco | 4,172 | 3,994 | 4,019 | 4,086 | local_questionnaire_and_codebooks_located | +| `GHA_2022_GSHS_v01::gha_sek_tak2022` | Ghana | 3,796 | 3,645 | 3,645 | 3,682 | local_questionnaire_and_codebooks_located | +| `IND_2022_GSHS_v01::ind_jaipur_2022` | India | 4,299 | 4,174 | 4,106 | 4,228 | local_questionnaire_and_codebooks_located | +| `JAM_2023_GSHS_v01::jam_st_cath_2023` | Jamaica | 3,041 | 2,879 | 2,850 | 2,936 | local_questionnaire_and_codebooks_located | +| `MNG_2023_GSHS_v01::mng2023` | Mongolia | 3,311 | 3,274 | 3,258 | 3,238 | local_questionnaire_and_codebooks_located | +| `SLB_2023_GSHS_v01::slb_2023` | Solomon Islands | 1,995 | 1,890 | 1,953 | 1,963 | pending_local_direct_source | +| `WLF_2023_GSHS_v01::wlf_2023` | Wallis and Futuna | 919 | 894 | 907 | 905 | local_questionnaire_and_codebooks_located | + +## Representation checks + +| Raw item | Binary representation | Result | Observed mapping | +|---|---|---|---| +| `raw_mh_considersui` | `raw_mh_b_considersui` | passed | ->: 652,749; 1->1: 4,854; 2->2: 15,896 | +| `raw_mh_plansui` | `raw_mh_b_plansui` | passed | ->: 652,761; 1->1: 4,363; 2->2: 16,375 | +| `raw_mh_attemptsui` | `raw_mh_b_attemptsui` | passed | ->: 652,461; 1->2: 16,732; 2->1: 2,457; 3->1: 1,139; 4->1: 325; 5->1: 385 | + +## Source boundary + +Local questionnaires plus raw and binary codebooks were located for 6 of the 7 components: Ghana, India, Jamaica, Mongolia, Morocco, and Wallis and Futuna. No country-specific Solomon Islands 2023 questionnaire/codebook was found locally, so that component remains pending direct-source acquisition. + +Available English/French/Mongolian files establish wording evidence but do not by themselves prove the language administered to every respondent. Exact sampled ages/grades, component-specific eligibility, and canonical missing reasons also remain unresolved. + +## Gate 1 decision + +Gate 1 remains **in progress**. This audit resolves the 191-component coverage question and the raw-versus-`_b_` representation issue, but it does not satisfy the population/missing-rule or two-human-reviewer requirements. All records remain provisional and are not approved for confirmatory analysis or anchor construction. + +## Reproduction + +Run `research/stage1/audit_gshs_primary_outcome_components.py` in the project Python environment. The implementation streams the consolidated CSV and does not load it into pandas memory. diff --git a/research/stage1/primary_outcome_registry.json b/research/stage1/primary_outcome_registry.json index 2f3080b..efe65e5 100644 --- a/research/stage1/primary_outcome_registry.json +++ b/research/stage1/primary_outcome_registry.json @@ -1,5 +1,5 @@ { - "schema_version": "1.1", + "schema_version": "1.2", "generated_on": "2026-09-20", "status": "provisional", "allowed_uses": [ @@ -16,11 +16,8 @@ "survey": "GSHS", "year": null, "source_variable": "raw_mh_attemptsui", - "construct": "suicide_attempt", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", "source_label": "Attempted suicide in past 12 mos", "answer_options": { "1": "0 times", @@ -30,140 +27,71 @@ "5": "6 or more times" }, "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", "source_url": null, - "page_or_section": "Master_Columns", + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", "review_status": "provisional", "reviewer_1": null, "reviewer_2": null, "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." - }, - { - "survey": "GSHS", - "year": null, - "source_variable": "raw_mh_b_attemptsui", "construct": "suicide_attempt", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, - "source_label": "Attempted suicide | Attempted suicide in past 12 mos", - "answer_options": { - "1": "Yes", - "2": "No" - }, - "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", - "source_url": null, - "page_or_section": "Master_Columns", - "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", - "review_status": "provisional", - "reviewer_1": null, - "reviewer_2": null, - "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." - }, - { - "survey": "GSHS", - "year": null, - "source_variable": "raw_mh_b_considersui", - "construct": "suicide_ideation", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, - "source_label": "Seriously considered attempting suicide | Seriously considered attempting suicide in past 12 mos", - "answer_options": { - "1": "Yes", - "2": "No" - }, - "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", - "source_url": null, - "page_or_section": "Master_Columns", - "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", - "review_status": "provisional", - "reviewer_1": null, - "reviewer_2": null, - "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." - }, - { - "survey": "GSHS", - "year": null, - "source_variable": "raw_mh_b_plansui", - "construct": "suicide_plan", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, - "source_label": "Made a plan about how they would attempt suicide | Made a plan about how they would attempt suicide in past 12 mos", - "answer_options": { - "1": "Yes", - "2": "No" - }, - "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", - "source_url": null, - "page_or_section": "Master_Columns", - "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", - "review_status": "provisional", - "reviewer_1": null, - "reviewer_2": null, - "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." + "record_type": "administered_raw_candidate", + "question_text": "During the past 12 months, how many times did you attempt suicide?", + "notes": "Country questionnaires and ordinary codebooks identify this as an administered item. Solomon Islands 2023 direct local source remains pending; population and missing rules are not approved." }, { "survey": "GSHS", "year": null, "source_variable": "raw_mh_considersui", - "construct": "suicide_ideation", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", "source_label": "Considered suicide in past 12 mos", "answer_options": { "1": "Yes", "2": "No" }, "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", "source_url": null, - "page_or_section": "Master_Columns", + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", "review_status": "provisional", "reviewer_1": null, "reviewer_2": null, "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." + "construct": "suicide_ideation", + "record_type": "administered_raw_candidate", + "question_text": "During the past 12 months, did you seriously consider attempting suicide?", + "notes": "Country questionnaires and ordinary codebooks identify this as an administered item. Solomon Islands 2023 direct local source remains pending; population and missing rules are not approved." }, { "survey": "GSHS", "year": null, "source_variable": "raw_mh_plansui", - "construct": "suicide_plan", - "record_type": "raw_candidate", - "population": "school-attending students; exact component ages pending source review", - "time_window": "past 12 months (from source label; questionnaire verification pending)", - "question_text": null, + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", "source_label": "Made a suicide plan in past 12 mos", "answer_options": { "1": "Yes", "2": "No" }, "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", "source_url": null, - "page_or_section": "Master_Columns", + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", "present_in_local_data": true, - "source_verification_status": "pending_questionnaire_review", + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", "review_status": "provisional", "reviewer_1": null, "reviewer_2": null, "link_status": "not_evaluated", - "notes": "The `_b_` and unprefixed forms remain separate item versions; labels alone do not prove equivalence." + "construct": "suicide_plan", + "record_type": "administered_raw_candidate", + "question_text": "During the past 12 months, did you make a plan about how you would attempt suicide?", + "notes": "Country questionnaires and ordinary codebooks identify this as an administered item. Solomon Islands 2023 direct local source remains pending; population and missing rules are not approved." }, { "survey": "YRBS", @@ -2307,6 +2235,90 @@ } ], "derived_records_not_independent_items": [ + { + "survey": "GSHS", + "year": null, + "source_variable": "raw_mh_b_attemptsui", + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", + "source_label": "Attempted suicide | Attempted suicide in past 12 mos", + "answer_options": { + "1": "Yes", + "2": "No" + }, + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", + "source_url": null, + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", + "present_in_local_data": true, + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null, + "link_status": "not_evaluated", + "construct": "suicide_attempt", + "record_type": "derived_or_duplicate_binary_indicator", + "question_text": null, + "derived_from": "raw_mh_attemptsui", + "derivation_rule": "1=Yes when attempt frequency is one or more; 2=No when frequency is zero", + "notes": "Binary Codebooks and exact row-level mapping show this is not an independent administered item." + }, + { + "survey": "GSHS", + "year": null, + "source_variable": "raw_mh_b_considersui", + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", + "source_label": "Seriously considered attempting suicide | Seriously considered attempting suicide in past 12 mos", + "answer_options": { + "1": "Yes", + "2": "No" + }, + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", + "source_url": null, + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", + "present_in_local_data": true, + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null, + "link_status": "not_evaluated", + "construct": "suicide_ideation", + "record_type": "derived_or_duplicate_binary_indicator", + "question_text": null, + "derived_from": "raw_mh_considersui", + "derivation_rule": "identity binary representation", + "notes": "Binary Codebooks and exact row-level mapping show this is not an independent administered item." + }, + { + "survey": "GSHS", + "year": null, + "source_variable": "raw_mh_b_plansui", + "population": "school-attending students; exact component ages/grades pending source review", + "time_window": "past 12 months", + "source_label": "Made a plan about how they would attempt suicide | Made a plan about how they would attempt suicide in past 12 mos", + "answer_options": { + "1": "Yes", + "2": "No" + }, + "source_file": "Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx", + "component_audit_file": "research/stage1/gshs_primary_outcome_component_audit.json", + "source_url": null, + "page_or_section": "Master_Columns plus component-specific questionnaire/codebook references in component audit", + "present_in_local_data": true, + "source_verification_status": "direct_local_sources_verified_for_six_of_seven_observed_components", + "review_status": "provisional", + "reviewer_1": null, + "reviewer_2": null, + "link_status": "not_evaluated", + "construct": "suicide_plan", + "record_type": "derived_or_duplicate_binary_indicator", + "question_text": null, + "derived_from": "raw_mh_plansui", + "derivation_rule": "identity binary representation", + "notes": "Binary Codebooks and exact row-level mapping show this is not an independent administered item." + }, { "survey": "NSDUH", "year": 2021, diff --git a/research/stage1/primary_outcome_registry.md b/research/stage1/primary_outcome_registry.md index 436f822..274b4bf 100644 --- a/research/stage1/primary_outcome_registry.md +++ b/research/stage1/primary_outcome_registry.md @@ -1,6 +1,6 @@ # Primary outcome source registry -Version: 1.1 | Status: provisional | Generated: 2026-09-20 +Version: 1.2 | Status: provisional | Generated: 2026-09-20 ## Scope and decision boundary @@ -10,7 +10,7 @@ This registry captures source-linked candidates for suicide ideation, plan, and | Survey | Ideation | Plan | Attempt | Current evidence boundary | |---|---:|---:|---:|---| -| GSHS | 2 | 2 | 2 | Workbook labels/options only; component questionnaires still require direct review. | +| GSHS | 1 | 1 | 1 | Three administered items occur in 7/191 components; local direct sources cover 6/7, with Solomon Islands pending. | | YRBS | 17 | 17 | 17 | 51 annual candidates; 2021/2023 data remain quarantined; annual PDFs require direct review. | | NSDUH | 4 | 4 | 4 | Attempt is administered as YSUI03/YUSUICTRY, but the raw and recoded attempt fields are absent from the local public-use package. | @@ -18,7 +18,7 @@ Counts are source-record counts, not distinct item families. YRBS counts include ## Material conflicts and exclusions -- GSHS exposes both `_b_` and unprefixed variants. They differ in naming and, for attempt, response form (binary versus frequency). They remain separate until questionnaire/component provenance is verified. +- GSHS ordinary codebooks identify the three unprefixed variables as administered items. Binary Codebooks plus exact row-level relations identify the three `_b_` columns as derived or duplicate representations, not independent items. - GSHS self-harm variables are not included as suicide-attempt items. - YRBS metadata contains stale absolute paths from another machine and some automatically extracted neighboring-text contamination. Only exact primary-construct rows were retained, and their direct PDF review is still pending. - YRBS 2021 and 2023 item metadata are retained for future migration checks, but their respondent data are quarantined pending layout/import validation. @@ -28,7 +28,7 @@ Counts are source-record counts, not distinct item families. YRBS counts include ## Gate 1 status -Gate 1 remains **in progress**. Before any candidate can enter confirmatory analysis, the project still needs direct official questionnaire/codebook review, exact population and skip-logic verification, canonical response/missing rules, component-specific GSHS provenance, and two actual human reviewers for primary outcomes. +Gate 1 remains **in progress**. Before any candidate can enter confirmatory analysis, the project still needs direct YRBS and Solomon Islands GSHS source review, exact population and skip-logic verification, canonical response/missing rules, and two actual human reviewers for primary outcomes. ## Reproduction