| condition,campaign,run_id,study_id,pmid,status,termination_reason,started_at,ended_at,human_scientific_interventions,autonomous_continuations,infrastructure_restarts,num_transcript_files,num_trajectory_events,result_summary_json |
| self-driving-aeris,r8404,codex-aeris-self-driving-33227571-sao-paulo-ami-r8404-20260925T152739Z,,33227571,completed_blocker,,2026-09-25T15:27:46.588219+00:00,2026-09-25T15:45:41.721304+00:00,0,1,0,0,0,"{""schema_version"": 3, ""study_id"": ""33227571-sao-paulo-ami"", ""status"": ""completed_blocker"", ""fidelity"": ""none"", ""target"": {""outcome"": ""Daily acute myocardial infarction admissions and in-hospital mortality"", ""pollutant"": ""NO2, PM2.5, and PM10"", ""geography"": ""39 municipalities of metropolitan Sao Paulo, Brazil"", ""population"": ""Acute myocardial infarction patients admitted in the 39 metropolitan Sao Paulo municipalities"", ""period"": ""2012-01-01 to 2015-12-31"", ""effect_scale"": ""The supplied abstract reports cluster summaries and p-values; no article-verified effect scale or regression contrast was recovered."", ""exposure_assignment"": ""Daily municipality-region air-pollution and weather features clustered hierarchically; no usable daily pollutant series was recovered."", ""model"": ""Article model form not recoverable from supplied abstract; pollutant-weather cluster comparison cannot be fit without pollutant observations."", ""covariates"": [""temperature"", ""temperature variation"", ""rainfall"", ""relative humidity""], ""named_outcome_source"": ""DataSUS SIH-RD"", ""specification_evidence"": [""/output/article-specification-evidence.md"", ""/study/article.xml"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://api.laundos.com.br/api/ftp-download"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/outcome-checkpoint.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""65f5e2f55e4101fa283b32be44729ec0e0220c370f4fb24377c880372be34410"", ""evidence_artifact"": ""/output/openmeteo-weather-2012.json""}, {""role"": ""exposure"", ""url"": ""OpenAQ boundary route via AERIS"", ""route_origin"": ""agent_discovered"", ""retrieved"": false, ""sha256"": ""68e86022323230543e0754a99ea87595e5e15e57ece0afed884c4cc424d7a91e"", ""evidence_artifact"": ""/output/aeris-workspace/.aeris/artifacts/exposure_pm10_2026-09-25T153609.9356110000.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""construct_change"", ""published"": ""Pollutant-weather clusters with NO2, PM2.5, and PM10"", ""reanalysis"": ""No pollutant substitution used; a weather-only diagnostic was retained separately and is not a fit to the target."", ""reason"": ""The retained AERIS PM10 query contains zero stations and 0% temporal coverage; pollutant values were not imputed.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2012-2015"", ""reanalysis"": ""Jan-May 2012 outcome and weather diagnostic slice only"", ""reason"": ""Five verified monthly outcome files were retained before proxy rate limiting; this does not remedy absent pollutant exposure.""}], ""coverage"": {""eligible_units"": 39, ""included_units"": 0, ""eligible_times"": 1461, ""included_times"": 0, ""rule"": ""No outcome-pollutant analytic rows were created because no daily NO2, PM2.5, or PM10 observations overlap the retained outcome data."", ""notes"": ""The retained 152-day weather/outcome panel is a diagnostic bounded sensitivity only; it is excluded from the pollutant-analysis handoff. The AERIS PM10 probe reports 0 stations and 0% coverage.""}, ""artifacts"": {""code"": ""analyze_bounded_slice.py"", ""source_manifest"": ""source-manifest.json"", ""exposure"": ""aeris-workspace/.aeris/artifacts/exposure_pm10_2026-09-25T153609.9356110000.csv"", ""analysis_panel"": ""analysis-panel.csv"", ""model_output"": ""model-output.json"", ""decision_log"": ""decision-log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker-ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T153910.4922070000.json"", ""coverage_diagnostics"": ""coverage-diagnostics.json"", ""counterexample_review"": ""recovery-critic/recovery-counterexample-review.json"", ""boundary_route_evidence"": ""cetesb-no2-layer.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""No usable daily NO2, PM2.5, or PM10 series was recovered for the target geography and period. A fresh counterexample review executed the article-named CETESB portal/client route, catalog and archive routes, and public deposit searches; its retained evidence is /output/recovery-critic/recovery-counterexample-review.json."", ""The supplied article materials are an abstract/citation; the precise fitted model and cluster implementation were not recoverable from lawful full-text routes."", ""The retained DataSUS outcome records and weather series cannot form an article-aligned pollutant-exposure panel in the absence of pollutant observations.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": true, ""historical_fallback_tested"": true, ""geographic_batching_applicable"": false, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/aeris-workspace/.aeris/artifacts/exposure_pm10_2026-09-25T153609.9356110000.csv"", ""/output/openmeteo-weather-2012.json"", ""/output/outcome-checkpoint.json"", ""aeris-workspace/.aeris/artifacts/exposure_pm10_2026-09-25T153609.9356110000.csv"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T153910.4922070000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis-panel.csv"", ""analyze_bounded_slice.py"", ""blocker-ledger.json"", ""cetesb-no2-layer.json"", ""coverage-diagnostics.json"", ""decision-log.json"", ""model-output.json"", ""recovery-critic/recovery-counterexample-review.json"", ""source-manifest.json""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-33398753-italy-cities-r8404-20260925T154625Z,,33398753,completed_fit,,2026-09-25T15:46:33.426828+00:00,2026-09-25T15:56:39.667183+00:00,0,0,0,0,0,"{""schema_version"": 3, ""study_id"": ""33398753-italy-cities"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Cumulative confirmed COVID-19 infections on 17 March, 7 April, and 27 April 2020"", ""pollutant"": ""PM10"", ""geography"": ""Italian provincial-capital cities"", ""population"": ""Residents of 55 provincial-capital cities"", ""period"": ""2018 exposure; first-wave 2020 infection outcomes"", ""effect_scale"": ""Outcome ratio per doubling of annual PM10 exceedance days"", ""exposure_assignment"": ""Nearest EEA E1a validated daily PM10 monitor within 50 km of municipal-capital centroid"", ""model"": ""OLS log(infections) on log(PM10 exceedance days) and log(2019 municipal population density)"", ""covariates"": [""2019 municipal population density""], ""named_outcome_source"": ""Italian Civil Protection Department provincial daily COVID-19 archive"", ""specification_evidence"": [""/study/article.md (Data and study design; Table 6)"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""exposure"", ""url"": ""https://eeadmz1-downloads-api-appservice.azurewebsites.net/ParquetFile/urls"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/eea_pm10_urls.txt""}, {""role"": ""exposure"", ""url"": ""https://air.discomap.eea.europa.eu/arcgis/rest/services/AirQuality/AirQualityDownloadServiceEUMonitoringStations/MapServer/0/query"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/eea_stations_it.geojson""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-province/dpc-covid19-ita-province-20200407.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/covid_province_20200407.csv""}, {""role"": ""covariate"", ""url"": ""https://raw.githubusercontent.com/opendatasicilia/comuni-italiani/main/dati/gb_main_comuni_italiani.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/gb_main_comuni_italiani.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Regional environmental agency/Legambiente city values with unspecified assignments"", ""reanalysis"": ""EEA E1a daily validated monitor data assigned to city centroids"", ""reason"": ""Original exposure values and assignments were not supplied.""}, {""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""City infections from Ministry of Health"", ""reanalysis"": ""Official provincial cumulative cases joined to provincial capitals"", ""reason"": ""Public historical official outcome data are province-level.""}, {""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""Unidentified random sample of 55 cities"", ""reanalysis"": ""55 hash-selected cities among 97 eligible capitals"", ""reason"": ""Original city identities unavailable; hash selection is independent of values.""}], ""coverage"": {""eligible_units"": 97, ""included_units"": 55, ""eligible_times"": 365, ""included_times"": 365, ""rule"": ""Nearest monitor within 50 km, at least 75% valid 2018 daily data, positive exposure and outcomes; retain 55 eligible capitals by SHA256 rank."", ""notes"": ""All selected cities have 365 valid daily PM10 values (100% coverage); nearest-monitor distance 0.08-45.43 km.""}, ""artifacts"": {""code"": ""reanalysis/run_reanalysis.py"", ""source_manifest"": ""reanalysis/source_manifest.json"", ""exposure"": ""reanalysis/analysis_panel.csv"", ""analysis_panel"": ""reanalysis/analysis_panel.csv"", ""model_output"": ""reanalysis/model_output.json"", ""decision_log"": ""reanalysis/decision_log.json"", ""research_notebook"": ""research-notebook.json"", ""blocker_ledger"": ""reanalysis/blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T155524.0534200000.json"", ""coverage_diagnostics"": ""reanalysis/coverage_diagnostics.csv"", ""boundary_route_evidence"": ""reanalysis/eea_stations_it.geojson"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Original 55 city identities, city-level outcome counts, original monitor assignments, and original exposure values were not available. The fitted analysis therefore uses explicit bounded source/geographic substitutions.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/reanalysis/covid_province_20200407.csv"", ""/output/reanalysis/eea_pm10_urls.txt"", ""/output/reanalysis/eea_stations_it.geojson"", ""/output/reanalysis/gb_main_comuni_italiani.csv"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T155524.0534200000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""reanalysis/analysis_panel.csv"", ""reanalysis/blocker_ledger.json"", ""reanalysis/coverage_diagnostics.csv"", ""reanalysis/decision_log.json"", ""reanalysis/eea_stations_it.geojson"", ""reanalysis/model_output.json"", ""reanalysis/run_reanalysis.py"", ""reanalysis/source_manifest.json"", ""research-notebook.json""]}, ""design_provenance"": {""contract_id"": ""33398753-italy-cities-reanalysis-invariants"", ""contract_sha256"": ""1ebe60e3e36aedc05c8fa49daa8e9103c43ca3c1d54719c09c3b09d0fbb18678"", ""contract_author"": ""agent"", ""geographic_representation"": ""fixed_location"", ""assignment_method"": ""nearest EEA E1a validated PM10 monitor to municipal-capital centroid, restricted to 50 km"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Number of 2018 calendar days with valid daily PM10 concentration strictly above 50 \u00b5g/m\u00b3"", ""coverage_policy"": {""mode"": ""report_and_deterministic_subset"", ""minimum_percent"": 75, ""threshold_source"": ""feasibility criterion, not article-mandated"", ""evidence"": ""A full calendar year has 365 days; 75% valid daily coverage is a transparent eligibility rule for a bounded public-monitor reanalysis. Coverage will be reported for all cities and a deterministic 55-city subset chosen only among eligible cities.""}, ""decision_rationale"": ""The article does not report station assignments or a numeric completeness rule. The EEA E1a archive supplies complete public, validated, daily PM10 observations for 2018, enabling a city-centroid monitor assignment consistent with the article's city-level construct while making coverage and distance explicit."", ""evidence_basis"": [""Official EEA API contract identifies Parquet time-series download endpoints and country/pollutant filters."", ""EEA E1a PM10 request for Italy produced a positive file summary."", ""EEA monitoring-station service yielded 763 Italian stations with coordinates and station identifiers.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""2020-03-17 infections: adjusted outcome ratio per doubling PM10 exceedance days"", ""primary"": false, ""estimate"": 1.3435653925850417, ""ci_low"": 1.043821446504452, ""ci_high"": 1.7293838617680655, ""contrast"": ""doubling of 2018 annual PM10 exceedance days"", ""native_estimate"": 0.4260665403777016, ""native_ci_low"": 0.061874949193850004, ""native_ci_high"": 0.7902581315615531, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log exceedance days"", ""scale"": ""ratio"", ""metric"": ""outcome_ratio""}, {""label"": ""2020-04-07 infections: adjusted outcome ratio per doubling PM10 exceedance days"", ""primary"": true, ""estimate"": 1.2383041226221332, ""ci_low"": 1.0204380635960901, ""ci_high"": 1.5026851259342286, ""contrast"": ""doubling of 2018 annual PM10 exceedance days"", ""native_estimate"": 0.3083656782968981, ""native_ci_low"": 0.029188619357924717, ""native_ci_high"": 0.5875427372358715, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log exceedance days"", ""scale"": ""ratio"", ""metric"": ""outcome_ratio""}, {""label"": ""2020-04-27 infections: adjusted outcome ratio per doubling PM10 exceedance days"", ""primary"": false, ""estimate"": 1.225603992989012, ""ci_low"": 1.0093506536749286, ""ci_high"": 1.488189602059125, ""contrast"": ""doubling of 2018 annual PM10 exceedance days"", ""native_estimate"": 0.2934929026497094, ""native_ci_low"": 0.0134274612965401, ""native_ci_high"": 0.5735583440028786, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log exceedance days"", ""scale"": ""ratio"", ""metric"": ""outcome_ratio""}], ""analysis_diagnostics"": {""observations"": 55, ""estimated_parameters"": 3, ""exposure_unique_values"": 28, ""outcome_unique_values"": 52, ""joined_rows"": 55, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""17 March 2020"", ""7 April 2020 (primary)"", ""27 April 2020""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-33484722-oecd-covid-r8404-20260925T160112Z,,33484722,completed_fit,,2026-09-25T16:01:21.316498+00:00,2026-09-25T16:07:41.047802+00:00,0,0,0,0,0,"{""schema_version"": 3, ""study_id"": ""33484722-oecd-covid"", ""status"": ""completed_fit"", ""fidelity"": ""source_substitution"", ""target"": {""outcome"": ""Log cumulative confirmed COVID-19 case rate and log death rate at days 60 and 80 after each country's first confirmed case"", ""pollutant"": ""PM2.5"", ""geography"": ""36 OECD countries listed in article Methods 2.1"", ""population"": ""National populations of the 36 countries"", ""period"": ""2017 annual PM2.5; country-specific 2020 epidemic day 60 and day 80 outcomes"", ""effect_scale"": ""Rate ratio per 1 ug/m3 PM2.5, from exponentiated OLS coefficient on log rate"", ""exposure_assignment"": ""Direct national population-weighted annual World Bank PM2.5 indicator (EN.ATM.PM25.MC.M3)"", ""model"": ""Separate conventional OLS regressions of log case/death rate at days 60 and 80, adjusted for article Table 1 covariates"", ""covariates"": [""age 65+ percentage"", ""population density"", ""GDP per capita (thousand USD)"", ""physicians per 100,000"", ""hospital beds per 100,000"", ""population exposed above WHO PM2.5 guideline percentage""], ""named_outcome_source"": ""WHO daily COVID-19 data in article; independently recovered from JHU CSSE global time series"", ""specification_evidence"": [""/output/article-specification.md"", ""/study/article.md"", ""/study/supplements/mmc1.docx""]}, ""sources"": [{""role"": ""exposure"", ""url"": ""https://api.worldbank.org/v2/country/all/indicator/EN.ATM.PM25.MC.M3?format=json&per_page=20000"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/worldbank_EN.ATM.PM25.MC.M3.json""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/jhu_confirmed_global.csv""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/jhu_deaths_global.csv""}, {""role"": ""covariate"", ""url"": ""https://api.worldbank.org/v2/country/all/indicator/"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/source_manifest.json""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""WHO daily country COVID-19 data"", ""reanalysis"": ""JHU CSSE global historical country time series"", ""reason"": ""Independent executable public historical source used to reconstruct first-case dates and country-specific day 60/80 counts.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""US physician density in article's 2015-17 fallback window"", ""reanalysis"": ""2018 World Bank physician density for US"", ""reason"": ""Current WDI response contains no US value in 2015-17; nearest available WDI record retained the full 36-country model.""}], ""coverage"": {""eligible_units"": 36, ""included_units"": 36, ""eligible_times"": 2, ""included_times"": 2, ""rule"": ""Report-only completeness; article gives no numeric threshold."", ""notes"": ""All 36 countries have retrieved 2017 PM2.5, all specified covariates, and positive day-60/day-80 case and death rates. See coverage_report.json.""}, ""artifacts"": {""code"": ""retrieve_and_fit.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""analysis_panel.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T160603.9437680000.json"", ""coverage_diagnostics"": ""coverage_report.json"", ""boundary_route_evidence"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Exact WHO source snapshot not used; JHU source substitution documented."", ""US physician covariate uses 2018 due to absent 2015-17 current-WDI record.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 2, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""source_substitution""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/raw/jhu_confirmed_global.csv"", ""/output/raw/jhu_deaths_global.csv"", ""/output/raw/worldbank_EN.ATM.PM25.MC.M3.json"", ""/output/source_manifest.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T160603.9437680000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""coverage_report.json"", ""decision_log.json"", ""model_output.json"", ""retrieve_and_fit.py"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""33484722-oecd-covid-reanalysis-invariants"", ""contract_sha256"": ""192d816b2bc411e226f61c3669e1ba15b2057ddebc91fe5a93381afae5ab3980"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Direct retrieval of World Bank national population-weighted exposure indicator; no monitor assignment."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""provider_api"", ""exposure_metric"": ""2017 annual population-weighted PM2.5 mean (ug/m3), World Bank EN.ATM.PM25.MC.M3."", ""coverage_policy"": {""mode"": ""report-only"", ""minimum_percent"": null, ""threshold_source"": ""Article does not state a numerical coverage threshold."", ""evidence"": ""All 36 listed countries have independently retrieved 2017 PM2.5 values; documented in coverage_report.json.""}, ""decision_rationale"": ""The article's exposure is already an administrative population-weighted annual metric, so deriving unweighted monitor means would change the construct. Direct World Bank indicator retrieval preserves the specified spatial support."", ""evidence_basis"": [""36/36 eligible countries have 2017 PM2.5 exposure records and complete analysis rows."", ""Executable direct World Bank API retrieval and annual country-level integration.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Day-60 case-rate ratio"", ""primary"": true, ""estimate"": 1.1346876449, ""ci_low"": 0.9566246783, ""ci_high"": 1.3458946658, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 increase in 2017 population-weighted PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.1263574104, ""native_ci_low"": -0.0443441502, ""native_ci_high"": 0.2970589709, ""native_scale"": ""log rate difference"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""Day-60 death-rate ratio"", ""primary"": true, ""estimate"": 1.0569050086, ""ci_low"": 0.8657046289, ""ci_high"": 1.2903340931, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 increase in 2017 population-weighted PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.055344834, ""native_ci_low"": -0.1442115037, ""native_ci_high"": 0.2549011717, ""native_scale"": ""log rate difference"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""Day-80 case-rate ratio"", ""primary"": true, ""estimate"": 1.0752178952, ""ci_low"": 0.9442740176, ""ci_high"": 1.2243199544, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 increase in 2017 population-weighted PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.0725233343, ""native_ci_low"": -0.0573388821, ""native_ci_high"": 0.2023855506, ""native_scale"": ""log rate difference"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""Day-80 death-rate ratio"", ""primary"": true, ""estimate"": 1.0262037331, ""ci_low"": 0.8437855939, ""ci_high"": 1.2480588782, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 increase in 2017 population-weighted PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.0258662973, ""native_ci_low"": -0.1698568523, ""native_ci_high"": 0.2215894469, ""native_scale"": ""log rate difference"", ""native_contrast"": ""1 ug/m3 PM2.5""}], ""analysis_diagnostics"": {""observations"": 36, ""estimated_parameters"": 8, ""exposure_unique_values"": 36, ""outcome_unique_values"": 36, ""joined_rows"": 72, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""case day 60"", ""death day 60"", ""case day 80"", ""death day 80""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-34004167-northern-italy-covid-r8404-20260925T134455Z,,34004167,completed_fit,,2026-09-25T13:45:04.222346+00:00,2026-09-25T13:57:01.385918+00:00,0,0,0,0,0,"{""schema_version"": 3, ""study_id"": ""34004167-northern-italy-covid"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Incident daily reported COVID-19 cases and deaths"", ""pollutant"": ""NO2 (with all five article pollutants in native output)"", ""geography"": ""Lombardia and Veneto, Italy"", ""population"": ""Regional residents"", ""period"": ""24 February\u201319 May 2020; 86 of the article's intended 89 days"", ""effect_scale"": ""Rate ratio per 1 microgram per cubic metre"", ""exposure_assignment"": ""Unweighted mean of monitor-level daily means within each documented region polygon; LTAP is 2013\u201319 May 2020 monitor-day mean"", ""model"": ""Pollutant-specific Poisson GEE with log link, AR(1) working correlation, STAP, LTAP, and lockdown"", ""covariates"": [""lockdown""], ""named_outcome_source"": ""Italian Protezione Civile regional COVID-19 series"", ""specification_evidence"": [""/study/article.txt"", ""/study/supplements/mmc1.docx"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""3438a0a85bdb0bca56a48a2edd0c69f3005d6c1c20c4a2a75bed668a8f01ead7"", ""evidence_artifact"": ""/output/recovery/dpc-regioni.csv""}, {""role"": ""exposure"", ""url"": ""https://eeadmz1-downloads-api-appservice.azurewebsites.net/ParquetFile/urls"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/eea_full_transfer.json""}, {""role"": ""boundary"", ""url"": ""https://www.geoboundaries.org/api/current/gbOpen/ITA/ADM2/"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""9baf79eab109cf61989ff45db54ed5a9e5219acc0103062f08d10875855650b1"", ""evidence_artifact"": ""/output/recovery/lombardy_veneto.geojson""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Legacy EEA AirQualityExport route"", ""reanalysis"": ""Current official EEA E1a parquet download API"", ""reason"": ""Legacy route returned HTTP 401; current official EEA records were usable.""}, {""dimension"": ""outcome"", ""change_type"": ""coverage_subset"", ""published"": ""21 February\u201319 May 2020"", ""reanalysis"": ""24 February\u201319 May 2020"", ""reason"": ""The retained public regional outcome CSV starts 24 February; no data were fabricated.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Meteorology-adjusted supplementary sensitivity"", ""reanalysis"": ""Primary lockdown-adjusted model only"", ""reason"": ""Meteorology is supplementary in the article; primary model is retained.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 89, ""included_times"": 86, ""rule"": ""Report-only completeness; retain all dates with at least one regional monitor and retain all two regions."", ""notes"": ""No retained region/pollutant/date has missing STAP. Full retrieval has 408 retained EEA station series and 13,651,225 normalized observations.""}, ""artifacts"": {""code"": ""recovery/recover_eea.py"", ""source_manifest"": ""recovery/source_manifest.json"", ""exposure"": ""recovery/eea_normalized_observations.parquet"", ""analysis_panel"": ""recovery/regional_analysis_panel.csv"", ""model_output"": ""recovery/gee_model_output.csv"", ""decision_log"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""recovery/audit_report.md"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T135504.2614860000.json"", ""coverage_diagnostics"": ""recovery/coverage_diagnostics.json"", ""boundary_route_evidence"": ""recovery/aeris_openaq_checkpoint.json.summary.csv"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Only two regional clusters: GEE robust uncertainty is not reliable for inference."", ""Three intended early dates are absent from retained public outcome data."", ""Meteorology-adjusted supplementary variants were not fit.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/recovery/dpc-regioni.csv"", ""/output/recovery/eea_full_transfer.json"", ""/output/recovery/lombardy_veneto.geojson"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T135504.2614860000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""recovery/aeris_openaq_checkpoint.json.summary.csv"", ""recovery/audit_report.md"", ""recovery/coverage_diagnostics.json"", ""recovery/eea_normalized_observations.parquet"", ""recovery/gee_model_output.csv"", ""recovery/recover_eea.py"", ""recovery/regional_analysis_panel.csv"", ""recovery/source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""34004167-northern-italy-covid-reanalysis-invariants"", ""contract_sha256"": ""a0fbdaa6abd52882b0a1025103a4d38334960095c016479b8ab55d20865b6a52"", ""contract_author"": ""agent"", ""geographic_representation"": ""fixed_location"", ""assignment_method"": ""For each region/pollutant/date, mean each monitor's within-day values then take the unweighted mean across contributing monitors. This is a regional monitor summary, not population-weighted or personal exposure."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""STAP = regional daily mean for 21 February\u201319 May 2020. LTAP = mean of all valid monitor-day concentrations from 1 January 2013 through 19 May 2020 within the same region and pollutant."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only: retain a region/pollutant/day if at least one monitor contributes, and report days and monitor counts. No post-hoc exclusion threshold.""}, ""decision_rationale"": ""The article defines regional daily concentrations and an eight-year regional mean but does not specify a population weighting or numeric completeness threshold. Equal weighting of daily monitor means is an explicit, reproducible regional-monitor interpretation. The current official EEA parquet service is a source/transport modernization of the article-named EEA database, not a change in pollutant, period, region, or metric."", ""evidence_basis"": [""Deterministic 3-sampling-point-per-region/pollutant probe retrieved 29 valid EEA E1a parquet objects; one missing object preserved as a failure."", ""Probe yields 86/89 target-date records per region/pollutant with no missing STAP among retained rows and 2\u20133 contributing monitors per region/pollutant."", ""Executable acquisition, point-in-polygon assignment, validity handling, daily aggregation, and diagnostics code.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""NO2 STAP\u2014incident cases"", ""primary"": true, ""estimate"": 1.0056411416, ""ci_low"": 1.003269188, ""ci_high"": 1.008018703, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3"", ""metric"": ""RR"", ""native_estimate"": 0.0056252899, ""native_ci_low"": 0.003263858, ""native_ci_high"": 0.007986722, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""NO2 LTAP\u2014incident cases"", ""primary"": true, ""estimate"": 1.2700541556, ""ci_low"": 1.2678302168, ""ci_high"": 1.2722819954, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3"", ""metric"": ""RR"", ""native_estimate"": 0.2390595418, ""native_ci_low"": 0.237307, ""native_ci_high"": 0.240812, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""NO2 STAP\u2014incident deaths"", ""primary"": true, ""estimate"": 1.0053099211, ""ci_low"": 1.0041015542, ""ci_high"": 1.0065197422, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3"", ""metric"": ""RR"", ""native_estimate"": 0.0052958732, ""native_ci_low"": 0.004092, ""native_ci_high"": 0.0065, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""NO2 LTAP\u2014incident deaths"", ""primary"": true, ""estimate"": 1.3954764404, ""ci_low"": 1.3942635186, ""ci_high"": 1.3966904175, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3"", ""metric"": ""RR"", ""native_estimate"": 0.3332358913, ""native_ci_low"": 0.332367, ""native_ci_high"": 0.334105, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}], ""analysis_diagnostics"": {""observations"": 172, ""estimated_parameters"": 4, ""exposure_unique_values"": 86, ""outcome_unique_values"": 114, ""joined_rows"": 172, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""incident cases"", ""incident deaths"", ""cumulative-count sensitivity"", ""all five pollutants in native output""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-34488764-france-covid-r8404-20260925T134647Z,,34488764,completed_fit,,2026-09-25T13:46:55.171230+00:00,2026-09-25T14:10:29.516005+00:00,0,1,0,0,0,"{""schema_version"": 3, ""study_id"": ""34488764-france-covid"", ""status"": ""completed_fit"", ""fidelity"": ""source_substitution"", ""target"": {""outcome"": ""Cumulative in-hospital COVID-19 deaths on 1 May 2020"", ""pollutant"": ""PM2.5"", ""geography"": ""96 mainland French departments (NUTS 3)"", ""population"": ""Residents of mainland French departments"", ""period"": ""PM2.5 annual means 1999-2016; COVID-19 outcome through 2020-05-01"", ""effect_scale"": ""mortality rate ratio"", ""exposure_assignment"": ""Unweighted department-polygon mean of annual PM2.5 rasters, then mean across 1999-2016"", ""model"": ""NB2 negative-binomial count regression with log population offset"", ""covariates"": [""temperature"", ""resuscitation beds"", ""intensive-care beds"", ""medical density"", ""age 60+ share"", ""male share"", ""unemployment"", ""poverty"", ""urban population"", ""population density"", ""diabetes""], ""named_outcome_source"": ""French Ministry of Health data.gouv.fr hospital dataset"", ""specification_evidence"": [""/output/article-specification.md""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://static.data.gouv.fr/resources/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/20230331-180159/covid-hospit-2023-03-31-18h01.csv"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/outcome_may1.csv""}, {""role"": ""exposure"", ""url"": ""https://gis.earthdata.nasa.gov/portal/rest/services/sdei/sdei-global-annual-gwr-pm2-5-modis-misr-seawifs-aod-v4-gl-03/ImageServer/exportImage"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/exposure_pm25_department.csv""}, {""role"": ""weather"", ""url"": ""https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_2.5m_tavg.zip"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/temperature_department.csv""}, {""role"": ""boundary"", ""url"": ""https://github.com/wmgeolab/geoBoundaries/raw/9469f09/releaseData/gbOpen/FRA/ADM2/geoBoundaries-FRA-ADM2.geojson"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/source-recovery.md""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Article-described NASA SEDAC/GOME-era gridded PM2.5 product"", ""reanalysis"": ""NASA SEDAC V4.GL.03 ImageServer annual rasters, same 1999-2016 window"", ""reason"": ""Direct public, executable source version.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""WorldClim department temperature mean stated for 2001-2012"", ""reanalysis"": ""WorldClim v2.1 1970-2000 tavg normal zonal mean"", ""reason"": ""Exact time-specific public raster was not directly recovered.""}], ""coverage"": {""eligible_units"": 96, ""included_units"": 96, ""eligible_times"": 18, ""included_times"": 18, ""rule"": ""Report-only coverage; no article-supported numeric exclusion threshold."", ""notes"": ""All 96 departments had all 18 PM2.5 annual means; minimum valid cells per department-year was 129.""}, ""artifacts"": {""code"": ""reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""exposure_pm25_department.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_native_output.json"", ""decision_log"": ""decision_log.md"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.md"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T140521.6565680000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.csv"", ""boundary_route_evidence"": ""source-recovery.md"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""audit"": ""audit.md""}, ""blockers"": [], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""source_substitution""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/exposure_pm25_department.csv"", ""/output/outcome_may1.csv"", ""/output/source-recovery.md"", ""/output/temperature_department.csv"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T140521.6565680000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""audit.md"", ""blocker_ledger.md"", ""coverage_diagnostics.csv"", ""decision_log.md"", ""exposure_pm25_department.csv"", ""model_native_output.json"", ""reanalysis.py"", ""source-recovery.md"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""34488764-france-covid-reanalysis-invariants"", ""contract_sha256"": ""bc8982b466c649401de436c0e48a838cb0743db48ca110aab8ff3489e14a7f71"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""unweighted zonal mean of valid 0.01-degree annual raster cells whose centers lie within each department polygon"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""local_model"", ""exposure_metric"": ""mean of annual mean PM2.5 (\u00b5g/m\u00b3) across 1999\u20132016 for each department"", ""coverage_policy"": {""mode"": ""report-only"", ""minimum_percent"": null, ""threshold_source"": ""No article or source-supported exclusion threshold"", ""evidence"": ""Report raster-cell count and 18-year raster completeness per department; retain valid departments.""}, ""decision_rationale"": ""The article specifies 1 km-grid PM2.5 averaged to departments over 1999\u20132016. Direct extraction of the NASA/SEDAC gridded annual product preserves pollutant, time window, department spatial support, and mean aggregation. The source is a later V4 product/service rather than the article's unrecoverable exact 2016 release, a documented source-version substitution."", ""evidence_basis"": [""NASA/SEDAC ImageServer feasibility probe returned a readable France 1999 PM2.5 GeoTIFF and exposes annual 1998\u20132019 slices; public boundary source has 96 departments.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Continuous PM2.5, fully adjusted"", ""primary"": true, ""estimate"": 1.355144, ""ci_low"": 1.192515, ""ci_high"": 1.539952, ""scale"": ""ratio"", ""contrast"": ""per 1 ug/m3 higher 1999-2016 PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.303908, ""native_ci_low"": 0.176063, ""native_ci_high"": 0.431753, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""per 1 ug/m3""}, {""label"": ""PM2.5 Q2 vs Q1, fully adjusted"", ""primary"": false, ""estimate"": 1.390285, ""ci_low"": 0.938788, ""ci_high"": 2.058922, ""scale"": ""ratio"", ""contrast"": ""Q2 vs Q1"", ""metric"": ""RR"", ""native_estimate"": 0.329509, ""native_ci_low"": -0.063165, ""native_ci_high"": 0.722183, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q2 vs Q1""}, {""label"": ""PM2.5 Q3 vs Q1, fully adjusted"", ""primary"": false, ""estimate"": 2.840383, ""ci_low"": 1.712485, ""ci_high"": 4.711151, ""scale"": ""ratio"", ""contrast"": ""Q3 vs Q1"", ""metric"": ""RR"", ""native_estimate"": 1.043939, ""native_ci_low"": 0.537945, ""native_ci_high"": 1.549933, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q3 vs Q1""}, {""label"": ""PM2.5 Q4 vs Q1, fully adjusted"", ""primary"": false, ""estimate"": 3.747079, ""ci_low"": 1.838902, ""ci_high"": 7.635316, ""scale"": ""ratio"", ""contrast"": ""Q4 vs Q1"", ""metric"": ""RR"", ""native_estimate"": 1.320976, ""native_ci_low"": 0.609051, ""native_ci_high"": 2.032901, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q4 vs Q1""}], ""analysis_diagnostics"": {""observations"": 96, ""estimated_parameters"": 14, ""exposure_unique_values"": 96, ""outcome_unique_values"": 65, ""joined_rows"": 96, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""continuous_fully_adjusted"", ""quartile_fully_adjusted""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-36383802-sao-jose-covid-r8404-20260925T141131Z,,36383802,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T14:11:38.322885+00:00,2026-09-25T14:22:51.024707+00:00,0,0,0,0,0,"{""schema_version"": 3, ""study_id"": ""36383802-sao-jose-covid"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily hospital admissions for COVID-19 (bounded sensitivity uses SIVEP-Gripe resident COVID/SRAG hospital admissions)"", ""pollutant"": ""O3 and NO2"", ""geography"": ""Sao Jose dos Campos, Sao Paulo, Brazil"", ""population"": ""Residents admitted with COVID-19"", ""period"": ""Article: 2020-04-01 to 2021-04-30; sensitivity: 2020-04-01 to 2020-09-09"", ""effect_scale"": ""Rate ratio"", ""exposure_assignment"": ""Daily city-level unweighted mean of eligible in-city station-day means, lags 0-7"", ""model"": ""Separate negative-binomial log-link daily count regressions"", ""covariates"": [""daily mean temperature"", ""daily mean relative humidity"", ""day of week"", ""linear calendar-day trend""], ""named_outcome_source"": ""Article: SIH-SUS B34.2; sensitivity: SIVEP-Gripe hospital extract"", ""specification_evidence"": [""/study/article.txt Material and Methods and Table 2"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CADDE-CENTRE/covid19_brazil_hfr/main/inst/data/SIVEP_hospital_31-01-2022-all.rds"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""1bdcb04998180ecc6bc3ed9f2ff196e36a42016ad8052634598f2caed91353db"", ""evidence_artifact"": ""/output/diagnostics/outcome_accounting.json""}, {""role"": ""exposure"", ""url"": ""https://www.kaggle.com/api/v1/datasets/download/amandalk/sp-air-quality"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""0a638a19fcf744f749e438d27c7338a8d763065598cd64086f326e42cce18013"", ""evidence_artifact"": ""/output/diagnostics/kaggle_air_metadata.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""de3a7932a9f359c85b8da0b96e1e335cefb99d9ab8373194ae401a62877b2886"", ""evidence_artifact"": ""/output/diagnostics/openmeteo_weather_full.log""}, {""role"": ""outcome"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/RDSP2004.dbc"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/diagnostics/outcome_route_ftp.log""}, {""role"": ""exposure"", ""url"": ""https://qualar.cetesb.sp.gov.br/qualar/home.do"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/diagnostics/cetesb_home.html""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""SIH-SUS admissions with ICD-10 B34.2"", ""reanalysis"": ""SIVEP-Gripe resident admissions classified COVID/SRAG"", ""reason"": ""Direct public SIH-SUS file transport timed out; recovered public hospital-level registry has resident municipality and admission date.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""CETESB daily pollution data with undocumented article aggregation"", ""reanalysis"": ""CETESB-derived public hourly archive, daily station-mean aggregation in source units"", ""reason"": ""QUALAR historical retrieval route required a registered account; archive has auditable hourly records through 2020-09-09.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2020-04-01 to 2021-04-30"", ""reanalysis"": ""2020-04-01 to 2020-09-09"", ""reason"": ""CETESB-derived public archive ends 2020-09-09; all days in this deterministic window meet completeness rule.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""CETESB temperature and relative humidity"", ""reanalysis"": ""Open-Meteo archive coordinate weather"", ""reason"": ""CETESB direct historical access required account.""}], ""coverage"": {""eligible_units"": 1, ""included_units"": 1, ""eligible_times"": 162, ""included_times"": 162, ""rule"": ""At least 18 hourly observations per station-day; daily value is unweighted mean of eligible station-day means."", ""notes"": ""Complete O3, NO2, and weather coverage in the bounded interval; two in-city stations.""}, ""artifacts"": {""code"": ""code/reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""data/exposure_daily_cetesb_archive_sensitivity.csv"", ""analysis_panel"": ""data/analysis_panel_sensitivity.csv"", ""model_output"": ""data/model_output_native.csv"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""diagnostics/blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T142112.3974850000.json"", ""coverage_diagnostics"": ""diagnostics/coverage_diagnostics.json"", ""boundary_route_evidence"": ""diagnostics/cetesb_arcgis_service.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""A full matched SIH-SUS ICD B34.2 daily outcome series was not recovered: both HTTPS and FTP DATASUS monthly-file attempts timed out."", ""CETESB QUALAR historical retrieval requires a registered account and public OpenAQ v3 requires an API key; neither yielded a full original-period record."", ""The public CETESB-derived archive ends 2020-09-09 and its metadata does not explicitly state the numerical units.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 2, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": false, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/diagnostics/cetesb_home.html"", ""/output/diagnostics/kaggle_air_metadata.json"", ""/output/diagnostics/openmeteo_weather_full.log"", ""/output/diagnostics/outcome_accounting.json"", ""/output/diagnostics/outcome_route_ftp.log"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T142112.3974850000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""code/reanalysis.py"", ""data/analysis_panel_sensitivity.csv"", ""data/exposure_daily_cetesb_archive_sensitivity.csv"", ""data/model_output_native.csv"", ""decision_log.json"", ""diagnostics/blocker_ledger.json"", ""diagnostics/cetesb_arcgis_service.json"", ""diagnostics/coverage_diagnostics.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""36383802-sao-jose-covid-reanalysis-invariants"", ""contract_sha256"": ""1b1d9cb35f4cfe59993a2722188d1b8a64647f70ee4e714da2ea8f2eedb031df"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Daily unweighted mean of eligible in-city CETESB station-day means (S.Jose Campos and Jd. Satelite)."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Daily arithmetic mean of hourly concentration values retained in archive source units."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""Analyst implementation decision after source inspection"", ""evidence"": ""All 162 days in bounded interval had O3 and NO2 under 18-hour station-day requirement.""}, ""decision_rationale"": ""The direct CETESB QUALAR historical query route requires a registered account, whereas the independently archived public hourly CETESB series offers a complete and auditable bounded window. A fixed city-wide station mean matches the ecological design but differs from the article's unspecified daily pollutant summary and source delivery route."", ""evidence_basis"": [""CETESB-derived archive yielded complete O3 and NO2 city-day coverage for 2020-04-01 to 2020-09-09 using two in-city stations."", ""Archive documentation says hourly data originate from CETESB and end 2020-09-09.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""O3 lag 0 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.7208039688831658, ""ci_low"": 0.5041650551315464, ""ci_high"": 1.030532275629776, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.03273880664834596, ""native_ci_low"": -0.06848515741836553, ""native_ci_high"": 0.0030075441216736096, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 1 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.6630714902161028, ""ci_low"": 0.4603648037862607, ""ci_high"": 0.9550334811032413, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.0410872466229091, ""native_ci_low"": -0.07757360520890813, ""native_ci_high"": -0.004600888036910077, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 2 (bounded sensitivity)"", ""primary"": true, ""estimate"": 0.6923651565024976, ""ci_low"": 0.4690487681117765, ""ci_high"": 1.0220035581129423, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.03676417797330042, ""native_ci_low"": -0.07570485327609738, ""native_ci_high"": 0.0021764973294965337, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 3 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.6327324048344833, ""ci_low"": 0.40290192006908815, ""ci_high"": 0.9936668856256081, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.045770768739595465, ""native_ci_low"": -0.09090621211742297, ""native_ci_high"": -0.000635325361767955, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 4 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.6169544208984002, ""ci_low"": 0.38823550037593346, ""ci_high"": 0.9804171877571958, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.04829601299311985, ""native_ci_low"": -0.09461431637526335, ""native_ci_high"": -0.001977709610976354, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 5 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.6390911518979315, ""ci_low"": 0.39636100725511625, ""ci_high"": 1.0304684188354982, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.04477081870502295, ""native_ci_low"": -0.0925429848531381, ""native_ci_high"": 0.0030013474430922032, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 6 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.642687356210198, ""ci_low"": 0.40126631166879, ""ci_high"": 1.0293588717046047, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.04420968997248184, ""native_ci_low"": -0.0913129953230131, ""native_ci_high"": 0.0028936153780494064, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""O3 lag 7 (bounded sensitivity)"", ""primary"": false, ""estimate"": 0.6452513745743549, ""ci_low"": 0.4045014547890703, ""ci_high"": 1.029290084029988, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": -0.043811531008834864, ""native_ci_low"": -0.09050999459781414, ""native_ci_high"": 0.0028869325801444204, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 0 (bounded sensitivity)"", ""primary"": false, ""estimate"": 1.8165323370322273, ""ci_low"": 0.5153398700918602, ""ci_high"": 6.403133005982191, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.05969293743550906, ""native_ci_low"": -0.06629286540583722, ""native_ci_high"": 0.18567874027685533, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 1 (bounded sensitivity)"", ""primary"": false, ""estimate"": 1.991801601212031, ""ci_low"": 0.6210862318113832, ""ci_high"": 6.387637360790225, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.06890395564170927, ""native_ci_low"": -0.047628534708910916, ""native_ci_high"": 0.18543644599232945, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 2 (bounded sensitivity)"", ""primary"": false, ""estimate"": 2.146160516407075, ""ci_low"": 0.6777020197525235, ""ci_high"": 6.796504699612165, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.07636804393642499, ""native_ci_low"": -0.03890475865397691, ""native_ci_high"": 0.1916408465268269, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 3 (bounded sensitivity)"", ""primary"": true, ""estimate"": 2.198039817831768, ""ci_low"": 0.6869599128448366, ""ci_high"": 7.032985404877874, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.07875659713004073, ""native_ci_low"": -0.037547933948871376, ""native_ci_high"": 0.19506112820895283, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 4 (bounded sensitivity)"", ""primary"": false, ""estimate"": 2.4180819230403143, ""ci_low"": 0.754262712502944, ""ci_high"": 7.752100282315789, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.08829746321150779, ""native_ci_low"": -0.02820145465898824, ""native_ci_high"": 0.20479638108200382, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 5 (bounded sensitivity)"", ""primary"": false, ""estimate"": 2.107035625593241, ""ci_low"": 0.6514947131747222, ""ci_high"": 6.814482201835549, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.0745282042886628, ""native_ci_low"": -0.04284859973009346, ""native_ci_high"": 0.19190500830741908, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 6 (bounded sensitivity)"", ""primary"": false, ""estimate"": 1.931819942699688, ""ci_low"": 0.5919418656156111, ""ci_high"": 6.304552030850316, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.06584625340867725, ""native_ci_low"": -0.052434684889369435, ""native_ci_high"": 0.18412719170672392, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}, {""label"": ""NO2 lag 7 (bounded sensitivity)"", ""primary"": false, ""estimate"": 1.5003016805215073, ""ci_low"": 0.452541616805871, ""ci_high"": 4.973918528119017, ""scale"": ""ratio"", ""contrast"": ""10 source concentration units"", ""metric"": ""RR"", ""native_estimate"": 0.040566620823385004, ""native_ci_low"": -0.07928755492295109, ""native_ci_high"": 0.16042079656972108, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 source concentration unit""}], ""analysis_diagnostics"": {""observations"": 162, ""estimated_parameters"": 11, ""exposure_unique_values"": 162, ""outcome_unique_values"": 34, ""joined_rows"": 162, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""O3 lags 0-7"", ""NO2 lags 0-7""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-38182658-uk-covid-r8404-20260925T142459Z,,38182658,completed_sensitivity,,2026-09-25T14:25:06.740723+00:00,2026-09-25T14:39:45.929368+00:00,0,1,0,0,0,"{""schema_version"": 3, ""study_id"": ""38182658-uk-covid"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Instantaneous COVID-19 case-fatality rate: article target D'/C; reanalysis uses stated fixed-delay proxy."", ""pollutant"": ""PM2.5"", ""geography"": ""England, Northern Ireland, Scotland, and Wales"", ""population"": ""Laboratory-confirmed COVID-19 cases in the four UK constituent nations"", ""period"": ""2020-03-26 through 2020-09-15"", ""effect_scale"": ""Odds ratio per 10 ug/m3 PM2.5"", ""exposure_assignment"": ""Article: daily country average. Reanalysis: daily mean of valid hourly values at one official UK-AIR representative monitor per nation."", ""model"": ""Article: binomial logistic GLMM/DLNM. Reanalysis: binomial-logit fixed-effect GLM with PM2.5, temperature and sunshine at lag 10 days."", ""covariates"": [""temperature"", ""sunshine duration"", ""nation fixed effects""], ""named_outcome_source"": ""Public Health England / Office for National Statistics (article); independently recovered Tom White historical UK data compilation (reanalysis)"", ""specification_evidence"": [""/output/estimand_ledger.json"", ""/study/article.md"", ""/study/supplements/41598_2023_50474_MOESM1_ESM.docx""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/tomwhite/covid-19-uk-data/master/data/covid-19-indicators-uk.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""151ecd06edb90e137ddddb822305ac642ca58297f2155362df2e4b7661d4a1f5"", ""evidence_artifact"": ""/output/retrieved/uk_covid_indicators.csv""}, {""role"": ""exposure"", ""url"": ""https://uk-air.defra.gov.uk/datastore/data_files/site_pol_data/{SITE}_PM25_2020.csv"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/exposure_daily.csv""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieved/openmeteo_EAGL.json""}, {""role"": ""boundary"", ""url"": ""OpenAQ archive S3 and v3 via AERIS"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-25T142941.5103370000.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Daily national average across monitors from DEFRA Air Information Resource"", ""reanalysis"": ""One official UK-AIR PM2.5 monitor per nation, daily hourly mean"", ""reason"": ""Direct regulator source provided reproducible fit-ready hourly records; retained analysis is explicitly representative-monitor exposure.""}, {""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""Non-parametric backprojected deaths D' divided by confirmed cases"", ""reanalysis"": ""Reported daily deaths shifted eight days and divided by daily incident cases"", ""reason"": ""Recovered public historical source does not contain original backprojection input/output.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""DLNM binomial GLMM with country random effects and stage-specific effects"", ""reanalysis"": ""Single linear 10-day lag binomial-logit model with nation fixed effects"", ""reason"": ""Fixed-delay proxy cannot defensibly identify separate stage effects and four clusters are not suitable for stable random-effect inference.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""ECA&D station aggregates"", ""reanalysis"": ""Open-Meteo archive at fixed representative coordinates"", ""reason"": ""Public, reproducible daily temperature and sunshine proxy.""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 4, ""eligible_times"": 174, ""included_times"": 466, ""rule"": ""Retain nation-days with nonmissing lag-10 PM2.5, temperature and sunshine and positive daily incident cases; no numeric PM completeness exclusion threshold imposed."", ""notes"": ""Joined panel has 696 nation-days; 13 have no daily PM2.5, and lag/missingness/zero-case rules leave 466 model rows. PM2.5 daily availability: England 166/174, Northern Ireland 174/174, Scotland 174/174, Wales 169/174. Full diagnostics are in coverage_report.json.""}, ""artifacts"": {""code"": ""reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""exposure_daily.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T143521.2130500000.json"", ""coverage_diagnostics"": ""coverage_report.json"", ""review_audit"": ""review_audit.json"", ""boundary_route_evidence"": ""aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-25T142941.5103370000.csv"", ""study_contract"": ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json""}, ""blockers"": [""Exact article all-monitor national PM2.5 average, backprojNP D' outcome, and DLNM stage-specific model were not recovered; this is a bounded sensitivity, not a matched replication.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-25T142941.5103370000.csv"", ""/output/exposure_daily.csv"", ""/output/retrieved/openmeteo_EAGL.json"", ""/output/retrieved/uk_covid_indicators.csv"", ""aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-25T142941.5103370000.csv"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T143521.2130500000.json"", ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""coverage_report.json"", ""decision_log.json"", ""exposure_daily.csv"", ""model_output.json"", ""reanalysis.py"", ""review_audit.json"", ""source_manifest.json""]}, ""effects"": [{""label"": ""Bounded PM2.5 lag-10 sensitivity"", ""primary"": true, ""estimate"": 1.0700745807495362, ""ci_low"": 1.06764487994319, ""ci_high"": 1.0725098109656321, ""scale"": ""ratio"", ""contrast"": ""10 ug/m3 increase in PM2.5 at lag 10 days"", ""metric"": ""OR"", ""native_estimate"": 0.006772834767984921, ""native_ci_low"": 0.006545517582800075, ""native_ci_high"": 0.007000151953169767, ""native_scale"": ""log odds coefficient"", ""native_contrast"": ""1 ug/m3 PM2.5""}], ""analysis_diagnostics"": {""observations"": 466, ""estimated_parameters"": 7, ""exposure_unique_values"": 443, ""outcome_unique_values"": 152, ""joined_rows"": 696, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 13, ""contrast_transformation_verified"": true, ""reported_variants"": [""lag-10 bounded sensitivity; article's three infection-stage variants not separately identifiable with fixed-delay proxy""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-38788590-brazil-cancer-r8404-20260925T144033Z,,38788590,policy_termination,credential-shaped content detected in retained artifacts,2026-09-25T14:40:40.899145+00:00,2026-09-25T15:01:47.333532+00:00,0,0,0,0,0,"{""schema_version"": 3, ""study_id"": ""38788590-brazil-cancer"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily all-cancer deaths (bounded slice; article also specified 25 site-specific outcomes)"", ""pollutant"": ""PM2.5"", ""geography"": ""Sao Paulo municipality/city, Brazil (bounded from 5,570 municipalities)"", ""population"": ""Individual SIM all-cancer death records with municipality of occurrence code 355030"", ""period"": ""2019-01-01 through 2019-12-31 (bounded from 2000-2019)"", ""effect_scale"": ""Odds ratio per 10 ug/m3"", ""exposure_assignment"": ""Daily Sao Paulo city-coordinate PM2.5 estimate, transformed to observed three-day lag 0-2 mean; explicit proxy for article population-weighted municipality grid mean"", ""model"": ""Time-stratified case-crossover conditional logistic regression; 3 or 4 same-weekday controls in same calendar month"", ""covariates"": [""NASA POWER coordinate daily temperature (linear and quadratic terms)"", ""NASA POWER coordinate relative humidity""], ""named_outcome_source"": ""Brazilian Mortality Information System (SIM)"", ""specification_evidence"": [""/output/article-evidence.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SIM/csv/Mortalidade_Geral_2019_csv.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""66501b7348ad77d8e88bcb6306d86dc555496fe65258333440998f2472c66480"", ""evidence_artifact"": ""/output/recovery-critic/sim2019.zip""}, {""role"": ""exposure"", ""url"": ""https://datacatalogfiles.worldbank.org/ddh-published/0067162/DR0096339/PM25_Latin_America_Caribbean.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""c4b60fbe718d6e6c7efddbfbc41189c7a9aa251bb1adb2c97a34b61709a108df"", ""evidence_artifact"": ""/output/recovery-critic/pm25-lac.zip""}, {""role"": ""weather"", ""url"": ""https://power.larc.nasa.gov/api/temporal/daily/point"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""42309a508fc62e298919bf45a827814ef51438bdd9481013d04c3f098b903a15"", ""evidence_artifact"": ""/output/recovery-critic/nasa-power-sp-2019.json""}], ""substitutions"": [{""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""5,570 Brazilian municipalities, 2000-2019"", ""reanalysis"": ""Sao Paulo municipality/city, 2019"", ""reason"": ""This was the first independently recovered daily outcome/exposure overlap suitable for an executable bounded fit.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Population-weighted within-municipality 0.25-degree daily grid PM2.5"", ""reanalysis"": ""Public daily city-coordinate PM2.5 estimate"", ""reason"": ""The recovered public city series preserves daily PM2.5 and lag calculation but not the article spatial support.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Population-weighted ERA5 temperature cross-basis, RH, and public holiday"", ""reanalysis"": ""NASA POWER coordinate temperature linear/quadratic terms and RH; no holiday term"", ""reason"": ""Bounded public-weather implementation; explicitly reduced adjustment.""}, {""dimension"": ""outcome"", ""change_type"": ""coverage_subset"", ""published"": ""All cancer plus 25 site-specific variants and subgroups"", ""reanalysis"": ""All-cancer only"", ""reason"": ""Only the principal all-cancer bounded slice was fit; variants remain unestimated.""}], ""coverage"": {""eligible_units"": 5570, ""included_units"": 1, ""eligible_times"": 365, ""included_times"": 329, ""rule"": ""Require three consecutive observed calendar days for lag 0-2 PM2.5 and weather on each case and referent date; no imputation."", ""notes"": ""353/365 PM2.5 source dates were recovered (all month-ends missing); 329 consecutive-date lagged days and 16,801 death strata were fitted.""}, ""artifacts"": {""code"": ""code/bounded_sp2019_reanalysis.py"", ""source_manifest"": ""source-manifest.json"", ""exposure"": ""bounded-sp2019/sp2019-daily-exposure-weather.csv"", ""analysis_panel"": ""bounded-sp2019/analysis-panel.csv"", ""model_output"": ""bounded-sp2019/model-output.json"", ""decision_log"": ""decision-log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""recovery-report.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T150022.3427420000.json"", ""coverage_diagnostics"": ""coverage-diagnostics.json"", ""boundary_route_evidence"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json""}, ""blockers"": [""The result does not recover the article's national 5,570-municipality, 2000-2019 population-weighted gridded PM2.5 panel."", ""The public daily city PM2.5 series omits all 2019 month-end dates and is a city-coordinate spatial proxy."", ""Site-specific, sex, age, and multi-period article variants were not fit in this one-city/one-year bounded analysis.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/recovery-critic/nasa-power-sp-2019.json"", ""/output/recovery-critic/pm25-lac.zip"", ""/output/recovery-critic/sim2019.zip"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T150022.3427420000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""bounded-sp2019/analysis-panel.csv"", ""bounded-sp2019/model-output.json"", ""bounded-sp2019/sp2019-daily-exposure-weather.csv"", ""code/bounded_sp2019_reanalysis.py"", ""coverage-diagnostics.json"", ""decision-log.json"", ""recovery-report.json"", ""source-manifest.json""]}, ""design_provenance"": {""contract_id"": ""38788590-brazil-cancer-reanalysis-invariants"", ""contract_sha256"": ""37d9e76cce70bd3b376425071b97528459ad2cd0b265c75570a6bf7e27af26dd"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Daily S\u00e3o Paulo city estimate at the catalogued city coordinate (-23.5475, -46.63611) assigned as an explicit city/municipality proxy; not a within-boundary population-weighted grid mean."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""Official Ministry of Health public S3 SIM 2019 CSV archive for outcomes; Global PM2.5 Watch World Bank public daily city estimates for PM2.5; NASA POWER daily coordinate weather for adjustment."", ""exposure_metric"": ""Arithmetic 3-day mean (index day plus prior two observed consecutive source dates) of PM2.5 in ug/m3."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Include a stratum only if its case and all referent dates have nonmissing lag 0-2 PM2.5 and weather. Report observed coverage: 353/365 PM source days and 351 lagged days.""}, ""decision_rationale"": ""The executable bounded panel preserves cancer mortality, PM2.5, daily lag 0-2 exposure calculation, time-stratified case-crossover matching, conditional-logistic family, and OR-per-10 contrast. The city proxy source is explicitly different from the article's national population-weighted gridded construct, so it is a source-substituted bounded analysis and is not selected for agreement with published results."", ""evidence_basis"": [""Official Ministry catalog page enumerates a public S3 2019 SIM CSV archive."", ""Downloaded official 2019 SIM CSV archive; SHA-256 66501b7348ad77d8e88bcb6306d86dc555496fe65258333440998f2472c66480."", ""Downloaded public daily Latin America city PM2.5 archive; SHA-256 c4b60fbe718d6e6c7efddbfbc41189c7a9aa251bb1adb2c97a34b61709a108df."", ""Retained S\u00e3o Paulo municipality/city daily panel with 353 source days and 351 valid three-day lag values.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""All-cancer mortality, Sao Paulo 2019 bounded slice"", ""primary"": true, ""estimate"": 0.9710111557808493, ""ci_low"": 0.9287615171656768, ""ci_high"": 1.0151827430665052, ""scale"": ""ratio"", ""contrast"": ""10 ug/m3 increase in observed PM2.5 lag 0-2 mean"", ""metric"": ""OR"", ""native_estimate"": -0.002941732179609983, ""native_ci_low"": -0.007390328230831152, ""native_ci_high"": 0.001506863871611186, ""native_scale"": ""conditional-logit coefficient"", ""native_contrast"": ""1 ug/m3 increase in PM2.5 lag 0-2 mean""}], ""analysis_diagnostics"": {""observations"": 67204, ""estimated_parameters"": 4, ""exposure_unique_values"": 329, ""outcome_unique_values"": 2, ""joined_rows"": 67204, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""All-cancer, Sao Paulo 2019 bounded slice; site-specific/subgroup/period variants not fit""]}}" |
| self-driving-aeris,r8404,codex-aeris-self-driving-39377000-us-stroke-r8404-20260925T150653Z,,39377000,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T15:07:01.942839+00:00,2026-09-25T15:26:44.733312+00:00,0,3,0,0,0,"{""schema_version"": 3, ""study_id"": ""39377000-us-stroke"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Article target: ischemic and hemorrhagic county stroke mortality among adults 65+; fitted sensitivity: CDC all-stroke county rate among adults 65+"", ""pollutant"": ""PM2.5"", ""geography"": ""United States counties; monitor-supported subset"", ""population"": ""United States residents aged 65 years and older"", ""period"": ""Article: 2016-2020; fitted sensitivity: 2016-2019"", ""effect_scale"": ""Article-native additive deaths per 100,000 per 1 ug/m3; outcome-ratio presentation below is evaluated at the fitted sample mean solely for schema transport"", ""exposure_assignment"": ""Unweighted within-county mean of qualifying EPA AQS PM2.5 monitor annual arithmetic means"", ""model"": ""OLS of all-stroke age-65+ county rate on PM2.5 with state fixed effects; reduced adjustment sensitivity"", ""covariates"": [""state fixed effects""], ""named_outcome_source"": ""CDC county heart disease and stroke mortality dataset (Socrata 7b9s-s8ck)"", ""specification_evidence"": [""../study/article.md: Methods and Statistical analysis"", ""../study/article.md: Results section establishes additive linear coefficients""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://data.cdc.gov/resource/7b9s-s8ck.csv"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""data/cdc_heart_stroke_2000_2019.csv""}, {""role"": ""exposure"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2018.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""evidence/epa2018.zip""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""Ischemic and hemorrhagic stroke, 2016-2020"", ""reanalysis"": ""All stroke, age 65+, 2016-2019"", ""reason"": ""The successful public CDC download did not separate article outcomes or include 2020.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Unspecified county annual PM2.5 assignment"", ""reanalysis"": ""EPA AQS within-county monitor mean"", ""reason"": ""Public decoded monitor archive was used; it is not a population-weighted surface.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Full clinical, socioeconomic, access, and park covariate set"", ""reanalysis"": ""State fixed effects only"", ""reason"": ""Article-identical covariate data were not recovered in fit-ready form.""}, {""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""3,142 county equivalents"", ""reanalysis"": ""301 joined monitor-supported counties"", ""reason"": ""Partial monitor coverage and usable outcome overlap.""}], ""coverage"": {""eligible_units"": 3142, ""included_units"": 301, ""eligible_times"": 5, ""included_times"": 4, ""rule"": ""EPA AQS PM2.5 monitor record with 24-hour Daily Mean metric, POC 1, local-condition units, and Observation Percent >=75; reported rather than article-specified threshold."", ""notes"": ""473 counties had qualifying EPA monitor records; 301 joined to the CDC outcome data. No individual dose or population-weighted area concentration is claimed.""}, ""artifacts"": {""code"": ""code/reanalysis.js"", ""code_artifact_audit"": ""code_artifact_audit.json"", ""executable_audit"": ""executable-audit/model_output.json"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""data/exposure_county_pm25.csv"", ""analysis_panel"": ""data/analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T151818.6237580000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""boundary_route_evidence.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""No fit-ready public county ischemic/hemorrhagic outcome route was recovered."", ""Full article covariate adjustment was not reconstructed."", ""EPA monitor coverage materially reduces county coverage.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T151818.6237580000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""blocker_ledger.json"", ""boundary_route_evidence.json"", ""code/reanalysis.js"", ""code_artifact_audit.json"", ""coverage_diagnostics.json"", ""data/analysis_panel.csv"", ""data/cdc_heart_stroke_2000_2019.csv"", ""data/exposure_county_pm25.csv"", ""decision_log.json"", ""evidence/epa2018.zip"", ""executable-audit/model_output.json"", ""model_output.json"", ""research-notebook.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""39377000-us-stroke-reanalysis-invariants"", ""contract_sha256"": ""ca210f0339070d98ef66698d92242088e4a4e1cbba7ec5d3777c6af68f3df356"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Within-county unweighted mean of qualifying EPA AQS PM2.5 monitor annual arithmetic means; county retained when monitor data were available in >=1 2016\u20132019 year."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Mean of annual PM2.5 local-condition 24-hour Daily Mean monitor arithmetic means (\u00b5g/m\u00b3), 2016\u20132019."", ""coverage_policy"": {""mode"": ""report_only inclusion"", ""minimum_percent"": 75, ""threshold_source"": ""AQS Observation Percent field; 75% is an explicit operational QC threshold, not article-specified"", ""evidence"": ""EPA AQS annual archive records were retained only for Observation Percent >=75; all county and time coverage are reported.""}, ""decision_rationale"": ""The article requires county-level annual PM2.5. 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| self-driving-aeris,r8406,codex-aeris-self-driving-33227571-sao-paulo-ami-r8406-20260925T235316Z,,33227571,completed_sensitivity,,2026-09-25T23:53:23.811771+00:00,2026-09-26T00:06:06.751700+00:00,0,1,0,2,211,"{""schema_version"": 3, ""study_id"": ""33227571-sao-paulo-ami"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily acute myocardial infarction admissions and in-hospital mortality"", ""pollutant"": ""NO2, PM2.5, and PM10 joint daily feature set"", ""geography"": ""39 municipalities in metropolitan Sao Paulo, Brazil"", ""population"": ""Acute myocardial infarction patients admitted 2012-2015"", ""period"": ""2012-01-01 through 2015-12-31"", ""effect_scale"": ""High-pollution versus low-pollution cluster comparison; exact article statistic absent from supplied abstract"", ""exposure_assignment"": ""Article assignment unspecified; sensitivity uses a fixed Pinheiros CETESB monitor"", ""model"": ""Article says hierarchical clustering; sensitivity uses Ward clustering with three clusters and GLM contrasts"", ""covariates"": [""temperature"", ""temperature variation"", ""rainfall"", ""relative humidity""], ""named_outcome_source"": ""DataSUS"", ""specification_evidence"": [""/output/article-specification-evidence.md""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://huggingface.co/datasets/SidneyBissoli/sih-rd"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/jan2014/sih_rd_sp_2014_06_selected.csv.gz""}, {""role"": ""exposure"", ""url"": ""https://sistemasinter.cetesb.sp.gov.br/Ar/php/ar_dados_horarios_resultado.php"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/jan2014/cetesb_pinheiros_2014-06-01.html""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/jan2014/openmeteo_weather.json""}], ""substitutions"": [{""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""39 metropolitan Sao Paulo municipalities"", ""reanalysis"": ""S\u00e3o Paulo municipality resident outcomes with one fixed Pinheiros monitor"", ""reason"": ""Abstract omits membership and monitor assignment.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2012-2015"", ""reanalysis"": ""June 2014"", ""reason"": ""Deterministic complete-observation feasibility slice.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""Meteorological Database for Teaching and Research"", ""reanalysis"": ""Open-Meteo archive daily weather"", ""reason"": ""Public weather-source substitution.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""Hierarchical clustering and unspecified comparison model"", ""reanalysis"": ""Ward three-cluster analysis; robust Poisson admissions and binomial mortality models"", ""reason"": ""Abstract lacks linkage, standardization, and comparison details.""}], ""coverage"": {""eligible_units"": 39, ""included_units"": 1, ""eligible_times"": 1461, ""included_times"": 30, ""rule"": ""Retain rows with observed values for all three pollutants and report hour coverage; no numerical exclusion threshold imposed."", ""notes"": ""NO2 mean 23.83 hours/day (22-24), PM2.5 23.40 (10-24), PM10 23.03 (11-24).""}, ""artifacts"": {""code"": ""reanalysis_jan2014.py"", ""source_manifest"": ""source_manifest_jun2014.json"", ""exposure"": ""exposure_daily_jun2014.csv"", ""analysis_panel"": ""analysis_panel_jun2014.csv"", ""model_output"": ""model_output_jun2014.json"", ""decision_log"": ""decision_log_jun2014.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker-ledger.md"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T000512.7217080000.json"", ""coverage_diagnostics"": ""coverage_diagnostics_jun2014.md"", ""boundary_route_evidence"": ""retrieval/jan2014/cetesb_pinheiros_2014-06-01.html"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-003.json""}, ""blockers"": [""Supplied article materials are abstract-only and omit exact assignment, clustering, and comparison procedures."", ""This is a one-month, one-municipality, one-monitor bounded sensitivity and not a matched replication.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/retrieval/jan2014/cetesb_pinheiros_2014-06-01.html"", ""/output/retrieval/jan2014/openmeteo_weather.json"", ""/output/retrieval/jan2014/sih_rd_sp_2014_06_selected.csv.gz"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T000512.7217080000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-003.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel_jun2014.csv"", ""blocker-ledger.md"", ""coverage_diagnostics_jun2014.md"", ""decision_log_jun2014.json"", ""exposure_daily_jun2014.csv"", ""model_output_jun2014.json"", ""reanalysis_jan2014.py"", ""retrieval/jan2014/cetesb_pinheiros_2014-06-01.html"", ""source_manifest_jun2014.json""]}, ""design_provenance"": {""contract_id"": ""33227571-sao-paulo-ami-reanalysis-invariants"", ""contract_sha256"": ""bb1061391c7ce965ed123f643672ea1b06005d45600d64283c9a55d66bbcd947"", ""contract_author"": ""agent"", ""geographic_representation"": ""fixed_location"", ""assignment_method"": ""fixed Ibirapuera monitor coordinate (-23.592,-46.661) represents a S\u00e3o Paulo municipality feasibility slice; no individual or municipality-wide interpolation"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""daily NO2, PM2.5, PM10 concentration features plus daily mean temperature, temperature range, precipitation, and mean relative humidity"", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""report daily component completeness and retain only complete rows for unsupervised clustering; no arbitrary source threshold""}, ""decision_rationale"": ""This is a strictly stronger recovery route than the previously planned monitor archive/model mixture. It preserves the bounded fixed-location/period sensitivity but replaces the failed PM10 model fallback with all three observed pollutants from the article-named regulator."", ""evidence_basis"": [""Direct POST to the legacy public result route returned dated Pinheiros hourly tables for NO2, MP10 and MP2.5 on 2014-06-01, with no credential."", ""Air-quality model route was rejected because its apparent historical values were actually null (the retained diagnostic had a counting mistake); no model concentrations will be used.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""AMI admissions, high-pollution versus low-pollution cluster"", ""primary"": true, ""estimate"": 0.6502463055, ""ci_low"": 0.2852171082, ""ci_high"": 1.482450546, ""scale"": ""ratio"", ""contrast"": ""High-pollution cluster versus low-pollution reference cluster"", ""metric"": ""RR"", ""native_estimate"": -0.4304040564, ""native_ci_low"": -1.2545045216, ""native_ci_high"": 0.3936964088, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Poisson GLM coefficient, high versus low cluster""}, {""label"": ""In-hospital mortality among AMI admissions, high-pollution versus low-pollution cluster"", ""primary"": false, ""estimate"": 1.2342857142, ""ci_low"": 0.4897463973, ""ci_high"": 3.1107145101, ""scale"": ""ratio"", ""contrast"": ""High-pollution cluster versus low-pollution reference cluster"", ""metric"": ""OR"", ""native_estimate"": 0.2104924337, ""native_ci_low"": -0.7138675785, ""native_ci_high"": 1.1348524458, ""native_scale"": ""log odds ratio"", ""native_contrast"": ""Binomial daily mortality coefficient, high versus low cluster""}], ""analysis_diagnostics"": {""observations"": 30, ""estimated_parameters"": 3, ""exposure_unique_values"": 30, ""outcome_unique_values"": 15, ""joined_rows"": 30, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""admissions IRR"", ""in-hospital mortality OR""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-33398753-italy-cities-r8406-20260925T220702Z,,33398753,completed_fit,,2026-09-25T22:07:09.521604+00:00,2026-09-25T22:26:39.230317+00:00,0,0,0,1,310,"{""schema_version"": 3, ""study_id"": ""33398753-italy-cities"", ""status"": ""completed_fit"", ""fidelity"": ""reduced_coverage"", ""target"": {""outcome"": ""Cumulative confirmed COVID-19 infections on 17 March, 7 April, and 27 April 2020"", ""pollutant"": ""PM10"", ""geography"": ""55 Italian provincial-capital cities"", ""population"": ""Residents of sampled provincial-capital cities"", ""period"": ""2018 exposure; 2020 outcomes"", ""effect_scale"": ""Outcome ratio per doubling annual PM10 exceedance-day count"", ""exposure_assignment"": ""Nearest monitor within 100 km of provincial-capital reference coordinate; daily series"", ""model"": ""OLS of log cumulative infections on log PM10 exceedance days and log 2019 population density"", ""covariates"": [""2019 population density (log)""], ""named_outcome_source"": ""Italian Ministry of Health / public Protezione Civile provincial archive substitution"", ""specification_evidence"": [""/study/article.md"", ""/run/contract/study-target.json""]}, ""sources"": [{""role"": ""covariate"", ""url"": ""https://data.mendeley.com/public-api/datasets/bbnyhp6gfh"", ""route_origin"": ""article_linked"", ""retrieved"": true, ""sha256"": ""eff39c6791990840d7b58d65a64c842507ff49d9cdcc7ad629242944b60a9c4b"", ""evidence_artifact"": ""/output/recovery/mendeley-record.json""}, {""role"": ""outcome"", ""url"": ""https://github.com/pcm-dpc/COVID-19/tree/master/dati-province"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/checksums.sha256""}, {""role"": ""exposure"", ""url"": ""https://api.openaq.org/v3/"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/pm10_daily_observations_raw.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Regional environmental agencies/Legambiente"", ""reanalysis"": ""OpenAQ v3 plus public S3 historical archive"", ""reason"": ""Independently retrieved monitor observations; published exposure values excluded.""}, {""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""Ministero della Salute"", ""reanalysis"": ""Protezione Civile provincial archive"", ""reason"": ""Public historical cumulative snapshots available for all article dates.""}, {""dimension"": ""exposure"", ""change_type"": ""coverage_subset"", ""published"": ""55 cities"", ""reanalysis"": ""32 positive-count complete cases"", ""reason"": ""13 missing series and 10 zero counts make log exposure undefined.""}], ""coverage"": {""eligible_units"": 55, ""included_units"": 32, ""eligible_times"": 365, ""included_times"": null, ""rule"": ""All units with retrieved series and strictly positive PM10>50 annual count; no numeric coverage cutoff."", ""notes"": ""42 units had 284\u2013343 observed days; 10 had zero count and 13 had no series.""}, ""artifacts"": {""code"": ""code"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""data/pm10_exposure_2018.csv"", ""analysis_panel"": ""data/analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.md"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T222340.8978740000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.md"", ""boundary_route_evidence"": ""data/aeris_city_cohort.csv"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""reduced_coverage""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/pm10_daily_observations_raw.csv"", ""/output/recovery/checksums.sha256"", ""/output/recovery/mendeley-record.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T222340.8978740000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger.md"", ""coverage_diagnostics.md"", ""data/aeris_city_cohort.csv"", ""data/analysis_panel.csv"", ""data/pm10_exposure_2018.csv"", ""decision_log.json"", ""model_output.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""33398753-italy-cities-reanalysis-invariants"", ""contract_sha256"": ""9980d508edc53481c41e55ac20b8f70773d80e7e620d54539a1a9406426a49a7"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Nearest available PM10 monitor within 100 km; one monitor per city after national catalog discovery."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Annual 2018 count of observed daily mean PM10 values strictly >50 \u00b5g/m\u00b3."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report observed daily coverage and distances; no precommitted numeric exclusion threshold. Fit deterministic complete-case feasible subset only if variation and coverage support it.""}, ""decision_rationale"": ""This operationalizes the locked PM10 target using a transparent city-monitor assignment; it does not alter outcome, pollutant, period, contrast, or model family."", ""evidence_basis"": [""55 fixed city-reference coordinates and the complete 2018 window loaded into AERIS."", ""AERIS catalog plan estimates 65 bounded calls and a public historical archive fallback."", ""Article specifies annual days exceeding PM10 limits, city-level analysis.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""COVID-19 infections 20200317"", ""primary"": false, ""estimate"": 1.2007807143024714, ""ci_low"": 0.8100296498507201, ""ci_high"": 1.7800266003923135, ""scale"": ""ratio"", ""contrast"": ""doubling annual 2018 PM10 >50 ug/m3 day count"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.26397271118214966, ""native_ci_low"": -0.3039533783595823, ""native_ci_high"": 0.8318988007238817, ""native_scale"": ""log-log OLS coefficient"", ""native_contrast"": ""one-unit increase in log PM10 count""}, {""label"": ""COVID-19 infections 20200407"", ""primary"": true, ""estimate"": 1.1503218860519138, ""ci_low"": 0.8942145943291312, ""ci_high"": 1.4797795181622706, ""scale"": ""ratio"", ""contrast"": ""doubling annual 2018 PM10 >50 ug/m3 day count"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.20203761632815598, ""native_ci_low"": -0.16130700282648697, ""native_ci_high"": 0.5653822354827989, ""native_scale"": ""log-log OLS coefficient"", ""native_contrast"": ""one-unit increase in log PM10 count""}, {""label"": ""COVID-19 infections 20200427"", ""primary"": false, ""estimate"": 1.1672914936694847, ""ci_low"": 0.9193376498072579, ""ci_high"": 1.4821207762771427, ""scale"": ""ratio"", ""contrast"": ""doubling annual 2018 PM10 >50 ug/m3 day count"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.22316487292125647, ""native_ci_low"": -0.12133327011193257, ""native_ci_high"": 0.5676630159544456, ""native_scale"": ""log-log OLS coefficient"", ""native_contrast"": ""one-unit increase in log PM10 count""}], ""analysis_diagnostics"": {""observations"": 32, ""estimated_parameters"": 3, ""exposure_unique_values"": 18, ""outcome_unique_values"": 32, ""joined_rows"": 55, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 13, ""contrast_transformation_verified"": true, ""reported_variants"": [""17 March 2020"", ""7 April 2020"", ""27 April 2020""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-33484722-oecd-covid-r8406-20260925T222641Z,,33484722,completed_fit,,2026-09-25T22:26:48.317827+00:00,2026-09-25T22:34:46.498862+00:00,0,0,0,1,101,"{""schema_version"": 3, ""study_id"": ""33484722-oecd-covid"", ""status"": ""completed_fit"", ""fidelity"": ""reduced_coverage"", ""target"": {""outcome"": ""Cumulative confirmed COVID-19 case rate and death rate per national population on days 60 and 80 after the first confirmed case"", ""pollutant"": ""Population-weighted annual PM2.5 concentration in 2017"", ""geography"": ""36 OECD member countries listed in article Methods section 2.1"", ""population"": ""National populations of the 36 article-listed OECD countries"", ""period"": ""Long-term exposure: 2017; COVID outcomes: 2020 epidemic day 60/day 80"", ""effect_scale"": ""Exponentiated coefficient from a linear regression of natural-log rate; outcome-rate ratio"", ""exposure_assignment"": ""Country-level population-weighted annual PM2.5 from World Bank indicator EN.ATM.PM25.MC.M3"", ""model"": ""OLS of natural-log case/death rate per 100,000 on PM2.5 and the five article-specified covariates"", ""covariates"": [""population age 65+ (%)"", ""population density (population / surface area)"", ""GDP per capita (current US dollars)"", ""physicians per 1,000 population"", ""hospital beds per 1,000 population""], ""named_outcome_source"": ""WHO COVID-19 website in article; daily JHU CSSE historical national series used as the documented retrieval substitution"", ""specification_evidence"": [""/study/article.md Methods sections 2.1-2.2"", ""/study/article.md Table 1"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""exposure"", ""url"": ""https://api.worldbank.org/v2/country/AUS;AUT;BEL;CAN;CHL;CZE;DNK;EST;FIN;FRA;DEU;GRC;HUN;ISL;IRL;ISR;ITA;JPN;KOR;LVA;LTU;LUX;MEX;NLD;NZL;NOR;POL;PRT;SVK;SVN;ESP;SWE;CHE;TUR;GBR;USA/indicator/EN.ATM.PM25.MC.M3?date=2017&format=json&per_page=1000"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/worldbank_EN_ATM_PM25_MC_M3_2017.json""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/time_series_covid19_confirmed_global.csv""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/time_series_covid19_deaths_global.csv""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""WHO daily national COVID-19 records"", ""reanalysis"": ""JHU CSSE daily national cumulative COVID-19 records"", ""reason"": ""The direct current WHO archive was recovered but is weekly, so it cannot provide exact values at days 60 and 80 without unsupported interpolation.""}, {""dimension"": ""population"", ""change_type"": ""coverage_subset"", ""published"": ""36 OECD countries"", ""reanalysis"": ""35 complete-case countries"", ""reason"": ""The US physician value is null in World Bank records for every article-authorized fallback year, 2015-2017.""}], ""coverage"": {""eligible_units"": 36, ""included_units"": 35, ""eligible_times"": 4, ""included_times"": 4, ""rule"": ""Complete-case only for the exact article covariate set; no imputation or year expansion."", ""notes"": ""All 36 have 2017 PM2.5 and each outcome. US is excluded only from fitted models for missing physician data in the stated fallback window.""}, ""artifacts"": {""code"": ""reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""analysis_panel.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""decision_log.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T223216.8141240000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": null, ""study_contract"": ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json""}, ""blockers"": [""The direct WHO archive is weekly rather than daily; a daily JHU source was used for the exact required epidemic days."", ""US physician data are absent for all article-authorized World Bank fallback years, so the full-adjustment models have 35 rather than 36 countries.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 2, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""reduced_coverage""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/time_series_covid19_confirmed_global.csv"", ""/output/time_series_covid19_deaths_global.csv"", ""/output/worldbank_EN_ATM_PM25_MC_M3_2017.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T223216.8141240000.json"", ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""coverage_diagnostics.json"", ""decision_log.json"", ""model_output.json"", ""reanalysis.py"", ""source_manifest.json""]}, ""effects"": [{""label"": ""Day-60 case rate"", ""primary"": true, ""estimate"": 1.111084, ""ci_low"": 0.98738, ""ci_high"": 1.250287, ""scale"": ""ratio"", ""contrast"": ""per 1 ug/m3 higher PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.105336, ""native_ci_low"": -0.012701, ""native_ci_high"": 0.223373, ""native_scale"": ""log outcome-rate slope"", ""native_contrast"": ""per 1 ug/m3 higher PM2.5""}, {""label"": ""Day-60 death rate"", ""primary"": true, ""estimate"": 1.18695, ""ci_low"": 1.004608, ""ci_high"": 1.402389, ""scale"": ""ratio"", ""contrast"": ""per 1 ug/m3 higher PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.171387, ""native_ci_low"": 0.004597, ""native_ci_high"": 0.338177, ""native_scale"": ""log outcome-rate slope"", ""native_contrast"": ""per 1 ug/m3 higher PM2.5""}, {""label"": ""Day-80 case rate"", ""primary"": true, ""estimate"": 1.064637, ""ci_low"": 0.967775, ""ci_high"": 1.171193, ""scale"": ""ratio"", ""contrast"": ""per 1 ug/m3 higher PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.062634, ""native_ci_low"": -0.032756, ""native_ci_high"": 0.158023, ""native_scale"": ""log outcome-rate slope"", ""native_contrast"": ""per 1 ug/m3 higher PM2.5""}, {""label"": ""Day-80 death rate"", ""primary"": true, ""estimate"": 1.077049, ""ci_low"": 0.932485, ""ci_high"": 1.244025, ""scale"": ""ratio"", ""contrast"": ""per 1 ug/m3 higher PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.074225, ""native_ci_low"": -0.069902, ""native_ci_high"": 0.218352, ""native_scale"": ""log outcome-rate slope"", ""native_contrast"": ""per 1 ug/m3 higher PM2.5""}], ""analysis_diagnostics"": {""observations"": 35, ""estimated_parameters"": 7, ""exposure_unique_values"": 35, ""outcome_unique_values"": 35, ""joined_rows"": 36, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""Day-60 case rate"", ""Day-60 death rate"", ""Day-80 case rate"", ""Day-80 death rate""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-34004167-northern-italy-covid-r8406-20260925T234155Z,,34004167,completed_sensitivity,,2026-09-25T23:42:04.976615+00:00,2026-09-25T23:47:57.282402+00:00,0,0,0,1,69,"{""schema_version"": 3, ""study_id"": ""34004167-northern-italy-covid"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily reported COVID-19 cases and deaths"", ""pollutant"": ""NO2 STAP; PM2.5 target was attempted but not fit"", ""geography"": ""Lombardia and Veneto, Italy"", ""population"": ""Residents of the two regions"", ""period"": ""Article target 2020-02-21 to 2020-05-19; retained complete overlap 2020-05-05 to 2020-05-19"", ""effect_scale"": ""Rate ratio per 1 \u00b5g/m3"", ""exposure_assignment"": ""Unweighted mean of monitor daily means within each administrative polygon"", ""model"": ""Log-link count models: AR(1) Poisson GEE for deaths; robust Poisson GLM fallback for cases after recorded GEE failure"", ""covariates"": [""None identifiable in bounded overlap; article lockdown is constant""], ""named_outcome_source"": ""Italian Civil Protection COVID-19 regional archive"", ""specification_evidence"": [""/study/article.md \u00a7\u00a72.1\u20132.3"", ""/study/supplements/mmc1.docx Tables S1\u2013S4""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""3438a0a85bdb0bca56a48a2edd0c69f3005d6c1c20c4a2a75bed668a8f01ead7"", ""evidence_artifact"": ""/output/reanalysis/dpc_regions.csv""}, {""role"": ""exposure"", ""url"": ""OpenAQ archive S3 and OpenAQ v3 via AERIS"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""a35c688461fc3f322b0f7b2c346e2e40c122b5491df90d3ea4dcbf4269beb8f0"", ""evidence_artifact"": ""/output/reanalysis/aeris_no2_stap_checkpoint.json.daily.csv""}, {""role"": ""boundary"", ""url"": ""https://www.geoboundaries.org/api/current/gbOpen/ITA/ADM2/"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/italy_adm2.geojson""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""EEA database"", ""reanalysis"": ""OpenAQ archive S3/v3 through AERIS"", ""reason"": ""Article-named legacy EEA export URL returned HTTP 404; OpenAQ yielded usable NO2 records.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""89 daily dates"", ""reanalysis"": ""16 complete-overlap dates"", ""reason"": ""AERIS OpenAQ retrieval covered 22.47% of target dates.""}, {""dimension"": ""exposure"", ""change_type"": ""coverage_subset"", ""published"": ""NO2, PM2.5 and LTAP"", ""reanalysis"": ""NO2 STAP only"", ""reason"": ""No PM2.5 records and no 8-year LTAP were recovered.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""lockdown and meteorology sensitivity"", ""reanalysis"": ""omitted"", ""reason"": ""Lockdown is constant and meteorology was not recovered.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""GEE AR(1)"", ""reanalysis"": ""case GLM fallback; death GEE AR(1)"", ""reason"": ""Case AR(1) GEE convergence failure retained in native output.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 89, ""included_times"": 15, ""rule"": ""Retain deterministic complete date-region overlap with recovered AERIS NO2; no imputation."", ""notes"": ""30 region-days across 5\u201319 May; dates outside the article end date were excluded.""}, ""artifacts"": {""code"": ""reanalysis/analyze.py"", ""source_manifest"": ""reanalysis/source_manifest.json"", ""exposure"": ""reanalysis/aeris_no2_stap_checkpoint.json.daily.csv"", ""analysis_panel"": ""reanalysis/analysis_panel.csv"", ""model_output"": ""reanalysis/model_output.json"", ""decision_log"": ""reanalysis/decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""reanalysis/coverage_diagnostics.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T234702.2082860000.json"", ""coverage_diagnostics"": ""reanalysis/coverage_diagnostics.json"", ""boundary_route_evidence"": ""reanalysis/italy_adm2.geojson"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""OpenAQ NO2 covered only 16 common dates across the two regions."", ""PM2.5 had no retrieved observations."", ""LTAP, meteorology, and variable lockdown could not be included."", ""Bounded panel has only two region clusters and is not a credible published-effect replication.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/reanalysis/aeris_no2_stap_checkpoint.json.daily.csv"", ""/output/reanalysis/dpc_regions.csv"", ""/output/reanalysis/italy_adm2.geojson"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T234702.2082860000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""reanalysis/aeris_no2_stap_checkpoint.json.daily.csv"", ""reanalysis/analysis_panel.csv"", ""reanalysis/analyze.py"", ""reanalysis/coverage_diagnostics.json"", ""reanalysis/decision_log.json"", ""reanalysis/italy_adm2.geojson"", ""reanalysis/model_output.json"", ""reanalysis/source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""34004167-northern-italy-covid-reanalysis-invariants"", ""contract_sha256"": ""035c1810b431582521a30e7b4cfa1c4a3571cb3a56adf429077def8279a5e268"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""For each named regional polygon, unweighted mean of daily means across OpenAQ-discovered monitors within the boundary; deterministic spatial-spread maximum 50 stations."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""NO2 STAP: regional same-day unweighted monitor mean in \u00b5g/m\u00b3."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only; retain the deterministic complete overlap of AERIS recovered NO2 dates for both regions (2020-05-05 through 2020-05-20 boundary outcome overlap expected; exact overlap determined after join). No unsupported completeness threshold.""}, ""decision_rationale"": ""The article's regional spatial support and same-day ambient concentration construct are preserved for NO2. OpenAQ is a source substitution and the recovered common time support is reduced; PM2.5 and the article's 8-year LTAP are not imputed or replaced."", ""evidence_basis"": [""Both target regional polygons yielded monitor-based NO2 observations; each has 22.47% of the 89-day target window under the first archive retrieval."", ""PM2.5 OpenAQ route yielded no observations for both target regions and cannot support a PM2.5 fit."", ""Article-named legacy EEA export URL returned HTTP 404 during direct retrieval probe.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""NO2 STAP and daily cases, bounded model"", ""primary"": true, ""estimate"": 1.1559907083, ""ci_low"": 1.0725488935, ""ci_high"": 1.2459241027, ""scale"": ""ratio"", ""contrast"": ""per 1 \u00b5g/m3"", ""metric"": ""RR"", ""native_estimate"": 0.1449577325, ""native_ci_low"": 0.070058958, ""native_ci_high"": 0.219856507, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""per 1 \u00b5g/m3""}, {""label"": ""NO2 STAP and daily deaths, bounded model"", ""primary"": false, ""estimate"": 0.9962815155, ""ci_low"": 0.9844977775, ""ci_high"": 1.0082062964, ""scale"": ""ratio"", ""contrast"": ""per 1 \u00b5g/m3"", ""metric"": ""RR"", ""native_estimate"": -0.0037254153, ""native_ci_low"": -0.015623638, ""native_ci_high"": 0.008172807, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""per 1 \u00b5g/m3""}], ""analysis_diagnostics"": {""observations"": 30, ""estimated_parameters"": 2, ""exposure_unique_values"": 30, ""outcome_unique_values"": 30, ""joined_rows"": 30, ""unmatched_outcome_rows"": 148, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""NO2 STAP cases bounded model"", ""NO2 STAP deaths bounded model""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-34488764-france-covid-r8406-20260926T000608Z,,34488764,agent_failure,result failed schema or autonomous-completion validation,2026-09-26T00:06:15.138875+00:00,2026-09-26T00:15:15.160859+00:00,0,0,0,1,162,"{""schema_version"": 3, ""study_id"": ""34488764-france-covid"", ""status"": ""completed_fit"", ""fidelity"": ""source_substitution"", ""target"": {""outcome"": ""Cumulative COVID-19 deaths in hospitals through 2020-05-01"", ""pollutant"": ""PM2.5"", ""geography"": ""96 mainland French departments (NUTS 3)"", ""population"": ""Department residents"", ""period"": ""PM2.5 annual means 1999\u20132016; mortality through 2020-05-01"", ""effect_scale"": ""Rate ratio per 1 microgram per cubic metre PM2.5"", ""exposure_assignment"": ""Unweighted polygon zonal mean of 18 annual NASA PM2.5 rasters"", ""model"": ""NB2 count regression with log department population offset"", ""covariates"": [""WorldClim temperature climatology"", ""combined resuscitation and intensive-care beds per 100k"", ""medical density"", ""age 60+ share"", ""male share"", ""unemployment"", ""poverty"", ""urban share"", ""population density"", ""diabetes""], ""named_outcome_source"": ""French Ministry of Health / Sant\u00e9 publique France data.gouv hospital COVID dataset"", ""specification_evidence"": [""/output/evidence/article.txt"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""exposure"", ""url"": ""https://gis.earthdata.nasa.gov/portal/rest/services/sdei/sdei-global-annual-gwr-pm2-5-modis-misr-seawifs-aod-v4-gl-03/ImageServer"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/nasa_imageserver.json""}, {""role"": ""outcome"", ""url"": ""https://www.data.gouv.fr/fr/datasets/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/covid_hospit.csv""}, {""role"": ""boundary"", ""url"": ""https://www.geoboundaries.org/api/current/gbOpen/FRA/ADM2/"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/geoboundaries.json""}, {""role"": ""weather"", ""url"": ""https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/retrieval/wc2.1_10m_bio.zip""}], ""substitutions"": [{""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""Article-stated WorldClim 2001\u20132012 temperature aggregation"", ""reanalysis"": ""WorldClim v2.1 BIO1 climatological department mean; centroid-cell fallback for Paris"", ""reason"": ""Exact article temperature aggregation was not recovered; complete public climatology is retained and explicitly classified as a substitution.""}], ""coverage"": {""eligible_units"": 96, ""included_units"": 96, ""eligible_times"": 18, ""included_times"": 18, ""rule"": ""Include departments with complete outcomes, covariates, and all 18 required annual PM2.5 slices."", ""notes"": ""All 96 departments met this rule. PM2.5 is 18/18 years for every unit.""}, ""artifacts"": {""code"": ""retrieve_exposure.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""retrieval/department_environment.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T001425.6974420000.json"", ""coverage_diagnostics"": ""coverage_report.json"", ""boundary_route_evidence"": ""retrieval/geoboundaries.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Exact article-stated WorldClim 2001\u20132012 temperature aggregation was not recovered; the temperature covariate is a declared source/time-window substitution.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""source_substitution""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/retrieval/covid_hospit.csv"", ""/output/retrieval/geoboundaries.json"", ""/output/retrieval/nasa_imageserver.json"", ""/output/retrieval/wc2.1_10m_bio.zip"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T001425.6974420000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""coverage_report.json"", ""decision_log.json"", ""model_output.json"", ""retrieval/department_environment.csv"", ""retrieval/geoboundaries.json"", ""retrieve_exposure.py"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""34488764-france-covid-reanalysis-invariants"", ""contract_sha256"": ""5b29ac517b34b018ee526b09cc6033d02a62a2ae6b8efe9901cdec37138bdc0e"", ""contract_author"": ""agent"", ""geographic_representation"": ""96 geoBoundaries France ADM2 department polygons (official IGN source stated in GeoBoundaries metadata); all mainland departments."", ""assignment_method"": ""Unweighted zonal mean over every valid 0.01-degree PM2.5 grid cell whose center falls in each department polygon; no monitor assignment."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""NASA Earthdata ImageServer public multidimensional Global Annual PM2.5 Grids (V4.GL.03), explicitly selecting each 1999\u20132016 annual slice; WorldClim v2.1 BIO1 used for temperature adjustment."", ""exposure_metric"": ""Arithmetic mean of 18 department annual PM2.5 zonal means, 1999\u20132016, \u00b5g/m\u00b3."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only: retain departments with all 18 valid annual PM2.5 means. WorldClim 10-arcminute cell containing the centroid is used only for Paris because its polygon contains no 10-arcminute cell center.""}, ""decision_rationale"": ""This directly implements the article's GOME/NASA SEDAC 1999\u20132016 department-level spatial mean construct using a maintained public NASA Earthdata distribution. It does not use author-published PM2.5 values. The covariate temperature source is a WorldClim climatology rather than the article-stated 2001\u20132012 aggregation, so that covariate substitution is declared separately."", ""evidence_basis"": [""NASA ImageServer metadata identifies the public global annual PM2.5 raster service, WGS84, 0.01-degree pixels, annual temporal dimension."", ""Independent zonal processing yielded 18/18 annual PM2.5 values for each of 96 departments; output includes mean/range and temperature coverage."", ""GeoBoundaries metadata reports France ADM2/Department, official IGN source, and 96 units.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Continuous PM2.5"", ""primary"": true, ""estimate"": 1.3536898948, ""ci_low"": 1.1923182787, ""ci_high"": 1.5369019866, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3 increase in long-term PM2.5"", ""metric"": ""RR"", ""native_estimate"": 0.3028341193, ""native_ci_low"": 0.175833639, ""native_ci_high"": 0.4298346, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""1 \u00b5g/m\u00b3 increase""}, {""label"": ""PM2.5 quartile Q2 versus Q1"", ""primary"": false, ""estimate"": 1.5308731566, ""ci_low"": 1.0436562288, ""ci_high"": 2.2455407794, ""scale"": ""ratio"", ""contrast"": ""Q2 versus Q1 derived from independent PM2.5 distribution"", ""metric"": ""RR"", ""native_estimate"": 0.4258382632, ""native_ci_low"": 0.042845, ""native_ci_high"": 0.808832, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q2 versus Q1""}, {""label"": ""PM2.5 quartile Q3 versus Q1"", ""primary"": false, ""estimate"": 3.0229027459, ""ci_low"": 1.8560172989, ""ci_high"": 4.9234137078, ""scale"": ""ratio"", ""contrast"": ""Q3 versus Q1 derived from independent PM2.5 distribution"", ""metric"": ""RR"", ""native_estimate"": 1.1062175439, ""native_ci_low"": 0.61837, ""native_ci_high"": 1.59407, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q3 versus Q1""}, {""label"": ""PM2.5 quartile Q4 versus Q1"", ""primary"": false, ""estimate"": 4.0383955331, ""ci_low"": 2.0244168091, ""ci_high"": 8.05596871596, ""scale"": ""ratio"", ""contrast"": ""Q4 versus Q1 derived from independent PM2.5 distribution"", ""metric"": ""RR"", ""native_estimate"": 1.3958474678, ""native_ci_low"": 0.70528, ""native_ci_high"": 2.08642, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""Q4 versus Q1""}], ""analysis_diagnostics"": {""observations"": 96, ""estimated_parameters"": 13, ""exposure_unique_values"": 96, ""outcome_unique_values"": 81, ""joined_rows"": 96, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""continuous PM2.5"", ""PM2.5 quartiles Q2/Q3/Q4 vs Q1""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-36383802-sao-jose-covid-r8406-recovery-20260926T034500Z,,36383802,completed_fit,,2026-09-26T06:21:57.964939+00:00,2026-09-26T06:39:46.484242+00:00,0,4,1,5,319,"{""schema_version"": 3, ""study_id"": ""36383802-sao-jose-covid"", ""status"": ""completed_fit"", ""fidelity"": ""source_substitution"", ""target"": {""outcome"": ""Daily COVID-19 hospital admissions among Sao Jose dos Campos residents"", ""pollutant"": ""O3 and NO2 (separate single-pollutant lag models)"", ""geography"": ""Sao Jose dos Campos, Sao Paulo, Brazil"", ""population"": ""Residents admitted for COVID-19"", ""period"": ""2020-04-01 through 2021-04-30"", ""effect_scale"": ""Rate ratio per 10 ug/m3"", ""exposure_assignment"": ""Daily mean of hourly values at municipal representative grid cell, America/Sao_Paulo local day"", ""model"": ""Negative-binomial log-link regression"", ""covariates"": [""daily mean temperature"", ""daily mean relative humidity"", ""day of week"", ""linear calendar day""], ""named_outcome_source"": ""Article: DATASUS SIH-SUS B34.2; reanalysis: official SIVEP-Gripe confirmed-COVID hospital notifications"", ""specification_evidence"": [""/study/article.txt lines 34-36, 73-103, 163-184"", ""/output/aeris-workspace/.aeris/contracts/agent-study-contract.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SRAG/2020/INFLUD20-23-03-2026.parquet"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""371723b91c0e4de1ae4067c8a6ee04887430869fa8d3c561d4b9106fb89e0c0b"", ""evidence_artifact"": ""/output/outcome_daily_sivep_proxy.csv""}, {""role"": ""outcome"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SRAG/2021/INFLUD21-23-03-2026.parquet"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""ecad01062f23715551a1e5e82fa1d9b28f0ea25e2c486a49518a15bf489ee790"", ""evidence_artifact"": ""/output/outcome_daily_sivep_proxy.csv""}, {""role"": ""exposure"", ""url"": ""https://opendap.nccs.nasa.gov/dods/gmao/geos-cf/assim/aqc_tavg_1hr_g1440x721_v1"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""cb3b4ab112a3a2564fc4cf23fc7c16cd76bc17348c686be9ff86ab9ccd9de2ba"", ""evidence_artifact"": ""/output/data/geoscf_provenance.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""b24f4fdc77a88ec730706c315d52e28355ad503bd716608fb22a75bed9b3cf24"", ""evidence_artifact"": ""/output/data/openmeteo_weather.json""}, {""role"": ""exposure"", ""url"": ""https://qualar.cetesb.sp.gov.br/qualar/home.do"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/qualar_home.html""}, {""role"": ""outcome"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/datasus_ftp_curl.log""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""SIH-SUS B34.2 admissions"", ""reanalysis"": ""SIVEP-Gripe confirmed-COVID hospital notifications"", ""reason"": ""SIH-SUS public transport timed out in retained attempt.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""CETESB daily measurements"", ""reanalysis"": ""NASA GEOS-CF hourly gridded model at nearest grid cell"", ""reason"": ""CETESB route required authentication; retained Open-Meteo pollutant payload was null.""}], ""coverage"": {""eligible_units"": 1, ""included_units"": 1, ""eligible_times"": 395, ""included_times"": 395, ""rule"": ""Retain only GEOS-CF local calendar days with 24 O3 and NO2 records; then apply the specified lag and complete-case covariate requirements."", ""notes"": ""All target-period local dates have complete hourly GEOS-CF coverage after retrieval of the three UTC edge hours needed for the final local date. SIVEP-Gripe notifications are a registry/source substitution for SIH-SUS B34.2 admissions.""}, ""artifacts"": {""code"": ""analyze_geoscf.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""exposure_daily_geoscf.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""native_model_output.txt"", ""decision_log"": ""aeris_analysis_artifacts.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""source_manifest.json"", ""fidelity_record"": ""aeris_analysis_artifacts.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""qualar_home.html"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-study-contract.json""}, ""blockers"": [""Article-named CETESB historical export was not publicly usable through tested route; GEOS-CF used as source substitute."", ""Article-named SIH-SUS transport timed out; SIVEP-Gripe used as source substitute.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 3, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": false, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""source_substitution""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/geoscf_provenance.json"", ""/output/data/openmeteo_weather.json"", ""/output/datasus_ftp_curl.log"", ""/output/outcome_daily_sivep_proxy.csv"", ""/output/qualar_home.html"", ""aeris-workspace/.aeris/contracts/agent-study-contract.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""aeris_analysis_artifacts.json"", ""analysis_panel.csv"", ""analyze_geoscf.py"", ""coverage_diagnostics.json"", ""exposure_daily_geoscf.csv"", ""native_model_output.txt"", ""qualar_home.html"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""36383802-sao-jose-covid-agent-authored"", ""contract_sha256"": ""d085fd7d62928d17280adc9e52703e6971c436676178c79d9b3cdbb446ec093c"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""nearest_monitor_to_unit_reference"", ""representative_location_rule"": ""Article-stated Sao Jose dos Campos coordinate, decimalized to latitude -23.1797, longitude -45.8872."", ""maximum_monitor_distance_km"": 200.0, ""monitor_distance_evidence"": ""Article calls the CETESB data city-level but does not identify station; source-substituted coordinate model has no monitor distance. Representative coordinate is article's stated municipal location."", ""source_strategy"": ""provider_api"", ""exposure_metric"": ""Daily arithmetic mean of hourly modeled/retrieved O3 and NO2 in ug/m3 at the city representative coordinate."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""The article gives no numeric completeness exclusion threshold; coverage will be reported, and analytic rows require nonmissing outcome, exposure and weather.""}, ""decision_rationale"": ""The article defines an ecological municipality-level daily comparison. The retained single coordinate represents the city monitor/model location rather than individuals. No article-supported coverage threshold exists, so missingness is reported. The initial regulator portal probe showed authentication; the design therefore permits independently recovered public gridded data while preserving pollutant, unit, period, lags, contrast, and model family."", ""evidence_basis"": [""/study/article.txt"", ""/study/article.xml"", ""/output/qualar_home.html"", ""/run/contract/study-target.json""], ""locked_before_exposure"": true}, ""effects"": [{""label"": ""O3 lag 2"", ""primary"": true, ""estimate"": 1.0263742977173338, ""ci_low"": 0.9953033539791288, ""ci_high"": 1.058415200554866, ""scale"": ""ratio"", ""contrast"": ""10 ug/m3 increase"", ""metric"": ""RR"", ""native_estimate"": 0.0026032492810638, ""native_ci_low"": -0.0004707710161001885, ""native_ci_high"": 0.005677269578227789, ""native_scale"": ""negative-binomial log rate coefficient per ug/m3"", ""native_contrast"": ""1 ug/m3 increase""}, {""label"": ""NO2 lag 3"", ""primary"": true, ""estimate"": 1.5249606083355989, ""ci_low"": 1.2130071598296124, ""ci_high"": 1.9171402560409747, ""scale"": ""ratio"", ""contrast"": ""10 ug/m3 increase"", ""metric"": ""RR"", ""native_estimate"": 0.0421968579126151, ""native_ci_low"": 0.019310253071928733, ""native_ci_high"": 0.06508346275330146, ""native_scale"": ""negative-binomial log rate coefficient per ug/m3"", ""native_contrast"": ""1 ug/m3 increase""}], ""analysis_diagnostics"": {""observations"": 392, ""estimated_parameters"": 12, ""exposure_unique_values"": 392, ""outcome_unique_values"": 36, ""joined_rows"": 395, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""o3 lag 0"", ""o3 lag 1"", ""o3 lag 2"", ""o3 lag 3"", ""o3 lag 4"", ""o3 lag 5"", ""o3 lag 6"", ""o3 lag 7"", ""no2 lag 0"", ""no2 lag 1"", ""no2 lag 2"", ""no2 lag 3"", ""no2 lag 4"", ""no2 lag 5"", ""no2 lag 6"", ""no2 lag 7""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-38182658-uk-covid-r8406-20260926T062342Z,,38182658,completed_fit,,2026-09-26T06:23:48.975906+00:00,2026-09-26T06:30:10.649238+00:00,0,0,0,1,103,"{""schema_version"": 3, ""study_id"": ""38182658-uk-covid"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Instantaneous COVID-19 case fatality: deaths back-projected to confirmation day among daily confirmed cases."", ""pollutant"": ""PM2.5"", ""geography"": ""England, Scotland, Wales, and Northern Ireland"", ""population"": ""Laboratory-confirmed COVID-19 cases among residents of the four UK constituent countries"", ""period"": ""Article target 2020-03-26 through 2020-09-15; bounded fitted effective dates 2020-03-26 through 2020-06-22."", ""effect_scale"": ""Odds ratio"", ""exposure_assignment"": ""Article: daily country averages. Bounded implementation: Open-Meteo gridded PM2.5 daily means at each national-capital coordinate, summarized over lags 0\u201310."", ""model"": ""Article Model 6 target is binomial-logit GLMM DLNM. Fitted bounded analogue is binomial GLM with flexible cubic bases of 0\u201310-day mean PM2.5, temperature and sunshine, plus country and weekday fixed effects."", ""covariates"": [""temperature"", ""sunshine duration"", ""weekday"", ""country""], ""named_outcome_source"": ""Public historical UK nation indicators archive derived from the sources documented in its retained sources file."", ""specification_evidence"": [""/study/article.txt"", ""/study/supplements/41598_2023_50474_MOESM1_ESM.docx"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/tomwhite/covid-19-uk-data/master/data/covid-19-indicators-uk.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""151ecd06edb90e137ddddb822305ac642ca58297f2155362df2e4b7661d4a1f5"", ""evidence_artifact"": ""/output/raw/covid-19-indicators-uk.csv""}, {""role"": ""exposure"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/openmeteo_air_England.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/openmeteo_weather_England.json""}, {""role"": ""other"", ""url"": ""OpenAQ historical archive via AERIS"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""6884d2ffb6fd6442fd9df84a5d26ca01deb2ca32b26ee01977b25bfb92724437"", ""evidence_artifact"": ""/output/aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-26T062823.6450900000.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""DEFRA Air Information Resource daily country average"", ""reanalysis"": ""Open-Meteo gridded daily PM2.5 at each national-capital coordinate"", ""reason"": ""Decoded, complete four-location historical public series retained; monitor-boundary feasibility route was also exercised through AERIS.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2020-03-26 through 2020-09-15"", ""reanalysis"": ""2020-03-26 through 2020-06-22 effective fit period"", ""reason"": ""The recovered four-nation health overlap ends 2020-06-30 and 8-day outcome alignment excludes its trailing days.""}, {""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""Non-parametric gamma back-projected deaths"", ""reanalysis"": ""Reported deaths shifted eight days earlier and capped at daily cases"", ""reason"": ""The paper gives a 7.92-day mean delay, but exact delay records/distribution and original outcome data were not recovered.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""Distributed-lag nonlinear mixed model"", ""reanalysis"": ""Flexible lag-mean binomial GLM with country/weekday fixed effects"", ""reason"": ""Transparent bounded analogue when exact cross-basis/mixed-effect implementation cannot be supported by recovered inputs.""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 4, ""eligible_times"": 174, ""included_times"": 89, ""rule"": ""Retain all country-days with observed positive daily cases, available shifted deaths, and complete 0\u201310 day environmental histories; no numeric environmental completeness exclusion was imposed."", ""notes"": ""351 fit rows: England 89, Scotland 89, Wales 89, Northern Ireland 84. Raw PM2.5 is complete in every recovered environmental country-day; the five missing Northern Ireland outcome rows explain the asymmetric fit count. See coverage_report.json.""}, ""artifacts"": {""code"": ""retrieve_and_fit.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""raw/openmeteo_air_England.json"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T062929.2255810000.json"", ""coverage_diagnostics"": ""coverage_report.json"", ""boundary_route_evidence"": ""boundary_route_evidence.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Not a matched reproduction: environmental support changed from country monitor averages to capital-coordinate gridded values."", ""Not a full-period reproduction: the retained common four-nation outcome series ends before the article period."", ""Not exact back-projection or DLNM: retained public inputs support only the documented bounded proxies.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/aeris-workspace/.aeris/artifacts/exposure_pm25_2026-09-26T062823.6450900000.csv"", ""/output/raw/covid-19-indicators-uk.csv"", ""/output/raw/openmeteo_air_England.json"", ""/output/raw/openmeteo_weather_England.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T062929.2255810000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""boundary_route_evidence.json"", ""coverage_report.json"", ""decision_log.json"", ""model_output.json"", ""raw/openmeteo_air_England.json"", ""retrieve_and_fit.py"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""38182658-uk-covid-reanalysis-invariants"", ""contract_sha256"": ""52c7a92e99acfcb22ed71db238e18ea0a4aefae7dd763bb17d2149182778719a"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""within_boundary_monitor_mean, separately by country and day; retain contributing monitor metadata."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""daily ambient PM2.5 country mean in \u00b5g/m\u00b3; raw gaps then article-specified trailing-7-day imputation only in analysis table."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""report_only: the article supplies no numeric threshold; report raw and imputed coverage.""}, ""decision_rationale"": ""This is the first executable exposure-design amendment, preserving the article's administrative country-day pollutant construct while keeping public source selection open pending feasibility probes."", ""evidence_basis"": [""Article environmental-data methods specify daily pollutant averages for every country and 7-day preceding-average replacement for missing observations."", ""Article model formulation specifies country-level daily outcomes and a maximum 10-day lag for air pollution.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Bounded PM2.5 lag-mean analogue"", ""primary"": true, ""estimate"": 1.7189892341, ""ci_low"": 1.7076838423, ""ci_high"": 1.7303694711, ""scale"": ""ratio"", ""contrast"": ""PM2.5 19 versus 10 \u00b5g/m\u00b3 for the fitted 0\u201310-day lag mean; covariate values held at medians, England/Monday design row."", ""metric"": ""OR"", ""native_estimate"": 0.5417364635, ""native_ci_low"": 0.5351383131, ""native_ci_high"": 0.5483346139, ""native_scale"": ""log odds ratio"", ""native_contrast"": ""19 versus 10 \u00b5g/m\u00b3""}], ""analysis_diagnostics"": {""observations"": 351, ""estimated_parameters"": 19, ""exposure_unique_values"": 335, ""outcome_unique_values"": 139, ""joined_rows"": 428, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""Article Model 6 target implemented as bounded lag-mean binomial-logit analogue""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-38788590-brazil-cancer-r8406-20260926T062401Z,,38788590,policy_termination,free disk fell below 10 GiB,2026-09-26T06:24:07.347828+00:00,2026-09-26T06:46:42.279216+00:00,0,2,0,3,285,"{""schema_version"": 3, ""study_id"": ""38788590-brazil-cancer"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily all-cancer deaths (ICD-10 C00-C97)"", ""pollutant"": ""PM2.5"", ""geography"": ""Brazilian municipalities (5570 in the article)"", ""population"": ""Individual Brazilian Mortality Information System cancer death records"", ""period"": ""2000-01-01 through 2019-12-31"", ""effect_scale"": ""Odds ratio per 10 micrograms per cubic metre"", ""exposure_assignment"": ""Population-weighted municipal mean of 0.25-degree daily PM2.5 grids; lag 0-2 three-day mean"", ""model"": ""Time-stratified case-crossover conditional logistic regression; same weekday within calendar month controls"", ""covariates"": [""temperature cross-basis"", ""relative humidity"", ""public holiday""], ""named_outcome_source"": ""Brazilian Mortality Information System (SIM)"", ""specification_evidence"": [""/study/article.txt"", ""ResearchGate full-text recovery, methods lines 424-790"", ""/output/recovery/pubmed-38788590.medline""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://redu.unicamp.br/api/access/datafile/17721?format=original"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/review2/sim_2019.parquet.sha256""}, {""role"": ""exposure"", ""url"": ""https://redu.unicamp.br/api/access/datafile/17719"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/cetesb_mp25.parquet""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""coverage_subset"", ""published"": ""All Brazilian municipalities, 2000-2019"", ""reanalysis"": ""Sao Paulo municipality, 2019"", ""reason"": ""The first complete public annual SIM member recovered under the predeclared byte-range design.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Population-weighted municipality-level 0.25-degree daily PM2.5 grid"", ""reanalysis"": ""Equal-station mean of observed CETESB PM2.5 monitors"", ""reason"": ""The public monitor archive supplied daily observed PM2.5 for a bounded city slice.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Temperature cross-basis, relative humidity, public holiday"", ""reanalysis"": ""None"", ""reason"": ""No daily covariate series was recovered into the bounded fit.""}], ""coverage"": {""eligible_units"": 5570, ""included_units"": 1, ""eligible_times"": 7305, ""included_times"": 365, ""rule"": ""Predeclared Sao Paulo 2019 subset; retain days with a complete three-day PM2.5 mean."", ""notes"": ""363 of 365 days had complete lag 0-2 exposure. The daily input panel is expanded by death event and same-weekday/calendar-month referents into 68,454 conditional-logistic rows for 15,647 cancer-death events.""}, ""artifacts"": {""code"": ""recovery/review2_recover_2019.sh"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""recovery/cetesb_mp25.parquet"", ""analysis_panel"": ""recovery/review2/bounded_casecrossover_analysis_panel.csv"", ""model_output"": ""recovery/review2/bounded_model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T064353.4276410000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""blocker_ledger.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""daily_source_panel"": ""recovery/review2/bounded_panel_2019_sao_paulo.csv"", ""row_accounting_audit"": ""recovery/review2/casecrossover_row_accounting_audit.json"", ""skeptical_audit"": ""recovery/review2/skeptical_postreview_audit.json""}, ""blockers"": [""This is not a nationwide replication: it covers one municipality and one year."", ""The exposure is a city monitor-network mean rather than the published population-weighted grid."", ""Temperature, relative humidity, and holiday adjustment are omitted.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/recovery/cetesb_mp25.parquet"", ""/output/recovery/review2/sim_2019.parquet.sha256"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T064353.4276410000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger.json"", ""coverage_diagnostics.json"", ""decision_log.json"", ""recovery/cetesb_mp25.parquet"", ""recovery/review2/bounded_casecrossover_analysis_panel.csv"", ""recovery/review2/bounded_model_output.json"", ""recovery/review2/bounded_panel_2019_sao_paulo.csv"", ""recovery/review2/casecrossover_row_accounting_audit.json"", ""recovery/review2/skeptical_postreview_audit.json"", ""recovery/review2_recover_2019.sh"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""38788590-brazil-cancer-reanalysis-invariants"", ""contract_sha256"": ""bb139cd2c5ec66a0ee6df9ac5136a0a1aec63465f43ecb400b5f99832fa5264e"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Municipality-code assignment joining CODMUNRES to CODE_MUNI; use population weighting only when public grid/population support is recovered."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""local_model"", ""exposure_metric"": ""Municipality-level PM2.5 lag 0\u20132 three-day arithmetic mean in micrograms per cubic metre."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only; fit requires nonmissing daily cancer outcome, three PM2.5 values, and recoverable covariates; no unsupported numeric threshold.""}, ""decision_rationale"": ""Defines an executable exposure and panel plan for the required fresh recovery attempt without modifying outcome, pollutant, lag construct, geography, contrast, or model family."", ""evidence_basis"": [""Abstract specifies individual cancer deaths in Brazilian municipalities, daily PM2.5, 2000\u20132019, and a three-day PM2.5 mean."", ""Target supplies time-stratified case-crossover conditional regression and weather/holiday covariates."", ""Public source documents daily municipality linkage via CODMUNRES and CODE_MUNI."", ""Review requires an evidence-backed executable design and fresh counterexample recovery.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""All-cancer mortality, Sao Paulo 2019 bounded sensitivity"", ""primary"": true, ""estimate"": 1.017754138136571, ""ci_low"": 0.9858916320293315, ""ci_high"": 1.0506463915937743, ""scale"": ""ratio"", ""contrast"": ""per 10 micrograms per cubic metre PM2.5"", ""metric"": ""OR"", ""native_estimate"": 0.001759837435836515, ""native_ci_low"": -0.001421149598364593, ""native_ci_high"": 0.004940824470037623, ""native_scale"": ""conditional logistic coefficient"", ""native_contrast"": ""per 1 microgram per cubic metre PM2.5""}], ""analysis_diagnostics"": {""observations"": 68454, ""estimated_parameters"": 1, ""exposure_unique_values"": 363, ""outcome_unique_values"": 365, ""joined_rows"": 68454, ""unmatched_outcome_rows"": 2, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""Unadjusted bounded Sao Paulo 2019 all-cancer sensitivity; event-expanded case-crossover panel""]}}" |
| self-driving-aeris,r8406,codex-aeris-self-driving-39377000-us-stroke-r8406-20260926T062408Z,,39377000,completed_sensitivity,,2026-09-26T06:24:15.031685+00:00,2026-09-26T06:30:25.192304+00:00,0,0,0,1,136,"{""schema_version"": 3, ""study_id"": ""39377000-us-stroke"", ""status"": ""completed_sensitivity"", ""fidelity"": ""supported_sensitivity"", ""target"": {""outcome"": ""County ischemic and hemorrhagic stroke mortality rate"", ""pollutant"": ""PM2.5"", ""geography"": ""US counties and county equivalents"", ""population"": ""Adults aged 65 years and older"", ""period"": ""Article: 2016-2020; recovered sensitivity: 2020-2022"", ""effect_scale"": ""Additive deaths per 100,000 per 1 ug/m3 PM2.5"", ""exposure_assignment"": ""County-level annual PM2.5"", ""model"": ""Ordinary linear regression"", ""covariates"": [""Article specified: CAD, hypertension, diabetes, high cholesterol, obesity, smoking, income, Gini, poverty, insurance, park access""], ""named_outcome_source"": ""CDC WONDER and Interactive Atlas on Heart Disease and Stroke"", ""specification_evidence"": [""/output/article-specification.json"", ""/study/article.md""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://heart-stroke-atlas.cdc.gov/api/api/data"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/ischemic.json""}, {""role"": ""exposure"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2020.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/exposure_county_pm25.csv""}, {""role"": ""covariate"", ""url"": ""https://api.census.gov/data/2021/acs/acs5"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/raw/acs2021.json""}], ""substitutions"": [{""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2016-2020"", ""reanalysis"": ""2020-2022"", ""reason"": ""Current Atlas API exposed usable subtype outcome records in 2020-2022.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""Unnamed county PM2.5 source"", ""reanalysis"": ""EPA AQS unweighted county monitor mean"", ""reason"": ""Article source not named; public AQS records were usable.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Full article covariate set"", ""reanalysis"": ""Unadjusted OLS"", ""reason"": ""Census route required unavailable key and remaining covariates were not recovered.""}, {""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""3142 units"", ""reanalysis"": ""551 ischemic and 430 hemorrhagic observed-overlap units"", ""reason"": ""Outcome suppression and monitor availability.""}], ""coverage"": {""eligible_units"": 3226, ""included_units"": 551, ""eligible_times"": 3, ""included_times"": 3, ""rule"": ""Observed AQS annual PM2.5 plus non-suppressed CDC Atlas outcome; report-only coverage policy."", ""notes"": ""See coverage_diagnostics.json; hemorrhagic model has 430 rows.""}, ""artifacts"": {""code"": ""reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""exposure_county_pm25.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.csv"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T062942.0135020000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""blocker_ledger.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""The ratio-shaped fields are schema placeholders only: the scientifically valid effects are native additive slopes; no exponentiation was performed."", ""Original-period county subtype outcome panel and article covariates were not recovered through usable public routes.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""supported_sensitivity""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/exposure_county_pm25.csv"", ""/output/raw/acs2021.json"", ""/output/raw/ischemic.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T062942.0135020000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""coverage_diagnostics.json"", ""decision_log.json"", ""exposure_county_pm25.csv"", ""model_output.csv"", ""reanalysis.py"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""39377000-us-stroke-reanalysis-invariants"", ""contract_sha256"": ""fca4111bbf2552b58e27aa8139bb3dcf56cd5794e5af66d777dae32edaaaa01b"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Within-county unweighted mean of EPA AQS annual PM2.5 monitor arithmetic means, then equal-weight mean across 2020\u20132022"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""County mean of annual PM2.5 monitor means (\u00b5g/m\u00b3)"", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only; include counties with observed EPA annual PM2.5 and non-suppressed CDC Atlas outcome; no unsupported completeness cutoff.""}, ""decision_rationale"": ""The complete article does not name an exposure source. EPA AQS is a public regulatory monitor archive with usable 2020\u20132022 annual PM2.5 records. The current public Atlas exposes 2020\u20132022 rather than 2016\u20132020. This is a bounded analysis retaining county ecological spatial support, target outcomes, PM2.5, and OLS model family while explicitly changing exposure implementation, period, and adjustment."", ""evidence_basis"": [""EPA annual archives yield 643 counties with PM2.5 and 551 ischemic-outcome/exposure overlaps; CDC Atlas produces 2020\u20132022 age-65+ county outcome records."", ""CDC Atlas configuration documents Ischemic Stroke and Hemorrhagic Stroke death-rate themes and age/race/sex/time filters.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Ischemic stroke, unadjusted OLS"", ""primary"": true, ""estimate"": 1.0, ""ci_low"": null, ""ci_high"": null, ""scale"": ""ratio"", ""contrast"": ""No ratio conversion: native article-compatible additive slope below"", ""metric"": ""outcome_ratio"", ""native_estimate"": 2.3557099746, ""native_ci_low"": 0.6641957406, ""native_ci_high"": 4.0472242086, ""native_scale"": ""deaths per 100,000"", ""native_contrast"": ""per 1 ug/m3 PM2.5""}, {""label"": ""Hemorrhagic stroke, unadjusted OLS"", ""primary"": false, ""estimate"": 1.0, ""ci_low"": null, ""ci_high"": null, ""scale"": ""ratio"", ""contrast"": ""No ratio conversion: native article-compatible additive slope below"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.6559801668, ""native_ci_low"": -0.0131970278, ""native_ci_high"": 1.3251573614, ""native_scale"": ""deaths per 100,000"", ""native_contrast"": ""per 1 ug/m3 PM2.5""}], ""analysis_diagnostics"": {""observations"": 551, ""estimated_parameters"": 2, ""exposure_unique_values"": 551, ""outcome_unique_values"": 551, ""joined_rows"": 551, ""unmatched_outcome_rows"": 1134, ""unmatched_exposure_rows"": 92, ""contrast_transformation_verified"": true, ""reported_variants"": [""ischemic_unadjusted"", ""hemorrhagic_unadjusted""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-33227571-sao-paulo-ami-r8407-20260925T214137Z,,33227571,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T21:41:44.475575+00:00,2026-09-25T22:02:56.872563+00:00,0,3,0,4,233,"{""schema_version"": 3, ""study_id"": ""33227571-sao-paulo-ami"", ""status"": ""completed_blocker"", ""fidelity"": ""none"", ""target"": {""outcome"": ""Daily acute myocardial infarction admissions and in-hospital deaths"", ""pollutant"": ""NO2, PM2.5, and PM10"", ""geography"": ""39 municipalities in metropolitan Sao Paulo, Brazil, aggregated daily"", ""population"": ""SUS acute myocardial infarction admissions"", ""period"": ""2012-10-01 through 2015-09-30"", ""effect_scale"": ""Article comparison scale not specified in the supplied record"", ""exposure_assignment"": ""Daily metropolitan pollutant-weather clusters"", ""model"": ""Hierarchical cluster comparison; exact inferential model not identified in supplied article materials"", ""covariates"": [""temperature"", ""temperature variation"", ""rainfall"", ""relative humidity""], ""named_outcome_source"": ""DataSUS SIH-RD public mirror"", ""specification_evidence"": [""/output/article-specification-evidence.md"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://huggingface.co/datasets/SidneyBissoli/sih-rd"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""d6a42d81fdce4a7c5c9485142726cd74f3dfa6d09ce278005d94ccdd0e86fc42"", ""evidence_artifact"": ""/output/outcomes_probe.parquet""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""b1d469a171320f7812719d03920e4e66df9fe7177162ba50401330d4663075ce"", ""evidence_artifact"": ""/output/analysis_panel.csv""}, {""role"": ""exposure"", ""url"": ""https://servicos.cetesb.sp.gov.br/arcgis/rest/services/QA_Hist/QA_Hist/MapServer"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/article-specification-evidence.md""}, {""role"": ""exposure"", ""url"": ""https://servicos.cetesb.sp.gov.br/arcgis/rest/services/QUALAR/CETESB_QUALAR/MapServer"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": ""1dc9b88f8b58970c674de4393c137e79d45d7e6d0774a1cdd3d2773df6172b44"", ""evidence_artifact"": ""/output/review/cetesb_qualar_service.json""}, {""role"": ""exposure"", ""url"": ""https://qualar.cetesb.sp.gov.br/qualar/exportaDados.do?method=pesquisar"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": ""87f69ced208dad313ed0363ace34c916d2c09818e1696352d7f694a1974f411a"", ""evidence_artifact"": ""/output/review/qualar_auth.body""}, {""role"": ""exposure"", ""url"": ""https://repositorio.cetesb.sp.gov.br/server/api/discover/search/objects"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": ""bba914578b1b7a7b68d009cb31067460194b433578766463f812cf5d703551dd"", ""evidence_artifact"": ""/output/review/cetesb_repo_bitstreams.tsv""}, {""role"": ""exposure"", ""url"": ""https://api.openaq.org/"", ""route_origin"": ""agent_discovered"", ""retrieved"": false, ""sha256"": ""7fbd3ede21f2d489539fa3fe9e652c25d32d02c152e08f91eb91f0e8e9bfb5e8"", ""evidence_artifact"": ""/output/aeris_pm25_openAQ_exposure.csv""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""construct_change"", ""published"": ""CETESB daily NO2, PM2.5 and PM10 monitor data included with weather in environmental clusters"", ""reanalysis"": ""No usable target-period pollutant series; weather-only proxy retained separately and not used to claim the article estimand"", ""reason"": ""All retained unauthenticated public pollutant routes yielded zero usable observations or required unavailable credentials.""}], ""coverage"": {""eligible_units"": 39, ""included_units"": 0, ""eligible_times"": 1095, ""included_times"": 0, ""rule"": ""No analytic pollutant-exposure panel was created because coverage for the required pollutant construct was 0%."", ""notes"": ""Outcome and weather records were recovered, but no usable daily NO2, PM2.5, or PM10 records overlap the article period.""}, ""artifacts"": {""code"": ""retrieve_outcomes.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""aeris_pm25_openAQ_exposure.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision_log.json"", ""research_notebook"": ""research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T215004.5644580000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""counterexample_review"": ""counterexample_review.md"", ""boundary_route_evidence"": ""aeris_pm25_openAQ_exposure.csv"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""No usable public daily NO2, PM2.5, or PM10 observations were recovered for 2012-10-01 through 2015-09-30; the locked pollutant-cluster estimand was therefore not fit."", ""Fresh counterexample review directly exercised four article-named CETESB routes: official QA_Hist service discovery, official QUALAR PM10/PM2.5/NO2 query transport, maintained qualR client authentication/export transport, and the CETESB repository API. The ArcGIS endpoints expose current 48-hour data only; the export requires an unavailable account; repository reports are summary documents rather than daily records. See /output/counterexample_review.md."", ""CAMS EAC4 is a plausible reanalysis substitution but its official download service requires an unavailable user API key; it was not represented as recovered data.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": true, ""historical_fallback_tested"": true, ""geographic_batching_applicable"": false, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/aeris_pm25_openAQ_exposure.csv"", ""/output/analysis_panel.csv"", ""/output/article-specification-evidence.md"", ""/output/outcomes_probe.parquet"", ""/output/review/cetesb_qualar_service.json"", ""/output/review/cetesb_repo_bitstreams.tsv"", ""/output/review/qualar_auth.body"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T215004.5644580000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris_pm25_openAQ_exposure.csv"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""counterexample_review.md"", ""coverage_diagnostics.json"", ""decision_log.json"", ""model_output.json"", ""research-notebook.json"", ""retrieve_outcomes.py"", ""source_manifest.json""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-33398753-italy-cities-r8407-20260925T220300Z,,33398753,completed_sensitivity,,2026-09-25T22:03:08.087545+00:00,2026-09-25T22:09:37.253301+00:00,0,0,0,1,94,"{""schema_version"": 3, ""study_id"": ""33398753-italy-cities"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Cumulative reported COVID-19 cases (three dates)"", ""pollutant"": ""PM10"", ""geography"": ""Italian provincial-capital cities"", ""population"": ""Article sample of 55 cities; bounded probe subset"", ""period"": ""2018 exposure; March-April 2020 outcomes"", ""effect_scale"": ""outcome ratio per doubling of annual PM10 exceedance days"", ""exposure_assignment"": ""nearest public monitor within 100 km"", ""model"": ""log-log OLS with log population density"", ""covariates"": [""2019 municipal population density proxy""], ""named_outcome_source"": ""Italian Civil Protection province-level historical feed"", ""specification_evidence"": [""/study/article.txt Tables 6-7"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-province/dpc-covid19-ita-province.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""d9f39377b0c3b0e8f4ac68b8e57cd9c1e953a4b922574b9438dc62094fb6446f"", ""evidence_artifact"": ""/output/raw/dpc_province.csv""}, {""role"": ""exposure"", ""url"": ""AERIS/OpenAQ public archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/pm10_daily_observations_combined.csv""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""city infected individuals"", ""reanalysis"": ""province-level cumulative cases matched to capital name"", ""reason"": ""Public national historical feed is published by province, while article city identities and city-level outcome source are unavailable.""}, {""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""55 randomly selected provincial-capital cities"", ""reanalysis"": ""four-city deterministic feasibility subset"", ""reason"": ""Article does not identify its sample; one of five exposure probes lacked a usable daily PM10 series.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""ISTAT 2019 city density"", ""reanalysis"": ""explicit municipal-density proxy values in executable code"", ""reason"": ""Bounded fit uses retained public-value proxy pending recoverable machine-readable ISTAT route.""}], ""coverage"": {""eligible_units"": 55, ""included_units"": 4, ""eligible_times"": 365, ""included_times"": 1332, ""rule"": ""Bounded feasibility subset; retained cities with usable 2018 PM10 daily records and positive threshold counts; coverage reported, no source-supported completeness threshold."", ""notes"": ""Four of five probe capitals had usable daily data; observed days range 316-343.""}, ""artifacts"": {""code"": ""code/reanalyze.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""data/exposure_exceedance_counts.csv"", ""analysis_panel"": ""data/analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""fidelity_record.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": null, ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Article city identities absent from supplied materials; exact 55-city replication cannot be verified."", ""Outcome public source is province-level, not city-level."", ""Four-city bounded model has one residual degree of freedom and is not substantively interpretable.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/pm10_daily_observations_combined.csv"", ""/output/raw/dpc_province.csv"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger.json"", ""code/reanalyze.py"", ""coverage_diagnostics.json"", ""data/analysis_panel.csv"", ""data/exposure_exceedance_counts.csv"", ""fidelity_record.json"", ""model_output.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""33398753-italy-cities-reanalysis-invariants"", ""contract_sha256"": ""9a5e7d4e76976ac046f8a12b04c5e0efe7e59e5199f7adf69ef8c0997692b69a"", ""contract_author"": ""agent"", ""geographic_representation"": ""fixed_location"", ""assignment_method"": ""nearest catalog-discovered PM10 monitor within 100 km of provincial-capital coordinate; retain city-monitor distance"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""count of observed 2018 daily PM10 means strictly greater than 50 ug/m3"", ""coverage_policy"": {""mode"": ""report_only_with_bounded_subset"", ""minimum_percent"": 0, ""threshold_source"": ""No article or source-supported numeric completeness threshold"", ""evidence"": ""Retain every city with a positive threshold count and report observed days/365; selection is a feasibility subset, not the complete article sample.""}, ""decision_rationale"": ""The locked metric requires a threshold count, so daily observations rather than the annual mean summary will be used. A 100-km search bound produced usable independent records for both feasibility cities; temporal coverage and monitor distances will be retained."", ""evidence_basis"": [""Milano and Roma have 670 daily PM10 records in 2018 via AERIS/OpenAQ and daily values support deriving threshold days."", ""Probe selected one catalog-discovered monitor per city with observed city-monitor distances up to 60.4 km.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""cases_2020_03_17"", ""primary"": true, ""estimate"": 0.7267035116644707, ""ci_low"": 1.9862305117427608e-05, ""ci_high"": 26587.95093234719, ""scale"": ""ratio"", ""contrast"": ""doubling of annual PM10 >50 ug/m3 days"", ""metric"": ""outcome_ratio"", ""native_estimate"": -0.46056121698311653, ""native_ci_low"": -15.619607410054964, ""native_ci_high"": 14.698484976088732, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log annual exceedance days""}, {""label"": ""cases_2020_04_07"", ""primary"": false, ""estimate"": 0.8410536744546437, ""ci_low"": 5.670732705393762e-05, ""ci_high"": 12474.072047882559, ""scale"": ""ratio"", ""contrast"": ""doubling of annual PM10 >50 ug/m3 days"", ""metric"": ""outcome_ratio"", ""native_estimate"": -0.24973022140030907, ""native_ci_low"": -14.106105319138097, ""native_ci_high"": 13.606644876337478, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log annual exceedance days""}, {""label"": ""cases_2020_04_27"", ""primary"": false, ""estimate"": 0.8333283142047269, ""ci_low"": 3.916886927238349e-05, ""ci_high"": 17729.285837334945, ""scale"": ""ratio"", ""contrast"": ""doubling of annual PM10 >50 ug/m3 days"", ""metric"": ""outcome_ratio"", ""native_estimate"": -0.26304309514630164, ""native_ci_low"": -14.639932993293183, ""native_ci_high"": 14.11384680300058, ""native_scale"": ""log outcome per log exposure"", ""native_contrast"": ""one-unit increase in log annual exceedance days""}], ""analysis_diagnostics"": {""observations"": 4, ""estimated_parameters"": 3, ""exposure_unique_values"": 4, ""outcome_unique_values"": 12, ""joined_rows"": 4, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""Multivariable log-log OLS for 17 March 2020"", ""Multivariable log-log OLS for 7 April 2020"", ""Multivariable log-log OLS for 27 April 2020"", ""Article-supported pollution-stratified density regressions: not identifiable in four-city bounded slice""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-33484722-oecd-covid-r8407-20260925T220938Z,,33484722,completed_fit,,2026-09-25T22:09:45.380808+00:00,2026-09-25T22:16:04.678274+00:00,0,0,0,1,59,"{""schema_version"": 3, ""study_id"": ""33484722-oecd-covid"", ""status"": ""completed_fit"", ""fidelity"": ""source_substitution"", ""target"": {""outcome"": ""National COVID-19 confirmed case and death rates at day 60 and day 80 after first confirmed case"", ""pollutant"": ""PM2.5"", ""geography"": ""36 OECD countries as of March 2020, excluding Colombia"", ""population"": ""National populations of those countries"", ""period"": ""2017 long-term PM2.5 and 2020 COVID-19 epidemics"", ""effect_scale"": ""Outcome ratio exp(beta) per 1 ug/m3 PM2.5"", ""exposure_assignment"": ""Direct ISO3 country assignment of World Bank population-weighted annual PM2.5"", ""model"": ""OLS of log(rate) at each epidemic day, with intercept"", ""covariates"": [""age 65+ percent"", ""population density"", ""GDP per capita"", ""physicians"", ""hospital beds"", ""PM2.5 percent above WHO guideline""], ""named_outcome_source"": ""WHO daily national COVID-19 data (article); JHU CSSE archive used after WHO route failure"", ""specification_evidence"": [""/output/specification-evidence.json""]}, ""sources"": [{""role"": ""exposure"", ""url"": ""https://api.worldbank.org/v2/country/all/indicator/EN.ATM.PM25.MC.M3?format=json&per_page=20000"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/wb_EN.ATM.PM25.MC.M3.json""}, {""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/jhu_confirmed_global.csv""}, {""role"": ""covariate"", ""url"": ""https://api.worldbank.org/v2/country/all/indicator/NY.GDP.PCAP.CD?format=json&per_page=20000"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/wb_NY.GDP.PCAP.CD.json""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""WHO daily country series"", ""reanalysis"": ""JHU CSSE archived daily country series"", ""reason"": ""WHO live historical CSV returned HTTP 403; JHU supplied all target records.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""OECD GDP 2019"", ""reanalysis"": ""World Bank GDP per capita 2019"", ""reason"": ""Stable public API with the same covariate construct.""}, {""dimension"": ""population"", ""change_type"": ""coverage_subset"", ""published"": ""36 countries"", ""reanalysis"": ""35 complete-case countries"", ""reason"": ""USA lacks a physician observation in the article's allowed 2015-2017 window.""}], ""coverage"": {""eligible_units"": 36, ""included_units"": 35, ""eligible_times"": 2, ""included_times"": 2, ""rule"": ""Complete-case per country and epidemic day; no exposure coverage threshold was applied."", ""notes"": ""All 36 countries have PM2.5 and both outcomes; USA is excluded only for missing physician covariate.""}, ""artifacts"": {""code"": ""reanalysis.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""analysis_panel.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""effects.json"", ""decision_log"": ""decision-log.json"", ""research_notebook"": ""research-notebook.json"", ""blocker_ledger"": ""data/who_route_error.txt"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T221426.2792680000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""WHO live historical CSV endpoint returned HTTP 403; source substitution retained all country-day outcome records."", ""USA lacks physician data in 2015-2017, producing a 35/36 complete-case sample.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""source_substitution""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/jhu_confirmed_global.csv"", ""/output/data/wb_EN.ATM.PM25.MC.M3.json"", ""/output/data/wb_NY.GDP.PCAP.CD.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T221426.2792680000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""analysis_panel.csv"", ""coverage_diagnostics.json"", ""data/who_route_error.txt"", ""decision-log.json"", ""effects.json"", ""reanalysis.py"", ""research-notebook.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""33484722-oecd-covid-reanalysis-invariants"", ""contract_sha256"": ""20502f9a7c2aeea76d76fcc552af3143dac6f2f0b264951599d3659479f1426c"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Direct assignment of public World Bank country-level population-weighted PM2.5 indicator to its ISO3 national administrative unit; no monitor interpolation is applicable."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""local_model"", ""exposure_metric"": ""2017 annual population-weighted mean PM2.5 concentration in \u00b5g/m\u00b3 (World Bank EN.ATM.PM25.MC.M3)."", ""coverage_policy"": {""mode"": ""report-only complete-case analytic coverage"", ""minimum_percent"": null, ""threshold_source"": ""Article specifies no numeric coverage threshold"", ""evidence"": ""All 36 countries have PM2.5; USA has no allowed-window physician value, leaving 35 complete countries per model.""}, ""decision_rationale"": ""The article itself defines population-weighted national PM2.5, so a public country indicator is the matching spatial and temporal support; monitor assignment would change the exposure construct."", ""evidence_basis"": [""All 36 ISO3 units contain a 2017 PM2.5 value; exposure is directly country-level and population-weighted."", ""The only complete-case loss is the USA physician covariate, not exposure coverage.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""day-60 case-rate ratio per 1 ug/m3 PM2.5"", ""primary"": true, ""estimate"": 1.1464274270821027, ""ci_low"": 0.9734368915470697, ""ci_high"": 1.350160300045027, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 higher 2017 population-weighted PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.13665052177643247, ""native_ci_low"": -0.026922282622439564, ""native_ci_high"": 0.3002233261753045, ""native_scale"": ""OLS coefficient on log rate"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""day-60 death-rate ratio per 1 ug/m3 PM2.5"", ""primary"": true, ""estimate"": 1.1809024534141734, ""ci_low"": 0.9356988001469596, ""ci_high"": 1.4903627152889276, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 higher 2017 population-weighted PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.16627893720289966, ""native_ci_low"": -0.06646164900636117, ""native_ci_high"": 0.3990195234121605, ""native_scale"": ""OLS coefficient on log rate"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""day-80 case-rate ratio per 1 ug/m3 PM2.5"", ""primary"": true, ""estimate"": 1.0736874861887384, ""ci_low"": 0.9399304761772739, ""ci_high"": 1.2264788164830922, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 higher 2017 population-weighted PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.07109897254113662, ""native_ci_low"": -0.0619493679669135, ""native_ci_high"": 0.20414731304918673, ""native_scale"": ""OLS coefficient on log rate"", ""native_contrast"": ""1 ug/m3 PM2.5""}, {""label"": ""day-80 death-rate ratio per 1 ug/m3 PM2.5"", ""primary"": true, ""estimate"": 1.0302730672642948, ""ci_low"": 0.8437717668573186, ""ci_high"": 1.2579972864980573, ""scale"": ""ratio"", ""contrast"": ""1 ug/m3 higher 2017 population-weighted PM2.5"", ""metric"": ""outcome_ratio"", ""native_estimate"": 0.029823880953907894, ""native_ci_low"": -0.1698732393713319, ""native_ci_high"": 0.22952100127914768, ""native_scale"": ""OLS coefficient on log rate"", ""native_contrast"": ""1 ug/m3 PM2.5""}], ""analysis_diagnostics"": {""observations"": 35, ""estimated_parameters"": 8, ""exposure_unique_values"": 36, ""outcome_unique_values"": 35, ""joined_rows"": 72, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""day-60 case rate"", ""day-60 death rate"", ""day-80 case rate"", ""day-80 death rate""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-34004167-northern-italy-covid-r8407-20260925T221606Z,,34004167,completed_fit,,2026-09-25T22:16:14.761818+00:00,2026-09-25T22:28:43.512013+00:00,0,0,0,1,154,"{""schema_version"": 3, ""study_id"": ""34004167-northern-italy-covid"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily incident reported COVID-19 cases and deaths"", ""pollutant"": ""NO2"", ""geography"": ""Lombardia and Veneto, Italy"", ""population"": ""Residents of the two regions"", ""period"": ""2020-02-21 through 2020-05-19 (outcomes available from 2020-02-24)"", ""effect_scale"": ""Rate ratio per 1 \u00b5g/m\u00b3"", ""exposure_assignment"": ""Unweighted mean of validated EEA station-day means within each public regional polygon; LTAP is the 2013-01-01 through 2020-05-19 mean."", ""model"": ""Poisson log-link GEE with AR(1) working correlation, clustered by region; STAP, LTAP, and lockdown."", ""covariates"": [""lockdown indicator from 2020-02-22""], ""named_outcome_source"": ""Italian Ministry of Health daily reports (article); public Italian Civil Protection regional series used as source substitution"", ""specification_evidence"": [""/output/evidence/article-specification.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/data/dpc-regioni.csv""}, {""role"": ""exposure"", ""url"": ""https://eeadmz1-downloads-api-appservice.azurewebsites.net/ParquetFile/urls"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/evidence/eea-urls3.txt""}, {""role"": ""boundary"", ""url"": ""https://www.geoboundaries.org/api/current/gbOpen/ITA/ADM2"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""a01b6408d7d9061318034f8f4f54b377b99b5f8dcf5a7f84c5fa1e8ee3c86549"", ""evidence_artifact"": ""/output/data/italy-adm2.geojson""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""Italian Ministry daily reports"", ""reanalysis"": ""Italian Civil Protection public regional time series"", ""reason"": ""Machine-readable public regional series; daily incidents derived from cumulative fields.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Meteorology and co-pollutant supplement variants"", ""reanalysis"": ""Primary lockdown-adjusted model only"", ""reason"": ""Exact meteorological covariates/source were not specified; primary article model preserved.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 86, ""included_times"": 86, ""rule"": ""Report-only completeness policy; include a region-day only when STAP and outcome are nonmissing."", ""notes"": ""Both regions have 86/86 exposure days after EEA recovery; all 172 joined rows were fitted.""}, ""artifacts"": {""code"": ""code/fit_reanalysis.py"", ""source_manifest"": ""source-manifest.json"", ""exposure"": ""data/eea_no2_daily.csv"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.json"", ""decision_log"": ""decision-log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker-ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T222719.2430000000.json"", ""coverage_diagnostics"": ""coverage_diagnostics.csv"", ""boundary_route_evidence"": ""data/italy-adm2.geojson"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Meteorology and co-pollutant sensitivity variants not reconstructed; primary article model is fitted."", ""Only two regions support the fixed LTAP contrast, limiting independent geographic inference.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/dpc-regioni.csv"", ""/output/data/italy-adm2.geojson"", ""/output/evidence/eea-urls3.txt"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T222719.2430000000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker-ledger.json"", ""code/fit_reanalysis.py"", ""coverage_diagnostics.csv"", ""data/eea_no2_daily.csv"", ""data/italy-adm2.geojson"", ""decision-log.json"", ""model_output.json"", ""source-manifest.json""]}, ""design_provenance"": {""contract_id"": ""34004167-northern-italy-covid-reanalysis-invariants"", ""contract_sha256"": ""c156a0d86034de1db7e244c5afdefb8753934e6155f4bafab5f5adb7cde630ff"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""For each explicit regional polygon, unweighted mean of all eligible daily station means whose coordinates fall within the polygon."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""NO2 concentration in \u00b5g/m\u00b3: daily regional monitor mean (STAP) and 2013-01-01 to 2020-05-19 regional monitor mean (LTAP)."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report completeness for every region and day; fit only rows with nonmissing outcome and STAP. No numeric exclusion threshold is asserted by article.""}, ""decision_rationale"": ""Records the complete executable implementation of the article-defined exposure construct and authorizes the historical period needed for LTAP, without modifying outcome period or invariants."", ""evidence_basis"": [""Article section 2.1 defines region-day mean STAP and the January 2013\u2013May 2020 LTAP mean."", ""Public ISTAT-sourced geoBoundaries file supplies the two named regional polygons.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Cases, STAP NO2"", ""primary"": true, ""estimate"": 1.0064636709840817, ""ci_low"": 1.0040938601550395, ""ci_high"": 1.0088390749190959, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3 higher region-day NO2"", ""metric"": ""RR"", ""native_estimate"": 0.0064428710439872975, ""native_ci_low"": 0.004085504117172845, ""native_ci_high"": 0.00880023797080175, ""native_scale"": ""log rate coefficient"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""Cases, LTAP NO2"", ""primary"": true, ""estimate"": 1.2706370933999962, ""ci_low"": 1.2681706376150437, ""ci_high"": 1.2731083461767407, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3 higher 2013-2020 regional NO2"", ""metric"": ""RR"", ""native_estimate"": 0.23951842303348622, ""native_ci_low"": 0.2375754192126132, ""native_ci_high"": 0.2414614268543592, ""native_scale"": ""log rate coefficient"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""Deaths, STAP NO2"", ""primary"": true, ""estimate"": 1.0073831565054678, ""ci_low"": 1.0064572801886127, ""ci_high"": 1.008309884569308, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3 higher region-day NO2"", ""metric"": ""RR"", ""native_estimate"": 0.007356034421388981, ""native_ci_low"": 0.006436521695211506, ""native_ci_high"": 0.008275547147566455, ""native_scale"": ""log rate coefficient"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}, {""label"": ""Deaths, LTAP NO2"", ""primary"": true, ""estimate"": 1.3891852498175954, ""ci_low"": 1.3880937920505902, ""ci_high"": 1.3902775657975428, ""scale"": ""ratio"", ""contrast"": ""1 \u00b5g/m\u00b3 higher 2013-2020 regional NO2"", ""metric"": ""RR"", ""native_estimate"": 0.3287174240784585, ""native_ci_low"": 0.327931433307104, ""native_ci_high"": 0.329503414849813, ""native_scale"": ""log rate coefficient"", ""native_contrast"": ""1 \u00b5g/m\u00b3""}], ""analysis_diagnostics"": {""observations"": 172, ""estimated_parameters"": 4, ""exposure_unique_values"": 172, ""outcome_unique_values"": 159, ""joined_rows"": 172, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""primary cases STAP+LTAP+lockdown"", ""primary deaths STAP+LTAP+lockdown""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-34488764-france-covid-r8407-20260925T222845Z,,34488764,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T22:28:52.019157+00:00,2026-09-25T22:38:47.021551+00:00,0,3,0,4,133,"{""schema_version"": 3, ""study_id"": ""34488764-france-covid"", ""status"": ""completed_blocker"", ""fidelity"": ""none"", ""target"": {""outcome"": ""Cumulative in-hospital COVID-19 deaths through 2020-05-01"", ""pollutant"": ""PM2.5"", ""geography"": ""96 mainland French department polygons"", ""population"": ""Residents of the 96 mainland French departments"", ""period"": ""PM2.5 1999\u20132016; outcome through 2020-05-01"", ""effect_scale"": ""mortality rate ratio"", ""exposure_assignment"": ""Department-polygon mean of annual PM2.5 values across 1999\u20132016"", ""model"": ""Negative-binomial death-count regression with log population offset"", ""covariates"": [""long-term temperature"", ""resuscitation beds"", ""intensive-care beds"", ""medical density"", ""age 60+"", ""male share"", ""unemployment"", ""poverty"", ""urban share"", ""population density"", ""diabetes prevalence""], ""named_outcome_source"": ""French Ministry of Health / data.gouv hospital COVID dataset"", ""specification_evidence"": [""/output/reanalysis/estimand-ledger.md""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://static.data.gouv.fr/resources/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/20230331-180159/covid-hospit-2023-03-31-18h01.csv"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": ""79945ede9e319d5d7289cdcbd4a686ff0e2d06ac9b4232fdde139b0b9e5cfc82"", ""evidence_artifact"": ""/output/reanalysis/derived/outcome_2020-05-01.csv""}, {""role"": ""exposure"", ""url"": ""https://data.earthdata.nasa.gov/nasa-earth/human-dimensions/sedac-root/downloads/data/sdei/sdei-global-annual-gwr-pm2-5-modis-misr-seawifs-aod/sdei-global-annual-gwr-pm2-5-modis-misr-seawifs-aod-2016-geotiff.zip"", ""route_origin"": ""article_named"", ""retrieved"": false, ""sha256"": null, ""evidence_artifact"": ""/output/reanalysis/logs/pm2016_range_headers.txt""}, {""role"": ""boundary"", ""url"": ""https://geodata.ucdavis.edu/gadm/gadm4.1/json/gadm41_FRA_1.json.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""da3d5b11019fcee25859a5931d53af0d6612b42e3c1454d01358f35d9ffc5554"", ""evidence_artifact"": ""/output/reanalysis/raw/gadm41_FRA_1.json.zip""}], ""substitutions"": [], ""coverage"": {""eligible_units"": 96, ""included_units"": 0, ""eligible_times"": 18, ""included_times"": 0, ""rule"": ""No fit: preserve locked numeric exposure construct rather than use a visual proxy."", ""notes"": ""All 96 outcomes were recovered; zero numeric department PM2.5 records were available.""}, ""artifacts"": {""code"": ""reanalysis/retrieve_and_audit.py"", ""source_manifest"": ""reanalysis/derived/recovery_audit.json"", ""exposure"": null, ""analysis_panel"": ""reanalysis/derived/analysis_panel.csv"", ""model_output"": ""reanalysis/derived/model_output.json"", ""decision_log"": ""reanalysis/decision-log.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""reanalysis/derived/recovery_audit.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T223613.5066440000.json"", ""coverage_diagnostics"": ""reanalysis/derived/coverage_diagnostics.json"", ""boundary_route_evidence"": ""reanalysis/raw/gadm41_FRA_1.json.zip"", ""study_contract"": ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json""}, ""blockers"": [""The exact public NASA/SEDAC 1998\u20132016 PM2.5 grid is catalogued but redirects to Earthdata Login (HTTP 302 then 401), and no approved credential is available. A retrieved public rendered 2011\u20132019 map is not numerical measurement data and was rejected.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": true, ""historical_fallback_tested"": true, ""geographic_batching_applicable"": false, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/reanalysis/derived/outcome_2020-05-01.csv"", ""/output/reanalysis/logs/pm2016_range_headers.txt"", ""/output/reanalysis/raw/gadm41_FRA_1.json.zip"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T223613.5066440000.json"", ""aeris-workspace/.aeris/contracts/reanalysis-invariants.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""reanalysis/decision-log.json"", ""reanalysis/derived/analysis_panel.csv"", ""reanalysis/derived/coverage_diagnostics.json"", ""reanalysis/derived/model_output.json"", ""reanalysis/derived/recovery_audit.json"", ""reanalysis/raw/gadm41_FRA_1.json.zip"", ""reanalysis/retrieve_and_audit.py""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-36383802-sao-jose-covid-r8407-20260925T223848Z,,36383802,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T22:38:55.992000+00:00,2026-09-25T22:40:34.492739+00:00,0,3,0,4,36,{} |
| self-driving-aeris,r8407,codex-aeris-self-driving-38182658-uk-covid-r8407-20260925T234200Z,,38182658,completed_sensitivity,,2026-09-25T23:42:07.407710+00:00,2026-09-25T23:48:56.093184+00:00,0,0,0,1,131,"{""schema_version"": 3, ""study_id"": ""38182658-uk-covid"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily instantaneous COVID-19 case-fatality risk (back-projected deaths / cases in article; fixed 8-day death-shift proxy in fitted sensitivity)"", ""pollutant"": ""PM2.5"", ""geography"": ""England, Northern Ireland, Scotland and Wales, nation-day"", ""population"": ""Laboratory-confirmed COVID-19 cases in the four UK nations"", ""period"": ""Article: 2020-03-26 to 2020-09-15; fit: 2020-03-26 to 2020-07-24"", ""effect_scale"": ""Odds ratio per 10 \u00b5g/m\u00b3 PM2.5"", ""exposure_assignment"": ""Article: daily nation monitor mean; fit: hourly modeled PM2.5 at nation centroid, daily mean, then 11-day mean"", ""model"": ""Article: binomial mixed DLNM; fit: binomial logit GLM with robust covariance and an 11-day linear lag-average predictor"", ""covariates"": [""temperature 11-day mean"", ""daylight duration 11-day mean"", ""relative humidity 11-day mean"", ""nation fixed effects"", ""weekday fixed effects""], ""named_outcome_source"": ""PHE/ONS in article; public GitHub preservation of UK dashboard indicators in fit"", ""specification_evidence"": [""/study/article.txt"", ""/study/supplements/41598_2023_50474_MOESM1_ESM.docx"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/tomwhite/covid-19-uk-data/master/data/covid-19-indicators-uk.csv"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""151ecd06edb90e137ddddb822305ac642ca58297f2155362df2e4b7661d4a1f5"", ""evidence_artifact"": ""/output/data/covid-19-indicators-uk.csv""}, {""role"": ""exposure"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""57116c2e313c39666aa087fa79e340312fc5ab6e8872496aff32b494f4728506"", ""evidence_artifact"": ""/output/data/openmeteo_air_england.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": ""2bbfc1e53f0763dd8bd021bb88ae85faf0f3a49723ec48b93ec0776173d4ca97"", ""evidence_artifact"": ""/output/data/openmeteo_all.json""}], ""substitutions"": [{""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""DEFRA country monitor averages"", ""reanalysis"": ""Open-Meteo atmospheric-composition PM2.5 at nation centroids"", ""reason"": ""AERIS historical monitor batch did not complete during this run.""}, {""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""backprojNP gamma delay reconstruction"", ""reanalysis"": ""daily reported deaths shifted 8 days"", ""reason"": ""Exact delay distribution and author outcome extract were unavailable.""}, {""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2020-03-26 to 2020-09-15"", ""reanalysis"": ""2020-03-26 to 2020-07-24"", ""reason"": ""Recovered archive ended 2020-08-01 and alignment removes subsequent dates.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""nonlinear DLNM cross-bases and country random effect"", ""reanalysis"": ""linear 11-day mean with country fixed effects"", ""reason"": ""A bounded, executable fit retained the binomial family and lag window but cannot reproduce spline DLNM.""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 4, ""eligible_times"": 174, ""included_times"": 121, ""rule"": ""Complete cases after 11 daily exposure/covariate observations and fixed 8-day death alignment; no numerical coverage threshold."", ""notes"": ""449 nation-day rows fitted. All four nations retained; public outcome archive and alignment limited usable calendar dates.""}, ""artifacts"": {""code"": ""code/reanalyse_uk_covid_pm25.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""data/openmeteo_air_england.json"", ""analysis_panel"": ""analysis_panel.csv"", ""model_output"": ""model_output.txt"", ""decision_log"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T234804.8334830000.json"", ""coverage_diagnostics"": ""coverage_report.csv"", ""boundary_route_evidence"": ""/output/aeris-pm25-checkpoint.json (not created"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""AERIS/OpenAQ administrative-boundary historical PM2.5 job remained running without durable output."", ""Exact backprojNP delay distribution and full-period official outcome extract were not recovered.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/data/covid-19-indicators-uk.csv"", ""/output/data/openmeteo_air_england.json"", ""/output/data/openmeteo_all.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T234804.8334830000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel.csv"", ""blocker_ledger.json"", ""code/reanalyse_uk_covid_pm25.py"", ""coverage_report.csv"", ""data/openmeteo_air_england.json"", ""model_output.txt"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""38182658-uk-covid-reanalysis-invariants"", ""contract_sha256"": ""f7816be29709755de2bfd452fb99714820b297673d8accf37f45a7a2d8d4a899"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Daily hourly PM2.5 values queried at the four centroids, then arithmetic daily mean and 11-day (lag 0 through 10) rolling mean per nation."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Nation-day PM2.5 concentration in \u00b5g/m\u00b3; main predictor is the 11-day mean, parameterized per 10 \u00b5g/m\u00b3."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only. Fit uses complete cases after necessary 11-day lag and fixed 8-day outcome alignment; no data-driven exposure threshold or outcome selection.""}, ""decision_rationale"": ""The article specifies daily country averages and a 10-day maximum lag. The selected implementation retains daily country-time support and lag scale, while explicitly labeling the coordinate-based modeled PM2.5 source as a substitution."", ""evidence_basis"": [""All four nations have hourly-derived daily PM2.5 and complete 11-day lag values over recovered outcome dates."", ""Fit-ready rows and outcome coverage are retained by nation."", ""Documents active but non-completing OpenAQ boundary route and the public source recovery choices.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Bounded PM2.5 association"", ""primary"": true, ""estimate"": 0.7022175276, ""ci_low"": 0.6962171726, ""ci_high"": 0.7082695968, ""scale"": ""ratio"", ""contrast"": ""Per 10 \u00b5g/m\u00b3 higher 11-day mean PM2.5"", ""metric"": ""OR"", ""native_estimate"": -0.3535120546, ""native_ci_low"": -0.362093638, ""native_ci_high"": -0.344930471, ""native_scale"": ""log odds ratio"", ""native_contrast"": ""Per 10 \u00b5g/m\u00b3 higher 11-day mean PM2.5""}], ""analysis_diagnostics"": {""observations"": 449, ""estimated_parameters"": 14, ""exposure_unique_values"": 448, ""outcome_unique_values"": 154, ""joined_rows"": 449, ""unmatched_outcome_rows"": 6, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""Article Model 6 specified but not exactly identifiable"", ""Bounded source-substituted linear 11-day binomial GLM fitted""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-38788590-brazil-cancer-r8407-20260925T235317Z,,38788590,agent_failure,result failed schema or autonomous-completion validation,2026-09-25T23:53:23.811770+00:00,2026-09-26T00:11:07.527436+00:00,0,3,0,4,351,"{""schema_version"": 3, ""study_id"": ""38788590-brazil-cancer"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily all-cancer and site-specific cancer deaths"", ""pollutant"": ""PM2.5"", ""geography"": ""Brazilian municipalities"", ""population"": ""Cancer deaths recorded across Brazilian municipalities"", ""period"": ""2000-01-01 through 2019-12-31"", ""effect_scale"": ""Odds ratio per 10 \u00b5g/m\u00b3"", ""exposure_assignment"": ""Population-weighted municipal mean of daily 0.25\u00b0 grid values; three-day lag 0-2 mean"", ""model"": ""Time-stratified case-crossover conditional logistic regression"", ""covariates"": [""temperature"", ""relative humidity"", ""public holidays""], ""named_outcome_source"": ""Brazilian Mortality Information System (SIM)"", ""specification_evidence"": [""/output/article-specification.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SIM/csv/Mortalidade_Geral_2000_csv.zip"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/sim-sp-cancer-2000-diagnostics.json""}, {""role"": ""exposure"", ""url"": ""https://api.osf.io/v2/nodes/dn7ya/files/osfstorage/"", ""route_origin"": ""article_linked"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/osf-pm-files.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/openmeteo-era5-sao-paulo-2000-05.json""}, {""role"": ""weather"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/openmeteo-era5-sao-paulo-2000-05.json""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""source"", ""published"": ""SIM individual deaths"", ""reanalysis"": ""Official SIM annual CSV transport"", ""reason"": ""Outcome construct preserved.""}, {""dimension"": ""geography"", ""change_type"": ""coverage_subset"", ""published"": ""5,570 Brazilian municipalities, 2000-2019"", ""reanalysis"": ""Sao Paulo municipality, May 2000"", ""reason"": ""Retained decoded PM partition and outcome slice overlap here.""}, {""dimension"": ""exposure"", ""change_type"": ""construct_change"", ""published"": ""Population-weighted municipal grid mean"", ""reanalysis"": ""Unweighted mean of three in-polygon grid centres"", ""reason"": ""Population weights unavailable in retained bounded slice.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""ERA5 municipality weather"", ""reanalysis"": ""Open-Meteo ERA5-backed point weather"", ""reason"": ""Fit-ready bounded public route.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""Public-holiday adjustment"", ""reanalysis"": ""Holiday field retained but omitted"", ""reason"": ""Zero analytic-panel variation.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""Conditional logistic model with temperature cross-basis"", ""reanalysis"": ""Conditional logistic model with linear daily temperature term"", ""reason"": ""Exact cross-basis specification was unavailable and the 29-day bounded panel does not support a defensible reconstruction of that flexible term.""}], ""coverage"": {""eligible_units"": 5570, ""included_units"": 1, ""eligible_times"": 7305, ""included_times"": 29, ""rule"": ""Deterministic bounded overlap: Sao Paulo municipality, May 2000, with complete PM2.5 lag 0-2 and weather."", ""notes"": ""922 of 991 May cancer deaths included; 69 deaths on May 1-2 lacked preceding retained PM days; three grid centres contributed daily.""}, ""artifacts"": {""code"": ""decode_pm_rds.py"", ""source_manifest"": ""source-manifest-independent.json"", ""exposure"": ""sao-paulo-pm25-daily-2000-05.csv"", ""analysis_panel"": ""bounded-case-crossover-panel.csv"", ""model_output"": ""bounded-case-crossover-model-output.json"", ""decision_log"": ""aeris-bounded-fit-registration.json"", ""research_notebook"": ""research-notebook.json"", ""blocker_ledger"": ""blocker-ledger.json"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T001003.4147090000.json"", ""coverage_diagnostics"": ""bounded-case-crossover-coverage.json"", ""boundary_route_evidence"": ""sao-paulo-boundary.geojson"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json""}, ""blockers"": [""National 2000-2019 coverage and population-weighted municipal aggregation are unavailable in retained bounded materials; this is a bounded feasibility estimate.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": false, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/openmeteo-era5-sao-paulo-2000-05.json"", ""/output/osf-pm-files.json"", ""/output/sim-sp-cancer-2000-diagnostics.json"", ""aeris-bounded-fit-registration.json"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-26T001003.4147090000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json"", ""blocker-ledger.json"", ""bounded-case-crossover-coverage.json"", ""bounded-case-crossover-model-output.json"", ""bounded-case-crossover-panel.csv"", ""decode_pm_rds.py"", ""research-notebook.json"", ""sao-paulo-boundary.geojson"", ""sao-paulo-pm25-daily-2000-05.csv"", ""source-manifest-independent.json""]}, ""design_provenance"": {""contract_id"": ""38788590-brazil-cancer-reanalysis-invariants"", ""contract_sha256"": ""a3b5d13dcbce18744ce6bd4265545f64f2e142ac574b38aa59b79f0a4b003b08"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""Unweighted mean of 0.25-degree grid-cell centres inside the Sao Paulo municipal polygon; declared substitute for population-weighted municipal aggregation."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""Official SIM annual CSV outcomes; article-linked OSF all-source PM2.5 0.25-degree product; Open-Meteo archival ERA5-backed daily weather."", ""exposure_metric"": ""Three-day lag 0-2 mean all-source PM2.5 in micrograms per cubic metre."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only; retain all events with complete lagged PM2.5 and weather in this bounded slice.""}, ""decision_rationale"": ""Recovered records support a stronger article-linked gridded analysis than the earlier monitor-proxy route. Bounded geography, unweighted aggregation, and holiday non-identifiability are explicit."", ""evidence_basis"": [""Decoded article-linked RDS contains daily PM2.5 grid-day records."", ""Three grid centres fall in the municipal polygon and yield 31 daily values."", ""Twenty-nine complete lag/weather days and 922 eligible death strata support a fit.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""All-cancer mortality, Sao Paulo May 2000 bounded slice"", ""primary"": true, ""estimate"": 0.7941872236440768, ""ci_low"": 0.6325054842161077, ""ci_high"": 0.9971982250575784, ""scale"": ""ratio"", ""contrast"": ""10 micrograms per cubic metre increase in lag 0-2 PM2.5"", ""metric"": ""OR"", ""native_estimate"": -0.23043604749059093, ""native_ci_low"": -0.45806638772064856, ""native_ci_high"": -0.00280570726053328, ""native_scale"": ""log odds ratio"", ""native_contrast"": ""10 micrograms per cubic metre increase in lag 0-2 PM2.5""}], ""analysis_diagnostics"": {""observations"": 3855, ""estimated_parameters"": 3, ""exposure_unique_values"": 29, ""outcome_unique_values"": 2, ""joined_rows"": 3855, ""unmatched_outcome_rows"": 69, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""All-cancer mortality, lag 0-2 PM2.5, conditional logistic regression""]}}" |
| self-driving-aeris,r8407,codex-aeris-self-driving-39377000-us-stroke-r8407-20260926T001108Z,,39377000,completed_sensitivity,,2026-09-26T00:11:15.422194+00:00,2026-09-26T00:19:42.582720+00:00,0,0,0,1,135,"{""schema_version"": 3, ""study_id"": ""39377000-us-stroke"", ""status"": ""completed_sensitivity"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""County ischemic and hemorrhagic stroke mortality rates among adults age 65+ (article target); bounded fit uses all-stroke mortality age 35+"", ""pollutant"": ""PM2.5"", ""geography"": ""United States counties"", ""population"": ""US residents; article target age 65+, bounded outcome source age 35+"", ""period"": ""Article 2016-2020; bounded outcome 2018-2020 and exposure 2016-2020"", ""effect_scale"": ""Article-native additive deaths per 100,000 per 1 ug/m3; no native ratio was fitted"", ""exposure_assignment"": ""County daily EPA Downscaler predictions averaged over 2016-2020"", ""model"": ""OLS with HC3 uncertainty in bounded sensitivity"", ""covariates"": [""diabetes"", ""obesity"", ""smoking"", ""lack of insurance (bounded sensitivity only)""], ""named_outcome_source"": ""CDC Interactive Atlas of Heart Disease and Stroke"", ""specification_evidence"": [""/output/article_estimand_ledger.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://data.cdc.gov/api/views/g5fg-bgtw/rows.csv?accessType=DOWNLOAD"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/cdc_stroke_2018_2020.csv""}, {""role"": ""exposure"", ""url"": ""https://data.cdc.gov/resource/53mz-4zqd.json"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/cdc_pm25_county_2016_2020.json""}, {""role"": ""covariate"", ""url"": ""https://data.cdc.gov/api/views/dv4u-3x3q/rows.csv?accessType=DOWNLOAD"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/raw/cdc_places_2020.csv""}], ""substitutions"": [{""dimension"": ""outcome"", ""change_type"": ""construct_change"", ""published"": ""age-65+ ischemic/hemorrhagic mortality"", ""reanalysis"": ""age-35+ all-stroke 2018-2020 rate"", ""reason"": ""Only the latter was recovered as a public, fit-ready county bulk product.""}, {""dimension"": ""exposure"", ""change_type"": ""source"", ""published"": ""article source unspecified"", ""reanalysis"": ""CDC EPA Downscaler county prediction"", ""reason"": ""Provides broad county coverage; monitor probes had uneven station coverage.""}, {""dimension"": ""covariate"", ""change_type"": ""covariate_omission"", ""published"": ""full 12-variable article adjustment"", ""reanalysis"": ""four PLACES risk-factor covariates"", ""reason"": ""Remaining article covariates were not recovered before bounded fit.""}], ""coverage"": {""eligible_units"": 3226, ""included_units"": 3103, ""eligible_times"": 1827, ""included_times"": 1461, ""rule"": ""Report-only, no numeric exclusion threshold."", ""notes"": ""Per-county PM2.5 days ranged 1461-1827; outcome/exposure intersection had 3103 counties.""}, ""artifacts"": {""code"": ""code/run_bounded_sensitivity.py"", ""source_manifest"": ""source_manifest.json"", ""exposure"": ""raw/cdc_pm25_county_2016_2020.json"", ""analysis_panel"": ""derived/bounded_analysis_panel.csv"", ""model_output"": ""derived/bounded_model_output.json"", ""decision_log"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.json"", ""fidelity_record"": ""reanalysis-fidelity_reanalysis-fidelity_2026-09-26T001909.1842150000"", ""coverage_diagnostics"": ""coverage_diagnostics.json"", ""boundary_route_evidence"": ""exposure_pm25_2026-09-26T001600.4546910000"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json""}, ""blockers"": [""Article-specific age-65+ ischemic and hemorrhagic outcome panel and full adjustment set not recovered. The completed fit is therefore a bounded sensitivity only.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/raw/cdc_places_2020.csv"", ""/output/raw/cdc_pm25_county_2016_2020.json"", ""/output/raw/cdc_stroke_2018_2020.csv"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-001.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger.json"", ""code/run_bounded_sensitivity.py"", ""coverage_diagnostics.json"", ""derived/bounded_analysis_panel.csv"", ""derived/bounded_model_output.json"", ""raw/cdc_pm25_county_2016_2020.json"", ""source_manifest.json""]}, ""design_provenance"": {""contract_id"": ""39377000-us-stroke-reanalysis-invariants"", ""contract_sha256"": ""464dcc4b5c5df0a408983cc20802296348c1d0eb31b2fdb0e4d128fae0880485"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""county-level annual aggregation of public modeled daily county predictions"", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""local_model"", ""exposure_metric"": ""mean of CDC Tracking Network daily county EPA Downscaler PM2.5 predictions across 2016-01-01 through 2020-12-31"", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": 0, ""threshold_source"": ""No article/source numeric exclusion threshold"", ""evidence"": ""CDC query returned days observed; retain and report per-county denominator rather than exclude.""}, ""decision_rationale"": ""After feasibility probes, use a public county-complete modeled surface for the bounded sensitivity rather than substitute monitor assignments with uneven county coverage. This changes the source/construct from the article-unspecified county annual PM2.5 to CDC EPA Downscaler county estimates and is explicitly labeled."", ""evidence_basis"": [""CDC describes 53mz-4zqd as EPA Downscaler modeled county PM2.5 2001-2022."", ""3109 counties returned; daily counts range to complete 1827 study days."", ""AERIS OpenAQ historical archive probe in Los Angeles recovered 2018 PM2.5 and 96.7% network day coverage, while the Autauga probe had no stations; monitor-only nationwide coverage would be unequal.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Bounded adjusted sensitivity; model-implied relative outcome change at sample-mean outcome for +10 ug/m3"", ""primary"": true, ""estimate"": 1.5171, ""ci_low"": 1.472, ""ci_high"": 1.5622, ""scale"": ""ratio"", ""contrast"": ""10 ug/m3; presentation-only rescaling at mean outcome, not article estimand"", ""metric"": ""outcome_ratio"", ""native_estimate"": 3.9546332431, ""native_ci_low"": 3.6094473028, ""native_ci_high"": 4.2998191834, ""native_scale"": ""additive deaths per 100,000"", ""native_contrast"": ""1 ug/m3 PM2.5""}], ""analysis_diagnostics"": {""observations"": 3101, ""estimated_parameters"": 6, ""exposure_unique_values"": 3103, ""outcome_unique_values"": 705, ""joined_rows"": 3103, ""unmatched_outcome_rows"": 123, ""unmatched_exposure_rows"": 6, ""contrast_transformation_verified"": true, ""reported_variants"": [""univariable OLS"", ""risk-factor-adjusted OLS HC3""]}}" |
| self-driving-aeris,repeatability,codex-aeris-self-driving-33227571-sao-paulo-ami-r8405-20260925T161051Z,,33227571,completed_fit,,2026-09-25T16:10:58.266670+00:00,2026-09-25T16:33:51.716108+00:00,0,1,0,0,0,"{""schema_version"": 3, ""study_id"": ""33227571-sao-paulo-ami"", ""status"": ""completed_fit"", ""fidelity"": ""bounded"", ""target"": {""outcome"": ""Daily acute myocardial infarction admissions and in-hospital mortality"", ""pollutant"": ""Joint daily NO2, PM2.5, and PM10 feature set"", ""geography"": ""39 municipalities of metropolitan S\u00e3o Paulo, Brazil"", ""population"": ""AMI patients admitted in the 39 municipalities"", ""period"": ""2012-01-01 through 2015-12-31; bounded fit uses 2014-01-01 through 2014-02-28"", ""effect_scale"": ""Exploratory rate ratios from robust Poisson models comparing environmental clusters"", ""exposure_assignment"": ""Bounded Congonhas CETESB station daily-mean proxy, not municipality-specific or population-weighted exposure"", ""model"": ""Ward hierarchical clustering (k=3) of standardized weather and joint-pollutant features, followed by robust Poisson cluster comparisons; exact article test unavailable in abstract-only materials"", ""covariates"": [""temperature"", ""temperature variation"", ""rainfall"", ""relative humidity""], ""named_outcome_source"": ""DataSUS SIH-RD"", ""specification_evidence"": [""/study/article.pdf"", ""/output/aeris-workspace/.aeris/contracts/reanalysis-invariants.json""]}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://huggingface.co/datasets/SidneyBissoli/sih-rd"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/review2/sih_ami_rmsp_201401_201402_deduplicated.csv""}, {""role"": ""exposure"", ""url"": ""https://sistemasinter.cetesb.sp.gov.br/Ar/php/ar_dados_horarios_resultado.php"", ""route_origin"": ""article_named"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/review2/cetesb-legacy-selector-scan.json""}, {""role"": ""weather"", ""url"": ""https://power.larc.nasa.gov/api/temporal/daily/point"", ""route_origin"": ""agent_discovered"", ""retrieved"": true, ""sha256"": null, ""evidence_artifact"": ""/output/recovery/review2/nasa_power_congonhas_201401.csv""}], ""substitutions"": [{""dimension"": ""period"", ""change_type"": ""coverage_subset"", ""published"": ""2012-2015"", ""reanalysis"": ""2014-01-01 through 2014-02-28"", ""reason"": ""Complete public overlap was recovered only for this bounded slice.""}, {""dimension"": ""exposure"", ""change_type"": ""construct_change"", ""published"": ""Unspecified study-wide CETESB environmental construct"", ""reanalysis"": ""Congonhas station daily means"", ""reason"": ""Public legacy route supplied all three pollutants; proxy limitation is explicit.""}, {""dimension"": ""covariate"", ""change_type"": ""source"", ""published"": ""Meteorological Database for Teaching and Research"", ""reanalysis"": ""NASA POWER MERRA-2 daily point weather"", ""reason"": ""Public source-substituted covariates.""}, {""dimension"": ""model"", ""change_type"": ""construct_change"", ""published"": ""Exact comparison test unspecified in supplied abstract"", ""reanalysis"": ""Ward clustering plus robust Poisson comparisons"", ""reason"": ""Exploratory fitting choice retained the three-cluster comparison structure.""}], ""coverage"": {""eligible_units"": 39, ""included_units"": 39, ""eligible_times"": 59, ""included_times"": 59, ""rule"": ""Report-only completeness: retain dates with nonmissing NO2, PM2.5, PM10, weather, and deduplicated outcome counts."", ""notes"": ""All 59 bounded-window dates were complete. Minimum contributing hours were 11 for NO2, 21 for PM2.5, and 21 for PM10.""}, ""artifacts"": {""code"": ""reanalysis_bounded.py"", ""source_manifest"": ""source_manifest_bounded.json"", ""exposure"": ""recovery/review2/cetesb_congonhas_20140101_20140131.csv"", ""analysis_panel"": ""analysis_panel_bounded.csv"", ""model_output"": ""model_output_bounded.txt"", ""decision_log"": ""decision_log_bounded.json"", ""research_notebook"": ""aeris-workspace/.aeris/research-notebook.json"", ""blocker_ledger"": ""blocker_ledger.md"", ""fidelity_record"": ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T163137.2531190000.json"", ""coverage_diagnostics"": ""coverage_diagnostics_bounded.json"", ""boundary_route_evidence"": ""recovery/review2/cetesb-legacy-selector-scan.json"", ""study_contract"": ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json""}, ""blockers"": [""A full 2012-2015 municipality-specific daily exposure panel was not recovered."", ""The supplied article materials are abstract-only, so exact preprocessing and inferential specifications remain unknown."", ""The bounded fit uses a single-station proxy and source-substituted weather; it is not a full replication.""], ""stopping_checklist"": {""target_specification_complete"": true, ""complete_article_checked"": true, ""outcome_routes_attempted"": 1, ""normal_exposure_source_tested"": true, ""historical_fallback_applicable"": false, ""historical_fallback_tested"": false, ""geographic_batching_applicable"": true, ""geographic_batching_attempted"": true, ""fidelity_levels_evaluated"": [""bounded""], ""pending_requests"": 0, ""evidence_artifacts"": [""/output/recovery/review2/cetesb-legacy-selector-scan.json"", ""/output/recovery/review2/nasa_power_congonhas_201401.csv"", ""/output/recovery/review2/sih_ami_rmsp_201401_201402_deduplicated.csv"", ""aeris-workspace/.aeris/artifacts/reanalysis-fidelity_reanalysis-fidelity_2026-09-25T163137.2531190000.json"", ""aeris-workspace/.aeris/contracts/agent-contract-amendment-002.json"", ""aeris-workspace/.aeris/research-notebook.json"", ""analysis_panel_bounded.csv"", ""blocker_ledger.md"", ""coverage_diagnostics_bounded.json"", ""decision_log_bounded.json"", ""model_output_bounded.txt"", ""reanalysis_bounded.py"", ""recovery/review2/cetesb-legacy-selector-scan.json"", ""recovery/review2/cetesb_congonhas_20140101_20140131.csv"", ""source_manifest_bounded.json""]}, ""design_provenance"": {""contract_id"": ""33227571-sao-paulo-ami-reanalysis-invariants"", ""contract_sha256"": ""5c8835f7d5d4a3284bda61b6f6860109237823b34891f75a5643f68cf84db348"", ""contract_author"": ""agent"", ""geographic_representation"": ""administrative_area"", ""assignment_method"": ""One fixed CETESB station selected after bounded multi-station/multi-date selector scan demonstrated all-three-pollutant coverage."", ""representative_location_rule"": null, ""maximum_monitor_distance_km"": null, ""monitor_distance_evidence"": ""Not applicable to the selected assignment method."", ""source_strategy"": ""public_monitor_network"", ""exposure_metric"": ""Daily arithmetic mean of valid hourly NO2, PM2.5, and PM10 values."", ""coverage_policy"": {""mode"": ""report_only"", ""minimum_percent"": null, ""threshold_source"": ""none"", ""evidence"": ""Report-only; include dates with nonmissing joint features, retaining per-pollutant contributing-hour counts; January-February 2014 has 59/59 complete days.""}, ""decision_rationale"": ""The public recovery routes yielded a valid overlapping outcome-exposure panel. This amendment records the evidence-based implementation design while preserving the locked outcome, pollutants, clustering construct, and target geography."", ""evidence_basis"": [""Public legacy selector scan identified Congonhas as having NO2, PM10, and PM2.5 data on representative 2014 and 2015 dates."", ""59 complete daily joint records and retained hour-count diagnostics.""], ""locked_before_exposure"": false}, ""effects"": [{""label"": ""Admissions: high-pollution vs low-pollution reference"", ""primary"": true, ""estimate"": 0.9275675676, ""ci_low"": 0.770240803, ""ci_high"": 1.1170293616, ""scale"": ""ratio"", ""contrast"": ""High-pollution cluster versus low-pollution reference"", ""metric"": ""RR"", ""native_estimate"": -0.07519, ""native_ci_low"": -0.261052, ""native_ci_high"": 0.110667, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""high versus low cluster""}, {""label"": ""Admissions: intermediate-pollution vs low-pollution reference"", ""primary"": false, ""estimate"": 0.9837837838, ""ci_low"": 0.824416838, ""ci_high"": 1.1739577464, ""scale"": ""ratio"", ""contrast"": ""Intermediate-pollution cluster versus low-pollution reference"", ""metric"": ""RR"", ""native_estimate"": -0.016349, ""native_ci_low"": -0.193933, ""native_ci_high"": 0.160377, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""intermediate versus low cluster""}, {""label"": ""Mortality: high-pollution vs low-pollution reference"", ""primary"": false, ""estimate"": 0.8590909091, ""ci_low"": 0.5667986354, ""ci_high"": 1.3021153264, ""scale"": ""ratio"", ""contrast"": ""High-pollution cluster versus low-pollution reference"", ""metric"": ""RR"", ""native_estimate"": -0.151872, ""native_ci_low"": -0.567744, ""native_ci_high"": 0.264033, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""high versus low cluster""}, {""label"": ""Mortality: intermediate-pollution vs low-pollution reference"", ""primary"": false, ""estimate"": 0.7933884298, ""ci_low"": 0.5304661895, ""ci_high"": 1.1866264297, ""scale"": ""ratio"", ""contrast"": ""Intermediate-pollution cluster versus low-pollution reference"", ""metric"": ""RR"", ""native_estimate"": -0.23197, ""native_ci_low"": -0.634999, ""native_ci_high"": 0.171059, ""native_scale"": ""log rate ratio"", ""native_contrast"": ""intermediate versus low cluster""}], ""analysis_diagnostics"": {""observations"": 59, ""estimated_parameters"": 3, ""exposure_unique_values"": 59, ""outcome_unique_values"": 29, ""joined_rows"": 59, ""unmatched_outcome_rows"": 0, ""unmatched_exposure_rows"": 0, ""contrast_transformation_verified"": true, ""reported_variants"": [""admissions cluster comparison"", ""in-hospital mortality cluster comparison""]}}" |
| raw-agent-control,r1,codex-baseline-33227571-sao-paulo-ami-r1-20260919T161709Z,,33227571,completed_blocker,,2026-09-19T16:17:10.226771+00:00,2026-09-19T16:25:09.633692+00:00,0,0,0,1,79,"{""study_id"": ""PMID:33227571"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily SUS hospital admissions with principal ICD-10 I21 (acute myocardial infarction)"", ""pollutant"": ""PM2.5, PM10, and nitrogen dioxide in a joint environmental cluster"", ""geography"": ""39 municipalities of the S\u00e3o Paulo metropolitan region, Brazil"", ""period"": ""Reported as 2012\u20132015; reanalysis panel used 2012-01-01 through 2015-12-31"", ""effect_scale"": ""Difference in daily AMI admissions between hierarchical environmental clusters (reported 9% increase)""}, ""sources"": [{""role"": ""study citation/full-text metadata"", ""url"": ""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33227571&retmode=xml"", ""retrieved"": true, ""sha256"": ""9d9e00109ca8d7f56baaeed6117e210d0be3b0d6093fe985d7da8825be4b50f6""}, {""role"": ""publisher full-text landing page"", ""url"": ""https://www.sciencedirect.com/science/article/pii/S0147956320301564"", ""retrieved"": false, ""sha256"": null}, {""role"": ""publisher article API metadata"", ""url"": ""https://api.elsevier.com/content/article/PII:S0147956320301564?httpAccept=text/xml"", ""retrieved"": true, ""sha256"": ""d196c19d06be12e6d2e4da2a68c74b1abf13cb38d353012d129b98d8b5543ac7""}, {""role"": ""health outcome: SIH-RD public DATASUS mirror, 2012-01 through 2016-04, SP"", ""url"": ""https://data.sidneybissoli.com/sih/rd/ano=YYYY/mes=MM/uf=SP/part-0.parquet"", ""retrieved"": true, ""sha256"": null}, {""role"": ""municipality reference"", ""url"": ""https://servicodados.ibge.gov.br/api/v1/localidades/municipios"", ""retrieved"": true, ""sha256"": ""86ecdccdf97d72e7e5e46f0854cfcea8bacc28154cc1bc4ed0e6110e3a6c9c02""}, {""role"": ""weather covariates"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=-23.5505&longitude=-46.6333&start_date=2012-01-01&end_date=2015-12-31"", ""retrieved"": true, ""sha256"": ""0b412bf2a3f4fcf88b0333c6bf087d1c2248d4f9ba7707654c5869ffb7e17ab2""}, {""role"": ""independent historical PM2.5/PM10/NO2 exposure"", ""url"": ""not available: no credential-free source retrieved that provided all required daily pollutants"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""DataSUS daily MI admissions; exact filtering details unavailable from supplied abstract/citation"", ""reanalysis"": ""SIH-RD records with DIAG_PRINC beginning I21, admission date DT_INTER, and residence in the 39 RM S\u00e3o Paulo municipalities"", ""reason"": ""This is the directly available public microdata implementation; it produced 51,689 admissions, not the reported 30,423, so equivalence was not assumed.""}, {""dimension"": ""geography"", ""published"": ""39 municipalities of S\u00e3o Paulo"", ""reanalysis"": ""39 current RM S\u00e3o Paulo municipalities identified with IBGE codes and matched to SIH six-digit municipality stems"", ""reason"": ""Article did not provide municipality codes/list in supplied material.""}, {""dimension"": ""covariate"", ""published"": ""Daily temperature variation, rainfall, humidity, NO2, PM2.5, PM10"", ""reanalysis"": ""Open-Meteo daily temperature maximum/minimum, precipitation, and mean relative humidity at S\u00e3o Paulo city coordinate; pollutants unavailable"", ""reason"": ""Independent archived weather was retrieved, but no complete credential-free public historical pollution series was retrieved.""}, {""dimension"": ""model"", ""published"": ""Hierarchical cluster analysis of six environmental variables, then admissions compared among clusters"", ""reanalysis"": ""Not fitted"", ""reason"": ""All three pollutant variables are required for the published cluster definition; outcome total and clustered-day count also fail to reconcile.""}], ""coverage"": {""eligible_units"": 39, ""included_units"": 39, ""eligible_times"": 1461, ""included_times"": 1461, ""notes"": ""Outcome and weather are complete for every calendar day. SIH competence files through 2016-04 were read to mitigate billing lag, then deduplicated by AIH number and restricted to 2012\u20132015 admission dates. No pollutant days were available.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md""}, ""blockers"": [""No independent, credential-free daily historical source providing PM2.5, PM10, and NO2 was successfully retrieved; clusters cannot be reconstructed with pollutants missing."", ""The supplied article says 30,423 patients and three clusters totaling 1,092 days, whereas the transparent 2012\u20132015 I21/residence extraction has 51,689 admissions and 1,461 days. The supplied materials lack sufficient methods to resolve this without silently changing the outcome/period."", ""Publisher full text was inaccessible: ScienceDirect returned HTTP 403 and the Elsevier API returned metadata only (openaccess=false).""]}" |
| raw-agent-control,r2,codex-baseline-33227571-sao-paulo-ami-r2-20260922T143418Z,,33227571,completed_blocker,"Preflight free disk was 15.69 GiB, below the frozen campaign minimum of 20 GiB.",2026-09-22T14:34:19.520178+00:00,2026-09-22T14:37:06.497916+00:00,0,0,0,1,32,"{""study_id"": ""PMID-33227571"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily acute myocardial infarction admissions in the Brazilian public health system (secondary outcome: in-hospital mortality)"", ""pollutant"": ""Daily NO2, PM2.5, and PM10 as components of a joint weather-and-pollution hierarchical cluster exposure"", ""geography"": ""39 municipalities in metropolitan S\u00e3o Paulo, Brazil"", ""period"": ""2012-01-01 through 2015-12-31 (article reports 1,092 clustered days)"", ""effect_scale"": ""Published comparison was a 9% increase in daily admissions for the high-pollution cluster; no independently fitted effect scale is available""}, ""sources"": [{""role"": ""citation and study specification"", ""url"": ""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33227571&retmode=xml"", ""retrieved"": true, ""sha256"": ""9d9e00109ca8d7f56baaeed6117e210d0be3b0d6093fe985d7da8825be4b50f6""}, {""role"": ""publisher landing record"", ""url"": ""https://doi.org/10.1016/j.hrtlng.2020.04.018"", ""retrieved"": true, ""sha256"": ""1a905237757ad4c13e99784466e5fcbcf7a033fb348aac8d5d8c0be85f323384""}, {""role"": ""DataSUS portal availability check"", ""url"": ""https://datasus.saude.gov.br/transferencia-de-arquivos/"", ""retrieved"": true, ""sha256"": ""4a591e15aa3043dfd16db4292185fd9742159da4b20ddb8f2c8d74705118b1d9""}, {""role"": ""independent exposure (not retrieved)"", ""url"": ""CETESB public monitoring data"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [], ""coverage"": {""eligible_units"": 39, ""included_units"": 0, ""eligible_times"": 1092, ""included_times"": 0, ""notes"": ""No public inputs were acquired after the mandatory preflight disk guard failed. Eligible counts are article-reported target scope, not observed panel coverage.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": null, ""analysis_panel"": null, ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""run_summary"": ""/output/run_summary.json"", ""preflight_evidence"": ""/output/preflight_disk_check.json""}, ""blockers"": [""Policy termination at preflight: 15.69 GiB free at /output, below the mandatory 20 GiB minimum before a study."", ""Exact principal model and contrasts are not recoverable from the supplied abstract and lawful publisher landing response.""]}" |
| raw-agent-control,r3,codex-baseline-33227571-sao-paulo-ami-r3-20260922T143418Z,,33227571,completed_blocker,,2026-09-22T14:34:19.520177+00:00,2026-09-22T14:41:32.941651+00:00,0,0,0,1,81,"{""study_id"": ""pmid:33227571"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily acute myocardial infarction hospital admissions (intended DataSUS SIH-SUS, ICD-10 I21)"", ""pollutant"": ""PM2.5, PM10, and nitrogen dioxide as a clustered environmental mixture"", ""geography"": ""39 municipalities in metropolitan S\u00e3o Paulo, Brazil"", ""period"": ""2012-2015 as stated in the supplied abstract; exact analytic dates unresolved"", ""effect_scale"": ""Published comparison described as admissions/day and percent increase; no model-native scale was available""}, ""sources"": [{""role"": ""article citation and abstract"", ""url"": ""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33227571&retmode=xml"", ""retrieved"": true, ""sha256"": ""9d9e00109ca8d7f56baaeed6117e210d0be3b0d6093fe985d7da8825be4b50f6""}, {""role"": ""official DataSUS SIH-SUS outcome microdata"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/RDSP1201.dbc"", ""retrieved"": false, ""sha256"": null}, {""role"": ""independent Open-Meteo historical exposure endpoint"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": null}], ""substitutions"": [], ""coverage"": {""eligible_units"": 39, ""included_units"": 0, ""eligible_times"": 1461, ""included_times"": 0, ""notes"": ""No usable daily outcome or exposure rows. The four-year count follows the stated inclusive 2012-2015 calendar interval; supplied abstract metadata are internally inconsistent about analytic dates.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization"": ""/output/health_column_sanitization.json"", ""request_log"": ""/output/request_log.json""}, ""blockers"": [""Official DataSUS daily SIH-SUS outcome microdata were unreachable; the alternate official portal query returned HTTP 500."", ""Independent Open-Meteo archival exposure request rejected 2012 and returned all-null variables for 2013-2015."", ""The supplied article materials do not resolve the exact analytic period, clustering specification, or model.""]}" |
| raw-agent-control,r1,codex-baseline-33398753-italy-cities-r1-20260919T162515Z,,33398753,completed_fit,,2026-09-19T16:25:15.299152+00:00,2026-09-19T16:31:12.936931+00:00,0,0,0,1,58,"{""study_id"": ""PMID-33398753"", ""status"": ""completed_fit"", ""target"": {""outcome"": ""Cumulative confirmed COVID-19 cases (province-level public series; 17 March 2020 primary, with 7 and 27 April replications)"", ""pollutant"": ""2018 days exceeding PM10 daily mean >50 ug/m3 or ozone maximum 8-hour rolling mean >120 ug/m3"", ""geography"": ""Italian provinces, assigned exposure at each provincial-capital coordinate"", ""period"": ""Exposure: 2018; outcomes: 17 March, 7 April, and 27 April 2020"", ""effect_scale"": ""OLS elasticity: log cumulative cases regressed on log annual exceedance days and log population density""}, ""sources"": [{""role"": ""health outcome (official provincial daily cases)"", ""url"": 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""66862a58e51783aec254cea7350283c892e94f8645363cf81a5f86d13b6cadd0""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""990db7657c39aaa2229bbaf5175c6bdde5f94fccfa031a61eed8b3b987741042""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""220d0d8e51aa7dc90c793b6be6bb0fea66983398a80e6b5f2ee8747d259eee6b""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""3d1d8fd89338eb13896bb32dcbbed39882b56b8ee22528e81ae1bcb159c9567a""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""a4f472d6b1bd5cf47dc1c8e68862dcb11f2ea360ce7b678f3a011df882387228""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""c2e298377b316c437f317e026858a71b95c343554a9065527eb34f8124a65709""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""b19ea3ea161a8225aeaee1b94c176493a0a25a0364511183da3cdf3a6724f554""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""fdee17a5eaef28fc936a5f4903d0e5a4fa3767931c1599ee526dd8d2e72b3eeb""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""ccb5110d13dfe8cdcebabe73b85d48a26dba1de7ca0f4ceb4c7a190f5533ce26""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""2aefe7a42404ed22d644809227d9ee9b839bb012c84c87d06936f97598c37fe4""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""6dd554b3cda43cb3c141369f50b4fe6dac42cf37c42eea43028bf7e975c0b0b6""}, {""role"": ""independent pollution exposure, CAMS via Open-Meteo (additional coordinate batch)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""2a466d22d25766a38db2d06603d2bd0ce31300b23de5dbaa91de5e65f21da795""}], ""substitutions"": [{""dimension"": ""geography"", ""published"": ""55 randomly selected provincial-capital cities (identities not reported)"", ""reanalysis"": ""All 107 official reporting provinces initially eligible; 100 entered the complete-case model"", ""reason"": ""The article does not identify its random 55-city sample; public outcome data are provincial.""}, {""dimension"": ""outcome"", ""published"": ""Infected individuals attributed to cities"", ""reanalysis"": ""Official cumulative confirmed cases reported by province"", ""reason"": ""The publicly available national series is province-level; city-specific case totals were not supplied.""}, {""dimension"": ""exposure"", ""published"": ""Legambiente-derived regulatory-monitor total days exceeding PM10 or ozone limits in 2018"", ""reanalysis"": ""CAMS reanalysis hourly PM10 and ozone at provincial-capital coordinates, aggregated using stated EU thresholds"", ""reason"": ""Required independent public exposure source; avoids article-author values and makes assignment reproducible.""}, {""dimension"": ""covariate"", ""published"": ""2019 municipal population density"", ""reanalysis"": ""2019 Eurostat NUTS3/provincial population density"", ""reason"": ""Aligns the covariate\u2019s geographic unit to the official provincial outcome.""}], ""coverage"": {""eligible_units"": 107, ""included_units"": 100, ""eligible_times"": 3, ""included_times"": 3, ""notes"": ""Four provinces lacked a direct 2019 Eurostat NUTS3-density match; three further provinces had zero modeled exceedance days and cannot enter a log-exposure model. All included points had 365 complete modeled exposure days.""}, ""effect"": {""estimate"": 0.7103243434902615, ""ci_low"": 0.5209219964158393, ""ci_high"": 0.8997266905646838, ""scale"": ""OLS log-log coefficient adjusted for log 2019 population density"", ""contrast"": ""1% higher 2018 CAMS-derived limit-exceedance days at the provincial-capital coordinate""}, ""artifacts"": {""code"": ""/output/code/reanalyze.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""request_log"": ""/output/request_log.json"", ""model_estimates"": ""/output/model_estimates.csv""}, ""blockers"": [""Exact reproduction of the published 55-city sample is impossible: the article says it was randomly selected but does not identify the cities."", ""The public national COVID-19 series reports cumulative cases by province, not city."", ""Four eligible provinces could not be directly matched to 2019 Eurostat NUTS3 density and were not imputed."", ""Three further provinces had zero CAMS-derived exceedance days; log(0) is undefined, so they were excluded rather than transformed.""]}" |
| raw-agent-control,r2,codex-baseline-33398753-italy-cities-r2-20260922T143706Z,,33398753,completed_fit,,2026-09-22T14:37:07.092387+00:00,2026-09-22T14:45:52.642709+00:00,0,0,0,1,131,"{""study_id"": ""PMC7781409"", ""status"": ""completed_fit"", ""target"": {""outcome"": ""Cumulative confirmed COVID-19 cases"", ""pollutant"": ""2018 PM10 daily-maximum exceedance days (>50 ug/m3)"", ""geography"": ""Italian provincial capitals/provinces"", ""period"": ""2020-03-17 (primary); 2020-04-07 and 2020-04-27 (declared comparisons)"", ""effect_scale"": ""log-log OLS PM10 elasticity; transformed to outcome ratio for doubling PM10 exceedance days""}, ""sources"": [{""role"": ""health_outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-province/dpc-covid19-ita-province.csv"", ""retrieved"": true, ""sha256"": ""d9f39377b0c3b0e8f4ac68b8e57cd9c1e953a4b922574b9438dc62094fb6446f""}, {""role"": ""independent_exposure"", ""url"": ""https://eeadmz1-downloads-api-appservice.azurewebsites.net/ParquetFile/urls"", ""retrieved"": true, ""sha256"": null}, {""role"": ""covariate_population"", ""url"": ""https://esploradati.istat.it/SDMXWS/rest/data/IT1,22_289?format=csvfile"", ""retrieved"": true, ""sha256"": ""2d1b5ee3b2432d541bc2ef604c13fe2b2f5116442030221fea3156a0f4540e64""}], ""substitutions"": [{""dimension"": ""geography"", ""published"": ""Unidentified random sample of 55 provincial-capital cities"", ""reanalysis"": ""107 eligible province/capital frame; 18 complete cases"", ""reason"": ""The article does not supply the sampled-city roster or selection seed.""}, {""dimension"": ""outcome"", ""published"": ""City infected-individual counts"", ""reanalysis"": ""Civil Protection province cumulative confirmed-case counts"", ""reason"": ""The public official archive provides province, rather than municipal/capital, series.""}, {""dimension"": ""exposure"", ""published"": ""Author's PM10-or-ozone city exceedance series (Table 6 labels PM10)"", ""reanalysis"": ""Nearest-station EEA PM10 daily-max days >50 ug/m3 in 2018"", ""reason"": ""Required independent public exposure source; PM10 follows the principal-table wording.""}, {""dimension"": ""covariate"", ""published"": ""2019 city population density"", ""reanalysis"": ""Istat NUTS3 2019 population divided by GISCO NUTS3 area"", ""reason"": ""Article does not provide city-level covariate values or sample roster.""}], ""coverage"": {""eligible_units"": 107, ""included_units"": 18, ""eligible_times"": 3, ""included_times"": 3, ""notes"": ""64 nearest-station assignments were available; 35 had positive PM10 exceedance counts; 18 had all log-model inputs.""}, ""effect"": {""estimate"": 0.6801064566, ""ci_low"": 0.3239684352, ""ci_high"": 1.4277464777, ""scale"": ""outcome ratio"", ""contrast"": ""Primary 2020-03-17 model: fitted case ratio for doubling 2018 PM10 exceedance days, exp(beta_PM10*ln(2)); native log-log beta=-0.5561675 (95% CI -1.6260748, 0.5137398).""}, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.csv"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""sanitization_record"": ""/output/sanitization_record.json"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""The article's 55-city sample cannot be reconstructed because its roster and selection procedure are not supplied."", ""The fitted panel uses province outcomes and province density, not city values."", ""Only 18 complete positive-exposure records support the log-log model.""]}" |
| raw-agent-control,r3,codex-baseline-33398753-italy-cities-r3-20260922T144133Z,,33398753,completed_blocker,,2026-09-22T14:41:33.662018+00:00,2026-09-22T14:49:06.790425+00:00,0,0,0,1,94,"{""study_id"": ""33398753"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Confirmed COVID-19 infected individuals, city, 7 April 2020"", ""pollutant"": ""2018 days exceeding PM10 or ozone limits"", ""geography"": ""55 Italian provincial capitals"", ""period"": ""2018 exposure; March-April 2020 outcomes"", ""effect_scale"": ""log-log OLS elasticity and transformed outcome ratio per 1% exposure increase""}, ""sources"": [{""role"": ""article"", ""url"": ""https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7781409/fullTextXML"", ""retrieved"": true, ""sha256"": ""dc2e0d8ceca27033d2746cf45607e0058d07fe16288aae3206722a9ff5aed02f""}, {""role"": ""author_designated_outcome_and_covariate_table_sanitized"", ""url"": ""https://data.mendeley.com/datasets/bbnyhp6gfh/1"", ""retrieved"": true, ""sha256"": ""c0e25d564b2a64308488e043bd4bc51e757dd4373c55ce6604242b8449dfb16a""}, {""role"": ""independent_exposure_station_catalogue"", ""url"": ""https://air.discomap.eea.europa.eu/arcgis/rest/services/AirQuality/AirQualityDownloadServiceEUMonitoringStations/MapServer/0"", ""retrieved"": true, ""sha256"": ""274821aa486bc512bc9d0c5f3bbb450280a94bd39f22ac0549337e46678b2a57""}, {""role"": ""independent_exposure_historical_series_attempt"", ""url"": ""https://eeadmz1batchservice02.blob.core.windows.net/airquality-p-e1a/IT/SPO.IT1846A_5_BETA_2006-04-30_00_00_00.parquet"", ""retrieved"": false, ""sha256"": null}, {""role"": ""geographic_assignment"", ""url"": ""https://nominatim.openstreetmap.org/search"", ""retrieved"": true, ""sha256"": ""55d1ac906d1c0fbb0131b9435d589e0ed279630d7f1f4222c3986939d7f60b23""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""PM10-or-ozone exceedance days"", ""reanalysis"": ""EEA PM10 daily means >50 ug/m3"", ""reason"": ""Independent source required; unavailable after terminal 404.""}, {""dimension"": ""outcome"", ""published"": ""Ministero della Salute city counts"", ""reanalysis"": ""Sanitized author-designated Mendeley table"", ""reason"": ""Public deposited table; pollution field dropped before inspection.""}], ""coverage"": {""eligible_units"": 55, ""included_units"": 0, ""eligible_times"": 2, ""included_times"": 0, ""notes"": ""EEA historical series retrieval failed at the first deterministic station assignment; no model fit.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/run_analysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/derived/eea_pm10_exposure.csv"", ""analysis_panel"": ""/output/derived/analysis_panel.csv"", ""model_output"": ""/output/models/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""EEA advertised historical PM10 object returned terminal HTTP 404."", ""Independent exposure coverage is 0/55; model fitting would violate the contract.""]}" |
| raw-agent-control,r1,codex-baseline-33484722-oecd-covid-r1-20260919T163114Z,,33484722,completed_fit,,2026-09-19T16:31:14.600701+00:00,2026-09-19T16:37:00.746943+00:00,0,0,0,1,54,"{""study_id"": ""33484722_oecd_covid19"", ""status"": ""completed_fit"", ""target"": {""outcome"": ""log confirmed COVID-19 case rate per 10,000 population on day 80 after first confirmed case"", ""pollutant"": ""2017 annual population-weighted PM2.5 concentration (micrograms per cubic metre)"", ""geography"": ""36 OECD countries listed in the article (35 complete-case countries fitted)"", ""period"": ""country-specific first confirmed case through day 80, January--May 2020; exposure year 2017"", ""effect_scale"": ""OLS coefficient on log case rate per 10,000 for a 1 microgram/m3 PM2.5 increase""}, ""sources"": [{""role"": ""outcome"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"", ""retrieved"": true, ""sha256"": ""e6234a59eec4359d2577358b5220e1a7e3da74c162913cdb7d882db1413f98c2""}, {""role"": ""exposure"", ""url"": ""https://api.worldbank.org/v2/country/all/indicator/EN.ATM.PM25.MC.M3?format=json&per_page=20000"", ""retrieved"": true, ""sha256"": ""f437564441e74f3ee3438e13910a8697ad2358f769af970d3dfbe04dd3afeb35""}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""WHO daily COVID-19 data"", ""reanalysis"": ""JHU CSSE country cumulative confirmed-case time series"", ""reason"": ""Independently retrieved public historical outcome source; same cumulative confirmed-case outcome and country-specific day rule.""}, {""dimension"": ""covariate"", ""published"": ""OECD GDP data (unit not specified in article)"", ""reanalysis"": ""World Bank GDP per capita, current USD, 2019"", ""reason"": ""Public, reproducible GDP series; article did not identify its GDP unit.""}], ""coverage"": {""eligible_units"": 36, ""included_units"": 35, ""eligible_times"": 36, ""included_times"": 36, ""notes"": ""All country-specific day-80 outcome dates are available. United States excluded from fitted model because physician data were unavailable under the article's 2015--2017 fallback rule.""}, ""effect"": {""estimate"": 0.07341496980495785, ""ci_low"": -0.05931746193216067, ""ci_high"": 0.20614740154207636, ""scale"": ""change in log day-80 confirmed-case rate per 10,000"", ""contrast"": ""1 microgram/m3 higher 2017 PM2.5""}, ""artifacts"": {""code"": ""/output/code/reanalyze.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""model_summary"": ""/output/model_summary.json""}, ""blockers"": []}" |
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""e6234a59eec4359d2577358b5220e1a7e3da74c162913cdb7d882db1413f98c2""}, {""role"": ""COVID-19 deaths"", ""url"": ""https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"", ""retrieved"": true, ""sha256"": ""4e87757a3e059c45650a1e1856614f8e339ee3c70653c378a7ba6f7b0ee8c72e""}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""WHO daily COVID-19 country data, Jan 21-Jun 7 2020"", ""reanalysis"": ""JHU CSSE global country time-series data"", ""reason"": ""independent public historical country-level source; exact WHO archive extract was not supplied""}, {""dimension"": ""model"", ""published"": ""Table 1 includes PM2.5 exposure-above-guideline plus stated covariates"", ""reanalysis"": ""OLS with stated covariates and independent PM2.5; omitted exposure-above-guideline"", ""reason"": ""principal PM2.5 concentration comparison reconstructed; independent source selected for pollutant""}], ""coverage"": {""eligible_units"": 36, ""included_units"": 35, ""eligible_times"": 2, ""included_times"": 2, ""notes"": ""Each included country contributes day-60 and day-80 records. Exclusions listed in exclusions.json.""}, ""effect"": {""estimate"": 1.0674434397039396, ""ci_low"": 0.9713177376328631, ""ci_high"": 1.1730821468820538, ""scale"": ""rate ratio"", ""contrast"": ""day-80 confirmed-case rate per 100,000, per 1 ug/m3 higher 2017 PM2.5; exp(OLS beta)""}, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_pm25_worldbank_2017.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization"": ""/output/sanitization_record.json""}, ""blockers"": []}" |
| raw-agent-control,r1,codex-baseline-34004167-northern-italy-covid-r1-20260919T163702Z,,34004167,completed_blocker,,2026-09-19T16:37:03.092564+00:00,2026-09-19T16:40:37.569848+00:00,0,0,0,1,41,"{""study_id"": ""PMID:34004167"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""daily reported COVID-19 deaths"", ""pollutant"": ""sulfur dioxide (SO2), long-term exposure"", ""geography"": ""Lombardy and Veneto, Italy"", ""period"": ""2020-02-21 through 2020-05-19"", ""effect_scale"": ""mortality count ratio per 1 ug/m3 LTAP SO2 (Poisson log-link GEE)""}, ""sources"": [{""role"": ""supplied_article"", ""url"": ""https://pmc.ncbi.nlm.nih.gov/articles/PMC8123517/"", ""retrieved"": false, ""sha256"": null, ""note"": ""Supplied locally under /study; used to identify target and model.""}, {""role"": ""health_outcome"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""retrieved"": true, ""sha256"": ""3438a0a85bdb0bca56a48a2edd0c69f3005d6c1c20c4a2a75bed668a8f01ead7"", ""local_file"": ""/output/source_covid_regions.csv"", ""note"": ""Italian Civil Protection regional public archive; cumulative fields differenced for daily incident counts.""}, {""role"": ""independent_exposure_lombardia"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=45.466&longitude=9.19&hourly=sulphur_dioxide&start_date=2013-01-01&end_date=2020-05-19&timezone=GMT"", ""retrieved"": true, ""sha256"": ""3ffb28d8dfaaf84df435d718108fda25e48462378f78d42cbed79c3f6c01de7f"", ""local_file"": ""/output/source_openmeteo_so2_lombardia.json"", ""note"": ""Public modelled hourly SO2; Milan regional-capital grid-cell assignment, averaged to daily values.""}, {""role"": ""independent_exposure_veneto"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=45.438&longitude=12.327&hourly=sulphur_dioxide&start_date=2013-01-01&end_date=2020-05-19&timezone=GMT"", ""retrieved"": true, ""sha256"": ""63847e860f5588f4475f418d56c3fc75e4a5439339593c7cc4324d737f30b45d"", ""local_file"": ""/output/source_openmeteo_so2_veneto.json"", ""note"": ""Public modelled hourly SO2; Venice regional-capital grid-cell assignment, averaged to daily values.""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""EEA monitoring-station measurements aggregated by region"", ""reanalysis"": ""Open-Meteo public modelled SO2 at Milan and Venice regional-capital grid cells"", ""reason"": ""Independent public exposure source required; authors' values were not used.""}, {""dimension"": ""period"", ""published"": ""2020-02-21 to 2020-05-19 (89 dates)"", ""reanalysis"": ""2020-02-25 to 2020-05-19 (85 dates)"", ""reason"": ""Public regional archive begins 2020-02-24 and daily incident counts require a preceding cumulative report.""}, {""dimension"": ""other"", ""published"": ""LTAP construction ambiguously described as mean measurements in the coming 8 years"", ""reanalysis"": ""mean of all 2013-01-01 to 2020-05-19 hourly assigned grid-cell SO2 values"", ""reason"": ""Explicit, reproducible operationalization; not claimed equivalent to authors' undocumented aggregation.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 89, ""included_times"": 85, ""notes"": ""170 complete region-date rows. Four article-period dates lack derivable public daily outcomes; no coverage relaxation was made.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_so2_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""request_log"": ""/output/request_log.json""}, ""blockers"": [""The reconstructed panel has only two regional clusters (Lombardia and Veneto); cluster-robust GEE inference is not defensible with two clusters."", ""The long-term SO2 predictor has only two region-level values, so its principal between-region comparison is based on two exposure groups."", ""The publicly archived regional outcome series begins 2020-02-24; daily incident outcomes can only be derived from 2020-02-25, leaving four of the article's 89 target dates unavailable.""]}" |
| raw-agent-control,r2,codex-baseline-34004167-northern-italy-covid-r2-20260922T144948Z,,34004167,completed_blocker,,2026-09-22T14:49:48.891475+00:00,2026-09-22T15:07:58.798930+00:00,0,0,0,1,140,"{""study_id"": ""PMID:34004167"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Accumulated confirmed COVID-19 cases and deaths by region-day (principal published count outcomes)"", ""pollutant"": ""SO2 principal; NO2, O3, PM2.5, and PM10 reconstructed as additional declared contrasts"", ""geography"": ""Lombardy and Veneto, Italy"", ""period"": ""Published: 2020-02-21 to 2020-05-19; reconstructed: 2020-02-24 to 2020-05-19; LTAP window 2013-01-01 to 2020-05-19"", ""effect_scale"": ""Native log rate ratio and exp(beta) RR per 1 ug/m3""}, ""sources"": [{""role"": ""health outcomes"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""retrieved"": true, ""sha256"": ""3438a0a85bdb0bca56a48a2edd0c69f3005d6c1c20c4a2a75bed668a8f01ead7""}, {""role"": ""raw exposure"", ""url"": ""https://eeadmz1-downloads-api-appservice.azurewebsites.net/ParquetFile/urls"", ""retrieved"": true, ""sha256"": ""d09d890b61556bcdaa2c56c6ff60c0372bb4e2f95597312c0dbd2f9b4cdc47ec""}, {""role"": ""station metadata"", ""url"": ""https://discomap.eea.europa.eu/map/fme/metadata/PanEuropean_metadata.csv"", ""retrieved"": true, ""sha256"": ""7373040062adf22d4c7a4bb1a51aa01bdcebd7caf4e1c865b5911d559e9b22da""}, {""role"": ""boundary assignment"", ""url"": ""https://geodata.ucdavis.edu/gadm/gadm4.1/json/gadm41_ITA_1.json.zip"", ""retrieved"": true, ""sha256"": ""f42fb1f30d4c72695fa6e48d7ac0179af4c38f426514f41c58e9057604d3939c""}], ""substitutions"": [{""dimension"": ""period"", ""published"": ""2020-02-21 through 2020-05-19"", ""reanalysis"": ""2020-02-24 through 2020-05-19"", ""reason"": ""The independent national regional time series begins 2020-02-24; the unavailable dates were not imputed.""}, {""dimension"": ""exposure"", ""published"": ""Author-aggregated EEA regional STAP/LTAP"", ""reanalysis"": ""Independent aggregation of raw EEA E1a station observations with GADM polygon assignment"", ""reason"": ""Author-derived exposure fields were prohibited.""}, {""dimension"": ""other"", ""published"": ""Calendar-complete long-term mean implied by 2013--2020 period"", ""reanalysis"": ""Observed-day mean: 2,331 days per pollutant-region"", ""reason"": ""No gap filling was used.""}, {""dimension"": ""model"", ""published"": ""GEE adjusted for lockdown"", ""reanalysis"": ""No valid principal fit; specified-form diagnostic fits retained only"", ""reason"": ""The substituted outcome period has no pre-lockdown observations, so lockdown is constant and collinear with intercept; only two GEE clusters also invalidate robust inference.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 89, ""included_times"": 86, ""notes"": ""Both regions have all 86 available outcome dates and complete STAP values. Long-term exposure has 2,331 observed dates rather than 2,696 calendar dates per pollutant-region.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.csv"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization"": ""/output/sanitization.json"", ""machine_readable_run_summary"": ""/output/run_summary.json""}, ""blockers"": [""The lockdown covariate is constant after the unavoidable public-outcome date substitution and is perfectly collinear with the intercept."", ""Only two regional clusters are available for AR(1) GEE; robust covariance warnings and diagnostic intervals are not valid inferential confidence intervals.""]}" |
| raw-agent-control,r3,codex-baseline-34004167-northern-italy-covid-r3-20260922T145312Z,,34004167,completed_blocker,,2026-09-22T14:53:13.514116+00:00,2026-09-22T14:57:20.850222+00:00,0,0,0,1,47,"{""study_id"": ""PMID_34004167"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily reported COVID-19 cases and deaths (with fatality rate as secondary outcome)"", ""pollutant"": ""NO2, O3, PM2.5, PM10, and SO2"", ""geography"": ""Lombardy and Veneto, Italy"", ""period"": ""2020-02-21 through 2020-05-19"", ""effect_scale"": ""Published comparison: outcome ratio per 1 microgram/m3 increment in STAP or LTAP""}, ""sources"": [{""role"": ""COVID-19 outcomes"", ""url"": ""https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"", ""retrieved"": true, ""sha256"": ""3438a0a85bdb0bca56a48a2edd0c69f3005d6c1c20c4a2a75bed668a8f01ead7""}, {""role"": ""independent Lombardy exposure candidate"", ""url"": ""https://www.arpalombardia.it/media/lo4mdame/013_aria_qa_dati_2020.xls"", ""retrieved"": true, ""sha256"": ""b2776a8572dda17e5d44564600c272da0b20cca78ddd48b911b03e251ae3d919""}, {""role"": ""independent Veneto exposure candidate"", ""url"": ""https://www.arpa.veneto.it/dati-ambientali/dati-storici/aria/dati-parametro"", ""retrieved"": true, ""sha256"": ""be9423e013de6fd6f2366c48aea63ac06835d3af8a3edd087cb8de2515b8b054""}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""Italian Ministry of Health daily reports cited by article"", ""reanalysis"": ""Italian Civil Protection regional public CSV"", ""reason"": ""Public machine-readable regional release; it preserves the target construct but starts on 2020-02-24.""}, {""dimension"": ""exposure"", ""published"": ""Authors' EEA-derived 2013-2020 STAP/LTAP values"", ""reanalysis"": ""No substituted exposure values used"", ""reason"": ""Contract prohibits author exposure fields; independent sources did not yield a complete comparable panel.""}], ""coverage"": {""eligible_units"": 2, ""included_units"": 2, ""eligible_times"": 89, ""included_times"": 86, ""notes"": ""Outcomes exist for both regions on 2020-02-24 through 2020-05-19 only. Exposure coverage is zero for the required complete independent STAP/LTAP panel.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""outcome_sanitization"": ""/output/outcome_sanitization.json"", ""fidelity_record"": ""/output/fidelity_record.json"", ""run_summary"": ""/output/run_summary.json""}, ""blockers"": [""No independent public daily STAP and 2013-2020 LTAP source was recovered for every pollutant in both regions."", ""The outcome release begins after the paper's LOCK start date, making LOCK identically one and the stated adjusted model non-estimable."", ""Three of 89 target dates are absent from the outcome release.""]}" |
| raw-agent-control,r1,codex-baseline-34488764-france-covid-r1-20260919T164040Z,,34488764,completed_blocker,,2026-09-19T16:40:40.672864+00:00,2026-09-19T16:44:24.028115+00:00,0,0,0,1,52,"{""study_id"": ""PMID:34488764"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Cumulative COVID-19 deaths in hospital"", ""pollutant"": ""Long-term annual mean PM2.5"", ""geography"": ""96 mainland-France departments (NUTS 3)"", ""period"": ""01 May through 31 December 2020 at nine specified cumulative snapshots; exposure period 1999\u20132016"", ""effect_scale"": ""Negative-binomial mortality-rate ratio (exponentiated coefficient)""}, ""sources"": [{""role"": ""official outcome data"", ""url"": ""https://static.data.gouv.fr/resources/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/20230331-180159/covid-hospit-2023-03-31-18h01.csv"", ""retrieved"": true, ""sha256"": ""79945ede9e319d5d7289cdcbd4a686ff0e2d06ac9b4232fdde139b0b9e5cfc82""}, {""role"": ""independent PM2.5 source catalogue"", ""url"": ""https://sites.wustl.edu/acag/surface-pm2-5/"", ""retrieved"": true, ""sha256"": ""41c0182b448b94327b201ef34036489cd37d22f7c8eb327a473bd3a0b81213fc""}, {""role"": ""independent PM2.5 Europe grid payload"", ""url"": ""https://wustl.box.com/v/ACAG-V5GL0502-GWRPM25c0p05"", ""retrieved"": false, ""sha256"": ""320054fc135b1910035decf29709dcc67b58f5725650ae4eaa7fdea472033404""}], ""substitutions"": [], ""coverage"": {""eligible_units"": 96, ""included_units"": 0, ""eligible_times"": 9, ""included_times"": 0, ""notes"": ""Official outcome extraction covers 96 departments x 9 snapshots. No analytic rows were included because independent department PM2.5 exposure values and a complete published-covariate panel were not retrieved.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/analysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""outcome"": ""/output/outcome_table.csv"", ""coverage_check"": ""/output/coverage_check.json"", ""run_summary"": ""/output/run_summary.json""}, ""blockers"": [""The independently identified ACAG PM2.5 catalogue was reachable but its nested Europe raster payload was not delivered through the public Box endpoint in this run; no 1999\u20132016 department exposure can be assigned without inventing values."", ""A complete independent 96-department panel for all ten published adjustment covariates was not retrieved."", ""Consequently the principal adjusted negative-binomial comparison was not executed.""]}" |
| raw-agent-control,r2,codex-baseline-34488764-france-covid-r2-20260922T150801Z,,34488764,completed_blocker,,2026-09-22T15:08:01.619439+00:00,2026-09-22T15:12:36.564480+00:00,0,0,0,1,59,"{""study_id"": ""PMID:34488764"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Cumulative COVID-19 deaths in hospital (all sexes), department level"", ""pollutant"": ""Long-term PM2.5"", ""geography"": ""96 metropolitan French departments (NUTS-3)"", ""period"": ""2020-05-01, 2020-06-01, 2020-07-01, 2020-08-01, 2020-09-01, 2020-10-01, 2020-11-01, 2020-12-01, and 2020-12-31"", ""effect_scale"": ""Mortality rate ratio; native negative-binomial log rate-ratio coefficient, exponentiated to a positive rate ratio""}, ""sources"": [{""role"": ""health outcome"", ""url"": ""https://static.data.gouv.fr/resources/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/20230331-180159/covid-hospit-2023-03-31-18h01.csv"", ""retrieved"": true, ""sha256"": ""79945ede9e319d5d7289cdcbd4a686ff0e2d06ac9b4232fdde139b0b9e5cfc82""}, {""role"": ""independent PM2.5 monitor exposure"", ""url"": ""https://air.discomap.eea.europa.eu/arcgis/rest/services/AirQuality/AQ_Statistics_WM/MapServer/0/query"", ""retrieved"": true, ""sha256"": ""4fde99e317af816c2c790c72b58b23ad27a838376b2808c97441f23b18156fc7""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""1999-2016 NASA/SEDAC GOME 1-km PM2.5 averaged by department"", ""reanalysis"": ""EEA validated 2016 French PM2.5 annual-mean monitor query"", ""reason"": ""Independent public source required; it was used only for coverage assessment and not as a scientific replacement because it covers two stations rather than 96 department means.""}, {""dimension"": ""other"", ""published"": ""Author says full dataset publicly accessible"", ""reanalysis"": ""No author table used"", ""reason"": ""No usable author-designated table URL or table was supplied; avoiding its use also avoids author-derived analysis fields.""}], ""coverage"": {""eligible_units"": 96, ""included_units"": 0, ""eligible_times"": 9, ""included_times"": 0, ""notes"": ""Outcome coverage was 96 departments at all nine dates; valid independent exposure coverage was zero departments because the EEA query returned two monitor points, not department exposure assignments.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalyse.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_eea_pm25_2016_stations.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""sanitization"": ""/output/sanitization.json"", ""request_log"": ""/output/request_log.json""}, ""blockers"": [""Independent PM2.5 source returned two 2016 station observations, not department-level 1999-2016 exposure for 96 departments."", ""Required adjusted covariates and population offset were not reconstructable from a usable public author-designated table."", ""The article does not state the negative-binomial offset; no unannounced model specification was chosen.""]}" |
| raw-agent-control,r3,codex-baseline-34488764-france-covid-r3-20260922T145738Z,,34488764,agent_failure,missing or schema-invalid result.json,2026-09-22T14:57:40.917780+00:00,2026-09-22T15:07:35.394676+00:00,0,0,0,1,105,"{""study_id"": ""PMID-34488764"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Cumulative COVID-19 hospital deaths by department"", ""pollutant"": ""Long-term PM2.5"", ""geography"": ""96 metropolitan French departments (NUTS 3)"", ""period"": ""Outcome dates 2020-05-01 through 2020-12-31; PM2.5 1999-2016"", ""effect_scale"": ""Mortality rate ratio, PM2.5 quartile Q2/Q3/Q4 versus Q1""}, ""sources"": [{""role"": ""health outcome"", ""url"": ""https://static.data.gouv.fr/resources/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/20230331-180159/covid-hospit-2023-03-31-18h01.csv"", ""retrieved"": true, ""sha256"": ""79945ede9e319d5d7289cdcbd4a686ff0e2d06ac9b4232fdde139b0b9e5cfc82""}, {""role"": ""department boundaries"", ""url"": ""https://france-geojson.gregoiredavid.fr/repo/departements.geojson"", ""retrieved"": true, ""sha256"": ""a5557a059bd4f848fbf92e81f716d7e2253226f31e943f67f85b844c9de91c5d""}, {""role"": ""author-designated covariate table (sanitized)"", ""url"": ""/study/supplements/12940_2021_784_MOESM1_ESM.docx"", ""retrieved"": true, ""sha256"": ""eb4378442d2f3a0f66717ab2d48ee4ba2ada3f1fc2e9e70d66f7b5b57e53db50""}, {""role"": ""independent PM2.5 grid 1999"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.199901-199912.nc"", ""retrieved"": true, ""sha256"": ""0194ac21b789cacc89e596f01ddd425f538703576beeb44e40170cce1aac8dc1""}, {""role"": ""independent PM2.5 grid 2000"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200001-200012.nc"", ""retrieved"": true, ""sha256"": ""09afbef9aea4f40f6214a69318f71680d1d277c6a88a0251474ea98cd5053c8c""}, {""role"": ""independent PM2.5 grid 2001"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200101-200112.nc"", ""retrieved"": true, ""sha256"": ""ba430c5e686455e09fa3dcd4a1994867edbecb42d5eae21fc2a7fc1327dc9ffc""}, {""role"": ""independent PM2.5 grid 2002"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200201-200212.nc"", ""retrieved"": true, ""sha256"": ""7c3aba72dcebe6054621d564db17430291121386bd747efef2c02fe736fd0b1f""}, {""role"": ""independent PM2.5 grid 2003"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200301-200312.nc"", ""retrieved"": true, ""sha256"": ""cf85ad3c06324e66d73bcb49d75c0f6a944cc3ad383f489d34636e0b0ac11c6c""}, {""role"": ""independent PM2.5 grid 2004"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200401-200412.nc"", ""retrieved"": true, ""sha256"": ""9eda232ba6b58b17d3bdf6c2740d90caaaabadfbc354f71cf2d14368c21eb800""}, {""role"": ""independent PM2.5 grid 2005"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200501-200512.nc"", ""retrieved"": true, ""sha256"": ""26ff6eee809d2bdb9da83bfa2defc8143e560a379dfed4c5206e5ded4d9ee005""}, {""role"": ""independent PM2.5 grid 2006"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200601-200612.nc"", ""retrieved"": true, ""sha256"": ""40747dd33fa973b0a176e12b6967f26d8d5928c7fa10b53088d337b054dc6c00""}, {""role"": ""independent PM2.5 grid 2007"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200701-200712.nc"", ""retrieved"": true, ""sha256"": ""ed5ae59c8fc00d1273189ba3afd539e3577456105bac5e77ab4f6424dd8fa14d""}, {""role"": ""independent PM2.5 grid 2008"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200801-200812.nc"", ""retrieved"": true, ""sha256"": ""0bd44dbc691283ee6f8d1a3419c0af6dcd05d292ff607b245b0f9fca0f6d0eb4""}, {""role"": ""independent PM2.5 grid 2009"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.200901-200912.nc"", ""retrieved"": true, ""sha256"": ""39f2ebd1734c58d67a722626dfc6d2d5ad4bfbc2d3474f1fa6d20939460a36f9""}, {""role"": ""independent PM2.5 grid 2010"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201001-201012.nc"", ""retrieved"": true, ""sha256"": ""4973a60961ad9024b7184384b147ca9bad069d9cded328ebb4d38b321569b4ac""}, {""role"": ""independent PM2.5 grid 2011"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201101-201112.nc"", ""retrieved"": true, ""sha256"": ""1a4d9a2cfe9eb9083211a0a29239de1d0653a664a0c747d0e9c9cb65f7c2195a""}, {""role"": ""independent PM2.5 grid 2012"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201201-201212.nc"", ""retrieved"": true, ""sha256"": ""47554091ff3f7c644a44ce6d3d12d301c0981c96ddf2428e89ff0a6539319953""}, {""role"": ""independent PM2.5 grid 2013"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201301-201312.nc"", ""retrieved"": true, ""sha256"": ""f9fd65d11d2af6ae06be3e9e10bb90cfcaeb2721bb73dc80811a2bcff2a8e173""}, {""role"": ""independent PM2.5 grid 2014"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201401-201412.nc"", ""retrieved"": true, ""sha256"": ""271abd66d324568c0225b2a3d97365ed197751398f3a7f6a0ea47bb979fc516a""}, {""role"": ""independent PM2.5 grid 2015"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201501-201512.nc"", ""retrieved"": true, ""sha256"": ""d11d1ea5486df96ed6cf1a30bfcf1d521ec3e9c5c51c2d88151078674eee23af""}, {""role"": ""independent PM2.5 grid 2016"", ""url"": ""https://satpmdata.s3.amazonaws.com/V6GL03/CoarseResolution/EU/Annual/V6GL03.CNNPM25.0p10.EU.201601-201612.nc"", ""retrieved"": true, ""sha256"": ""03e6d42f84286e66c2b755e077b6f047afeaf986f38f7aa152207728e3993369""}, {""role"": ""original SEDAC PM2.5 endpoint attempted"", ""url"": ""https://sedac.ciesin.columbia.edu/downloads/maps/sdei/sdei-global-annual-gwr-pm2-5-modis-misr-seawifs-aod-v4-gl-03/"", ""retrieved"": false, ""sha256"": null}, {""role"": ""WorldClim historical temperature attempt"", ""url"": ""https://geodata.ucdavis.edu/climate/worldclim/2_1/hist/cts4.09/"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""NASA SEDAC V4 PM2.5 1999-2016, stated 1 km"", ""reanalysis"": ""ACAG V6.GL.03 independently retrieved public PM2.5 annual 0.1 degree grids, polygonal department means"", ""reason"": ""Contract prohibits using authors\u2019 pollution values/derived exposure; independent public product used.""}], ""coverage"": {""eligible_units"": 96, ""included_units"": 95, ""eligible_times"": 9, ""included_times"": 9, ""notes"": ""Health outcome and covariates cover 96 departments and 9 dates. Independent 0.1-degree PM2.5 polygonal extraction has no in-polygon grid cell for Hauts-de-Seine (92), leaving 95 exposure-complete departments. No fill or geographic relaxation was made.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""sanitization"": ""/output/sanitization.json"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""Exact required independent long-term temperature (2001-2012) was not constructed; temperature is a declared covariate in every published principal model. The principal model was therefore not fit."", ""Hauts-de-Seine (92) has no in-polygon pixel in the 0.1-degree independent PM2.5 grid; it would be excluded from any exposure-complete model.""], ""fidelity_record"": {""status"": ""blocked"", ""published_target_locked"": true, ""outcome_independent"": true, ""exposure_independent"": true, ""covariates_sanitized"": true, ""principal_model_fit"": false, ""blocker"": ""Independent temperature reconstruction unavailable in this run; PM2.5 grid has no in-polygon cell for Hauts-de-Seine.""}}" |
| raw-agent-control,r1,codex-baseline-36383802-sao-jose-covid-r1-20260919T164424Z,,36383802,completed_blocker,,2026-09-19T16:44:25.248608+00:00,2026-09-19T16:55:17.736276+00:00,0,0,0,1,85,"{""study_id"": ""PMID-36383802"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily SIH/SUS COVID-19 hospitalizations among S\u00e3o Jos\u00e9 dos Campos residents (ICD-10 B34.2)"", ""pollutant"": ""O3, NO2, and PM10; lag 0 through 7 days"", ""geography"": ""S\u00e3o Jos\u00e9 dos Campos, S\u00e3o Paulo, Brazil (municipality code 354990)"", ""period"": ""2020-04-01 through 2021-04-30"", ""effect_scale"": ""relative risk per 10 \u00b5g/m\u00b3""}, ""sources"": [{""role"": ""article and methods"", ""url"": ""https://pmc.ncbi.nlm.nih.gov/articles/PMC9668087/"", ""retrieved"": true, ""sha256"": ""a42a246573ef4d63dc36cdd87fb76ff75090d5025e0e1c14fc8991d3658964dc""}, {""role"": ""independent air-pollution exposure"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=-23.1791&longitude=-45.8872&hourly=ozone,nitrogen_dioxide,pm10&timezone=America%2FSao_Paulo&start_date=2020-04-01&end_date=2021-04-30"", ""retrieved"": true, ""sha256"": ""68624e5396ba8c5b5e08ceb71cc5096b9170cf51852140cdd84693a7b95b3459""}, {""role"": ""meteorological covariates"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=-23.1791&longitude=-45.8872&daily=temperature_2m_max,relative_humidity_2m_mean&timezone=America%2FSao_Paulo&start_date=2020-04-01&end_date=2021-04-30"", ""retrieved"": true, ""sha256"": ""2e8de7635b3e2bbb044640a66696c418b093e45af15ac9e4bfe9589c1ce150ec""}, {""role"": ""SIH/SUS outcome microdata (first required monthly object; remaining URLs in decision log)"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/RDSP2004.dbc"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""CETESB station daily pollutant values"", ""reanalysis"": ""Open-Meteo/CAMS gridded hourly fields at municipal coordinates, aggregated O3 daily maximum and NO2/PM10 daily mean"", ""reason"": ""Independent public source required; no author exposure data used""}, {""dimension"": ""covariate"", ""published"": ""CETESB daily temperature and relative humidity"", ""reanalysis"": ""Open-Meteo ERA5-Land daily maximum 2-m temperature and mean 2-m relative humidity"", ""reason"": ""Independent public meteorology source required""}], ""coverage"": {""eligible_units"": 1, ""included_units"": 0, ""eligible_times"": 395, ""included_times"": 0, ""notes"": ""No analysis panel: official raw SIH/SUS outcome object could not be retrieved; the independent air-quality response also contains complete pollutant values for 0/395 requested days.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""retrieval_log"": ""/output/retrieval_log.json""}, ""blockers"": [""Official DATASUS SIH/SUS raw outcome microdata request failed by connect timeout; without daily hospitalization counts, the specified negative-binomial model cannot be fit."", ""Open-Meteo air-quality endpoint returned hourly timestamps but null O3, NO2, and PM10 values for the requested historical period (0/395 complete daily observations); coverage was not relaxed.""]}" |
| raw-agent-control,r2,codex-baseline-36383802-sao-jose-covid-r2-20260922T151237Z,,36383802,completed_blocker,,2026-09-22T15:12:38.044291+00:00,2026-09-22T15:23:29.919700+00:00,0,0,0,1,96,"{""study_id"": ""PMID:36383802"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""daily COVID-19 hospital admissions among S\u00e3o Jos\u00e9 dos Campos residents"", ""pollutant"": ""ozone, nitrogen dioxide, and PM10"", ""geography"": ""S\u00e3o Jos\u00e9 dos Campos, S\u00e3o Paulo, Brazil"", ""period"": ""2020-04-01 through 2021-04-30"", ""effect_scale"": ""relative risk for 10 \u00b5g/m\u00b3 increase""}, ""sources"": [{""role"": ""study article"", ""url"": ""https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9668087/fullTextXML"", ""retrieved"": true, ""sha256"": ""a42a246573ef4d63dc36cdd87fb76ff75090d5025e0e1c14fc8991d3658964dc""}, {""role"": ""independent air-pollution exposure (attempted)"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=-23.1797&longitude=-45.8872&hourly=ozone,nitrogen_dioxide,pm10&start_date=2020-04-01&end_date=2021-04-30&timezone=America%2FSao_Paulo"", ""retrieved"": true, ""sha256"": ""94a9ea8500c3d20b01907d4a70bb2370110991aebeceadfd34afc0c0de095a68""}, {""role"": ""weather covariates"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=-23.1797&longitude=-45.8872&hourly=temperature_2m,relative_humidity_2m&start_date=2020-04-01&end_date=2021-04-30&timezone=America%2FSao_Paulo"", ""retrieved"": true, ""sha256"": ""625aebaeaf1295118b35e5ea22a27300c270b4fc4e8c74b43d850d4c575b4a00""}, {""role"": ""health outcome (SIVEP-Gripe)"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SRAG/2020/INFLUD20-23-03-2026.parquet"", ""retrieved"": true, ""sha256"": ""371723b91c0e4de1ae4067c8a6ee04887430869fa8d3c561d4b9106fb89e0c0b""}, {""role"": ""health outcome (SIVEP-Gripe)"", ""url"": ""https://s3.sa-east-1.amazonaws.com/ckan.saude.gov.br/SRAG/2021/INFLUD21-23-03-2026.parquet"", ""retrieved"": true, ""sha256"": ""ecad01062f23715551a1e5e82fa1d9b28f0ea25e2c486a49518a15bf489ee790""}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""SIH-SUS hospitalizations coded B34.2"", ""reanalysis"": ""SIVEP-Gripe COVID-19 SRAG hospital-admission notifications by residence"", ""reason"": ""DATASUS SIH FTP timed out; this alternative was retrieved but does not resolve exposure coverage.""}, {""dimension"": ""exposure"", ""published"": ""CETESB monitor concentrations"", ""reanalysis"": ""Open-Meteo historical air-quality endpoint, requested at S\u00e3o Jos\u00e9 dos Campos coordinates"", ""reason"": ""Independent exposure request returned all-null pollutant observations, so no substitution series is available.""}], ""coverage"": {""eligible_units"": 1, ""included_units"": 0, ""eligible_times"": 395, ""included_times"": 0, ""notes"": ""Outcome source yielded 4871 qualifying records, but pollutant missingness is {'ozone': 395, 'nitrogen_dioxide': 395, 'pm10': 395}; no complete daily exposure rows.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.csv"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""Independent Open-Meteo historical air-quality response contained null ozone, nitrogen dioxide, and PM10 for all 395 study dates; a complete exposure panel cannot be constructed."", ""Original SIH-SUS daily B34.2 microdata FTP endpoint timed out; SIVEP outcome is a non-identical, disclosed substitution.""]}" |
| raw-agent-control,r3,codex-baseline-36383802-sao-jose-covid-r3-20260922T150736Z,,36383802,completed_blocker,,2026-09-22T15:07:36.906023+00:00,2026-09-22T15:16:41.782470+00:00,0,0,0,0,0,"{""study_id"": ""PMID:36383802"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""Daily SUS hospital admissions among S\u00e3o Jos\u00e9 dos Campos residents with principal ICD-10 B34.2, by admission date"", ""pollutant"": ""Ozone, nitrogen dioxide, and PM10; lags 0-7 days"", ""geography"": ""S\u00e3o Jos\u00e9 dos Campos, S\u00e3o Paulo, Brazil (IBGE 354990)"", ""period"": ""2020-04-01 through 2021-04-30"", ""effect_scale"": ""RR per 10 ug/m3, exp(beta*10), from negative-binomial regression""}, ""sources"": [{""role"": ""health_outcome_microdata"", ""url"": ""https://huggingface.co/datasets/SidneyBissoli/sih-rd/raw/main/README.md"", ""retrieved"": true, ""sha256"": null}, {""role"": ""independent_air_pollution_exposure"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=-23.1826&longitude=-45.8872&hourly=ozone,nitrogen_dioxide,pm10,temperature_2m,relative_humidity_2m&timezone=America%2FSao_Paulo&start_date=2020-03-25&end_date=2021-04-30"", ""retrieved"": true, ""sha256"": ""9566e3312e72b8bc8a7f31f4cd93fd5793ccf64a37ac0bceed94223cabbc0894""}, {""role"": ""weather_covariates"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=-23.1826&longitude=-45.8872&hourly=temperature_2m,relative_humidity_2m&timezone=America%2FSao_Paulo&start_date=2020-03-25&end_date=2021-04-30"", ""retrieved"": true, ""sha256"": ""0c5c97682cefad68281e9405ac7d9fc6696e1da4c47199c25d9d9ca1331abf9a""}], ""substitutions"": [{""dimension"": ""other"", ""published"": ""Direct DATASUS SIH-SUS source"", ""reanalysis"": ""Public SIH-RD re-release of official DATASUS microdata"", ""reason"": ""The direct FTP request timed out; the fallback preserves the same record-level outcome fields and definition.""}], ""coverage"": {""eligible_units"": 1, ""included_units"": 1, ""eligible_times"": 395, ""included_times"": 0, ""notes"": ""The health panel covers all 395 study days and reproduces 1,873 records. All pollutant values are missing in the independent historical response, so zero days support an exposure model.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalyze.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_daily.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.csv"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""Independent historical O3, NO2, and PM10 response contains no usable values for 2020-03-25 through 2021-04-30; the locked lagged exposure model cannot be fitted.""]}" |
| raw-agent-control,r1,codex-baseline-38182658-uk-covid-r1-20260919T110722Z,,38182658,completed_fit,,2026-09-19T11:07:22.805785+00:00,2026-09-19T11:15:52.792927+00:00,0,0,0,1,94,"{""study_id"": ""PMC10770173"", ""status"": ""completed_fit"", ""target"": {""outcome"": ""instantaneous COVID-19 case fatality (retrospectively attributed deaths among newly confirmed cases)"", ""pollutant"": ""PM2.5"", ""geography"": ""England, Northern Ireland, Scotland, and Wales"", ""period"": ""2020-03-26 to 2020-09-15"", ""effect_scale"": ""odds ratio""}, ""sources"": [{""role"": ""outcome_cases"", ""url"": ""https://archive.ukhsa-dashboard.data.gov.uk/coronavirus-dashboard/cases.zip"", ""retrieved"": true, ""sha256"": ""9376efeb41f60df24ceb850d9b8359d9ac1417b88e4267efbbf71a23cefebf9e""}, {""role"": ""outcome_deaths"", ""url"": ""https://archive.ukhsa-dashboard.data.gov.uk/coronavirus-dashboard/deaths.zip"", ""retrieved"": true, ""sha256"": ""fcb6b40fdb1b93e283b25e53093177d4c7acd848af969565992f8d3256ba1ea3""}, {""role"": ""exposure_and_weather"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": ""207bc81db86e01d895cf5ffdd680d70ce63976e514158e6af0eaf2836ca32541""}, {""role"": ""article"", ""url"": ""https://pmc.ncbi.nlm.nih.gov/articles/PMC10770173/"", ""retrieved"": true, ""sha256"": ""d88727b655e51183c8f8ece19f54c2e21e310c8e07e9ed839a349fcd352d132c""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""DEFRA UK-Air country daily monitor averages"", ""reanalysis"": ""Open-Meteo/CAMS hourly gridded PM2.5 at country centroids, daily mean"", ""reason"": ""required independent public exposure source; author-derived exposure values prohibited""}, {""dimension"": ""covariate"", ""published"": ""ECA&D stations and NOAA-derived humidity"", ""reanalysis"": ""Open-Meteo archive hourly gridded temperature, RH, sunshine at country centroids"", ""reason"": ""independent public covariates needed for adjusted reconstruction""}, {""dimension"": ""outcome"", ""published"": ""backprojNP using gamma confirmation-to-death delay (mean 7.92; distribution shape not reported)"", ""reanalysis"": ""reported deaths shifted back 8 days"", ""reason"": ""insufficient published delay-distribution parameterization to recreate backprojection""}, {""dimension"": ""model"", ""published"": ""binomial GLMM with DLNM cross-basis spline terms and country random effects"", ""reanalysis"": ""binomial-logit GLM with country fixed effects, weekday, RH and lag-window means"", ""reason"": ""closest fully executable model after the stated outcome/exposure substitution; exact spline specification and random-effects implementation unavailable""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 4, ""eligible_times"": 174, ""included_times"": 153, ""notes"": ""510 country-days retained after required lags, 2.5--97.5% predictor trimming, positive cases, and attributed deaths <= cases.""}, ""effect"": {""estimate"": 1.0959466737615946, ""ci_low"": 1.0931197472594876, ""ci_high"": 1.0987809110029583, ""scale"": ""odds ratio"", ""contrast"": ""per 1 ug/m3 increase in mean PM2.5 across confirmation-day through 10 days before confirmation""}, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md""}, ""blockers"": []}" |
| raw-agent-control,r2,codex-baseline-38182658-uk-covid-r2-20260922T152330Z,,38182658,agent_failure,missing or schema-invalid result.json,2026-09-22T15:23:30.716985+00:00,2026-09-22T15:27:07.118206+00:00,0,0,0,1,60,"{""study_id"": ""38182658"", ""status"": ""completed_fit"", ""target"": {""outcome"": ""instantaneous COVID-19 case fatality risk (assigned deaths among confirmed cases)"", ""pollutant"": ""PM2.5"", ""geography"": ""England, Scotland, Wales, and Northern Ireland"", ""period"": ""2020-03-26 to 2020-09-15"", ""effect_scale"": ""odds ratio""}, ""sources"": [{""role"": ""health_outcome_raw"", ""url"": ""https://storage.googleapis.com/covid19-open-data/v3/epidemiology.csv"", ""retrieved"": true, ""sha256"": ""acdcb8a6c8c16a8eae9f4b897b80576f1c3e1d6e6663f791dcd9a231017befd1""}, {""role"": ""pm25_GB_ENG.json"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=52.3555&longitude=-1.1743&hourly=pm2_5&start_date=2020-03-26&end_date=2020-09-15&timezone=UTC"", ""retrieved"": true, ""sha256"": ""0ea74eeae6713d57920afbc8f2cf691a198de97ba8ffaf569dd5ee670b17abe7""}, {""role"": ""weather_GB_ENG.json"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=52.3555&longitude=-1.1743&start_date=2020-03-26&end_date=2020-09-15&daily=temperature_2m_mean,relative_humidity_2m_mean,shortwave_radiation_sum&timezone=GMT"", ""retrieved"": true, ""sha256"": ""b13c4a5bd7dded02157a8638471acbdf9e0c18f06b6ed5bbedd1b6a37ae31939""}, {""role"": ""pm25_GB_SCT.json"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=56.4907&longitude=-4.2026&hourly=pm2_5&start_date=2020-03-26&end_date=2020-09-15&timezone=UTC"", ""retrieved"": true, ""sha256"": ""0718c4d49c9bd53bdc9f4a45977de1e7a4dfc38ac4dd3eb783c00f2b9da8a3d0""}, {""role"": ""weather_GB_SCT.json"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=56.4907&longitude=-4.2026&start_date=2020-03-26&end_date=2020-09-15&daily=temperature_2m_mean,relative_humidity_2m_mean,shortwave_radiation_sum&timezone=GMT"", ""retrieved"": true, ""sha256"": ""d1782f0d49af48e6826937b64648eeea81ee1c9eb0da7a5d1a88cc74d292a16b""}, {""role"": ""pm25_GB_WLS.json"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=52.1307&longitude=-3.7837&hourly=pm2_5&start_date=2020-03-26&end_date=2020-09-15&timezone=UTC"", ""retrieved"": true, ""sha256"": ""cbc888be156bd7d6f3715ba060d8e7394592cf7d944300135c76f52b6cb4cd31""}, {""role"": ""weather_GB_WLS.json"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=52.1307&longitude=-3.7837&start_date=2020-03-26&end_date=2020-09-15&daily=temperature_2m_mean,relative_humidity_2m_mean,shortwave_radiation_sum&timezone=GMT"", ""retrieved"": true, ""sha256"": ""c6cbb41676237e23b3252c565fd3e8f6e861799f25434d1b15fe4e73f23eacdd""}, {""role"": ""pm25_GB_NIR.json"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality?latitude=54.7877&longitude=-6.4923&hourly=pm2_5&start_date=2020-03-26&end_date=2020-09-15&timezone=UTC"", ""retrieved"": true, ""sha256"": ""b286386938bae5f87cd7f80233af92c8d9b817650062ba37736c254a76c17d13""}, {""role"": ""weather_GB_NIR.json"", ""url"": ""https://archive-api.open-meteo.com/v1/archive?latitude=54.7877&longitude=-6.4923&start_date=2020-03-26&end_date=2020-09-15&daily=temperature_2m_mean,relative_humidity_2m_mean,shortwave_radiation_sum&timezone=GMT"", ""retrieved"": true, ""sha256"": ""24f16bfa59ef71e534e454da9ef0d4364a3069d6688f35474e85293b62333375""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""DEFRA national daily PM2.5 and ECA&D/NOAA weather"", ""reanalysis"": ""Open-Meteo CAMS PM2.5 and ERA5 weather, national centroid"", ""reason"": ""independent public exposure source required""}, {""dimension"": ""covariate"", ""published"": ""sunlight duration (hours)"", ""reanalysis"": ""daily shortwave radiation (MJ/m2)"", ""reason"": ""ERA5 source supplies radiation but not sunshine duration""}, {""dimension"": ""outcome"", ""published"": ""backprojNP gamma back-projected deaths (mean confirmation-to-death 7.92 days)"", ""reanalysis"": ""daily deaths shifted 8 days to confirmation date"", ""reason"": ""public Python environment has no backprojNP implementation; deterministic disclosed approximation""}, {""dimension"": ""model"", ""published"": ""binomial GLMM with DLNM cross-bases and country random effect"", ""reanalysis"": ""binomial logistic GLM with linear PM and weather terms at lag 3, country/weekday fixed effects, HC1 covariance"", ""reason"": ""DLNM R dependencies unavailable; approximation preserves principal contrast timing and covariate set as closely as feasible""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 4, ""eligible_times"": 174, ""included_times"": 171, ""notes"": ""682 nation-days retained after 3 lag days and 0 rows excluded because fixed-delay assigned deaths exceeded cases; source coverage was complete before these rules.""}, ""effect"": {""estimate"": 1.4744625847488653, ""ci_low"": 1.4709096081485988, ""ci_high"": 1.4780241435506838, ""scale"": ""odds ratio"", ""contrast"": ""PM2.5 19 versus 10 ug/m3 at lag 3 days (nearest available proxy for one day after symptom onset)""}, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization"": ""/output/sanitization_columns.json""}, ""blockers"": [], ""fidelity_record"": {""procedure"": ""record_reanalysis_fidelity"", ""article_data_used"": false, ""health_data_public"": true, ""independent_exposure_source"": ""Open-Meteo CAMS global reanalysis PM2.5 at national centroid; Open-Meteo ERA5 weather at same centroid"", ""target_match"": ""four UK constituent nations and stated 2020 period"", ""outcome_reconstruction"": ""fixed 8-day shift in place of article backprojNP gamma backprojection"", ""model_reconstruction"": ""lag-3 linear logistic approximation, not the article DLNM spline mixed model"", ""fit_eligible"": true}}" |
| raw-agent-control,r3,codex-baseline-38182658-uk-covid-r3-20260922T151641Z,,38182658,completed_blocker,,2026-09-22T15:16:42.492237+00:00,2026-09-22T15:25:25.087454+00:00,0,0,0,1,72,"{""study_id"": ""PMID-38182658"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""instantaneous COVID-19 case-fatality probability"", ""pollutant"": ""PM2.5 (ug/m3)"", ""geography"": ""England, Northern Ireland, Scotland, and Wales"", ""period"": ""2020-03-26 through 2020-09-15"", ""effect_scale"": ""odds ratio""}, ""sources"": [{""role"": ""health outcomes: daily reported confirmed cases/deaths"", ""url"": ""https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv"", ""retrieved"": true, ""sha256"": ""8473d0f0fdf962e1ffbd5b85b18726fc96a49bab109e271186c339725a12b10c""}, {""role"": ""alternate health-outcome endpoint (terminal DNS failure; see failed_endpoint_evidence.txt)"", ""url"": ""https://api.coronavirus.data.gov.uk/v2/data?areaType=nation&metric=newCasesByPublishDate&metric=newDeaths28DaysByPublishDate&format=csv"", ""retrieved"": false, ""sha256"": null}, {""role"": ""independent PM2.5 exposure: Open-Meteo/CAMS country-centroid hourly values"", ""url"": ""https://air-quality-api.open-meteo.com/v1/air-quality"", ""retrieved"": true, ""sha256"": null}, {""role"": ""weather covariates: Open-Meteo historical archive"", ""url"": ""https://archive-api.open-meteo.com/v1/archive"", ""retrieved"": true, ""sha256"": null}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""DEFRA Air Information Resource"", ""reanalysis"": ""Open-Meteo/CAMS country-centroid values"", ""reason"": ""independent exposure required""}], ""coverage"": {""eligible_units"": 4, ""included_units"": 0, ""eligible_times"": 174, ""included_times"": 0, ""notes"": ""OWID rows for the four constituent countries contain zero nonmissing daily cases and deaths. UK aggregate data are not a permissible geographic substitution.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization"": ""/output/sanitization.json""}, ""blockers"": [""No public four-country outcome panel was obtained from the tested OWID release: zero nonmissing case and death values for England, Northern Ireland, Scotland, and Wales. The principal four-country binomial model therefore cannot execute.""]}" |
| raw-agent-control,r1,codex-baseline-38788590-brazil-cancer-r1-20260919T165517Z,,38788590,completed_blocker,,2026-09-19T16:55:18.133713+00:00,2026-09-19T17:05:06.953253+00:00,0,0,0,1,73,"{""study_id"": ""pmid-38788590"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""All-cancer mortality (ICD-10 C00\u2013C97) from Brazil's SIM individual death records"", ""pollutant"": ""Daily ambient PM2.5, 3-day moving average (lag 0\u20132)"", ""geography"": ""Brazil, 5,570 municipalities (residential municipality)"", ""period"": ""2000-01-01 to 2019-12-31"", ""effect_scale"": ""Odds ratio per 10 \u00b5g/m3 increase in lag 0\u20132 PM2.5""}, ""sources"": [{""role"": ""SIM API probe"", ""url"": ""https://apidadosabertos.saude.gov.br/vigilancia-e-meio-ambiente/sistema-de-informacao-sobre-mortalidade?ano=2019&limit=20&offset=0"", ""retrieved"": true, ""sha256"": ""94fc8652f51aa9bf519222ba41237cc471baea2a0147ebc0f5047116c101db40""}, {""role"": ""SIM API specification"", ""url"": ""https://apidadosabertos.saude.gov.br/static/swagger.json"", ""retrieved"": true, ""sha256"": ""a3ff1a1c6737a60a75b02017536a8400771598d65556cacfd6d907db427fc65d""}, {""role"": ""historical SIM archive"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DADOS/DO2000.dbc"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [], ""coverage"": {""eligible_units"": 5570, ""included_units"": 0, ""eligible_times"": 7305, ""included_times"": 0, ""notes"": ""No historical individual SIM records for 2000\u20132019 were retrieved. The official API query returned 2025 records despite ano=2019, and the historical archive timed out.""}, ""artifacts"": {""code"": ""/output/code/analysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.md"", ""decision_log"": ""/output/decision_log.md"", ""retry_log"": ""/output/logs/sim_archive_attempts.jsonl"", ""input_validation"": ""/output/raw/sim_api_validation.json""}, ""blockers"": [""Required public 2000\u20132019 individual-level Brazilian SIM mortality records were not retrieved. The current official API returned 2025 data despite a 2019 query and exposes no historical-period parameter; the official historical archive request timed out with zero bytes."", ""Without death dates and residential municipality for the target period, valid time-stratified case-crossover strata and municipality-specific exposure assignment cannot be constructed.""]}" |
| raw-agent-control,r2,codex-baseline-38788590-brazil-cancer-r2-20260922T152736Z,,38788590,completed_blocker,"Pre-study free disk was 12 GiB, below the retry policy's 20 GiB minimum.",2026-09-22T15:27:38.497635+00:00,2026-09-22T15:31:53.315829+00:00,0,0,0,1,37,"{""study_id"": ""PMID-38788590"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""All-cancer mortality (individual Brazilian SIM death records; underlying ICD-10 cancer causes)"", ""pollutant"": ""Daily PM2.5, primary three-day mean over lag 0-2"", ""geography"": ""Brazil; 5,570 residence municipalities"", ""period"": ""2000-01-01 to 2019-12-31"", ""effect_scale"": ""Odds ratio per 10 micrograms/m3 increase; intended transformation OR=exp(10*beta)""}, ""sources"": [{""role"": ""supplied_pubmed_record"", ""url"": ""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=38788590&retmode=xml"", ""retrieved"": true, ""sha256"": ""da1585735e550f7b8e4ab9c8a219f3a831658311f313f5f059ee9153594d0d28""}, {""role"": ""article_landing_page"", ""url"": ""https://research.monash.edu/en/publications/cancer-mortality-risk-from-short-term-pmsub25sub-exposure-and-tem/"", ""retrieved"": true, ""sha256"": ""ad2827946aec23f32cd72a27b53580a9d313ce623997cec3d03f76c00a7b4730""}, {""role"": ""public_health_outcome_candidate_SIM"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DADOS/"", ""retrieved"": false, ""sha256"": null}, {""role"": ""independent_PM25_candidate"", ""url"": ""https://disc.gsfc.nasa.gov/datasets/M2T1NXAER_5.12.4/summary"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [], ""coverage"": {""eligible_units"": 5570, ""included_units"": 0, ""eligible_times"": 7305, ""included_times"": 0, ""notes"": ""No data acquired: policy termination before study because free disk was 12 GiB, below the 20 GiB required minimum.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""sanitization_columns"": ""/output/sanitization_columns.json"", ""fidelity_record"": ""/output/fidelity_record.json"", ""run_summary"": ""/output/run_summary.json""}, ""blockers"": [""Campaign policy termination: 12 GiB free disk before study; retry policy requires at least 20 GiB."", ""No full eligible national health/exposure/covariate panel was constructed; no principal model was fit.""]}" |
| raw-agent-control,r3,codex-baseline-38788590-brazil-cancer-r3-20260922T152534Z,,38788590,completed_blocker,,2026-09-22T15:25:35.367548+00:00,2026-09-22T15:29:44.298660+00:00,0,0,0,1,45,"{""study_id"": ""pmid-38788590"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""All-cancer mortality (underlying ICD-10 C00-C97)"", ""pollutant"": ""PM2.5"", ""geography"": ""Brazil, 5,570 residential municipalities"", ""period"": ""2000-01-01 through 2019-12-31"", ""effect_scale"": ""Odds ratio per 10 \u00b5g/m3 increase in three-day mean PM2.5""}, ""sources"": [{""role"": ""article_record"", ""url"": ""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=38788590&retmode=xml"", ""retrieved"": true, ""sha256"": ""da1585735e550f7b8e4ab9c8a219f3a831658311f313f5f059ee9153594d0d28""}, {""role"": ""lawful_full_text"", ""url"": ""https://www.researchgate.net/publication/380561503_Cancer_Mortality_Risk_from_Short-Term_PM25_Exposure_and_Temporal_Variations_in_Brazil"", ""retrieved"": true, ""sha256"": ""9c5d16c75615b12d2610b37f485edc4172e451ff9cc579f6b8a3fe67d649f93f""}, {""role"": ""outcome_SIM_documentation"", ""url"": ""https://www.gov.br/saude/pt-br/acesso-a-informacao/sic/dados-em-transparencia-ativa/svsa/mortalidade"", ""retrieved"": true, ""sha256"": null}, {""role"": ""outcome_SIM_microdata_attempt"", ""url"": ""https://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DADOS/DO2000.dbc"", ""retrieved"": false, ""sha256"": null}, {""role"": ""independent_exposure_candidate_MERRA2_documentation"", ""url"": ""https://gmao.gsfc.nasa.gov/gmao-products/merra-2/"", ""retrieved"": true, ""sha256"": null}, {""role"": ""independent_exposure_candidate_MERRA2_data_attempt"", ""url"": ""https://goldsmr4.gesdisc.eosdis.nasa.gov/data/MERRA2/M2I1NXAER.5.12.4/2000/01/MERRA2_100.inst1_2d_aer_Nx.20000101.nc4"", ""retrieved"": false, ""sha256"": null}, {""role"": ""published_weather_ERA5_catalog"", ""url"": ""https://cds.climate.copernicus.eu/datasets/reanalysis-era5-single-levels"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [], ""coverage"": {""eligible_units"": 5570, ""included_units"": 0, ""eligible_times"": 7305, ""included_times"": 0, ""notes"": ""No municipality-day can enter the locked comparison because the required independent PM2.5 series was not retrieved. Outcome microdata are public in principle but were not processed after exposure validation failed.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization_columns"": ""/output/sanitization_columns.json""}, ""blockers"": [""No independent daily municipality PM2.5 table covering all 5,570 municipalities and 2000-01-01 through 2019-12-31 was retrieved. A complete matched exposure panel is required; partial sources were not substituted.""]}" |
| raw-agent-control,r1,codex-baseline-39377000-us-stroke-r1-20260919T170507Z,,39377000,completed_blocker,,2026-09-19T17:05:07.369341+00:00,2026-09-19T17:09:05.291302+00:00,0,0,0,1,39,"{""study_id"": ""PMID-39377000"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""county ischemic-stroke mortality among adults aged 65 years or older"", ""pollutant"": ""annual PM2.5 concentration (ug/m3)"", ""geography"": ""U.S. counties and county equivalents, excluding Puerto Rico, American Samoa, Guam, and U.S. Virgin Islands"", ""period"": ""2016-2020, as reported by article"", ""effect_scale"": ""adjusted linear-regression change in deaths per 100,000 per 1 ug/m3 PM2.5""}, ""sources"": [{""role"": ""public_health_outcome"", ""url"": ""https://data.cdc.gov/api/views/g5fg-bgtw/rows.csv?accessType=DOWNLOAD"", ""retrieved"": true, ""sha256"": ""7a08a1db579bbbcf1f98d253dfeba354267b449ea4c6ec6ae1bea45baa085b8c""}, {""role"": ""independent_pm25_monitor_data_2018"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2018.zip"", ""retrieved"": true, ""sha256"": ""0a6ab33afcfb48faa66d5554d69b731cf01adbe2ad3fc4f88a05ee6dd825a4b8""}, {""role"": ""independent_pm25_monitor_data_2019"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2019.zip"", ""retrieved"": true, ""sha256"": ""09808acc29300c80df07b0bced65b6d69d088049b26c2be5c2de297a1b08201f""}, {""role"": ""independent_pm25_monitor_data_2020"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2020.zip"", ""retrieved"": true, ""sha256"": ""b2c0c6b89dfc125e740cf9f941cf1b05a3ab0d5026db6315720cab45eb7a5a80""}], ""substitutions"": [{""dimension"": ""outcome"", ""published"": ""ischemic-stroke mortality, age 65+, 2016-2020"", ""reanalysis"": ""CDC public CSV offers all-stroke, age-adjusted age 35+, 2018-2020"", ""reason"": ""This public extract cannot reproduce the target outcome; it was retained only as evidence, not used to fit a substitute model.""}, {""dimension"": ""exposure"", ""published"": ""undisclosed county annual PM2.5 product"", ""reanalysis"": ""EPA AQS parameter 88101 county monitor averages, 2018-2020"", ""reason"": ""Independent public exposure source required; monitoring covers only a subset of counties.""}, {""dimension"": ""covariate"", ""published"": ""12-variable adjusted model specified in article"", ""reanalysis"": ""not fitted"", ""reason"": ""Joint public reconstruction of all stated covariates was not completed because target outcome and coverage already failed.""}], ""coverage"": {""eligible_units"": 3226, ""included_units"": 612, ""eligible_times"": 3, ""included_times"": 3, ""notes"": ""CDC public outcome extract has 3,226 county records. EPA AQS PM2.5 has 647 counties with any observation and 612 with all 2018-2020 observations; 612 is 19.0% of the article's stated 3,142 all-county target. Outcome definition also differs materially.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""outcome_extract"": ""/output/outcome_public_extract.csv"", ""coverage_summary"": ""/output/coverage_summary.json""}, ""blockers"": [""Available public CDC outcome extract is all-stroke age 35+ for 2018-2020, not ischemic stroke age 65+ for 2016-2020."", ""Independent EPA AQS monitor PM2.5 covers only 612 counties in all three 2018-2020 years, insufficient to represent the article's national all-county analysis."", ""The specified adjusted model cannot be executed without material outcome, coverage, and covariate substitutions.""]}" |
| raw-agent-control,r2,codex-baseline-39377000-us-stroke-r2-20260922T153548Z,,39377000,agent_failure,missing or schema-invalid result.json,2026-09-22T15:35:49.545126+00:00,2026-09-22T15:40:22.006209+00:00,0,0,0,1,49,"{""study_id"": ""PMC11456533"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""County ischemic stroke mortality rate among adults aged 65+ (ICD-10 I63, I65-I66)"", ""pollutant"": ""annual PM2.5 concentration (ug/m3)"", ""geography"": ""US counties and county equivalents, excluding territories stated by article"", ""period"": ""2016-2020"", ""effect_scale"": ""native OLS change in deaths per 100,000 per 1 ug/m3 PM2.5""}, ""sources"": [{""role"": ""article"", ""url"": ""https://pmc.ncbi.nlm.nih.gov/articles/PMC11456533/"", ""retrieved"": true, ""sha256"": ""b232c04c24ef27a2de52ad54a22154a5d72f1c1a28d3190bcb57024a9c8efedd""}, {""role"": ""outcome_request_form"", ""url"": ""https://wonder.cdc.gov/ucd-icd10.html"", ""retrieved"": true, ""sha256"": ""c39f20926aa2694a8ffa9bdc65021b34a52cb9d34fc2384688ffdfe4c1bf397c""}, {""role"": ""outcome_query_attempt"", ""url"": ""https://wonder.cdc.gov/controller/datarequest/D76"", ""retrieved"": false, ""sha256"": ""6824409d9667e94904995f488282e82042aa7b86714f2591a1b5cad5b80fac4e""}, {""role"": ""independent_exposure_2016"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2016.zip"", ""retrieved"": true, ""sha256"": ""e693e5f87409cf22147664a18546f54f91c9769493019fde87a8eaa5eb0ae157""}, {""role"": ""independent_exposure_2020"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2020.zip"", ""retrieved"": true, ""sha256"": ""b2c0c6b89dfc125e740cf9f941cf1b05a3ab0d5026db6315720cab45eb7a5a80""}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""unspecified county annual PM2.5 values"", ""reanalysis"": ""EPA AQS annual PM2.5 monitor arithmetic means aggregated to county"", ""reason"": ""independent public source required; monitor coverage is incomplete and only 2016/2020 retrieved before stop""}], ""coverage"": {""eligible_units"": 3142, ""included_units"": 0, ""eligible_times"": 5, ""included_times"": 0, ""notes"": ""No complete merged panel. EPA AQS monitor data were available locally for 2016 and 2020 only; no outcome table or locked covariate table was obtained.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_table.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.txt"", ""decision_log"": ""/output/decision_log.md"", ""blocker_ledger"": ""/output/blocker_ledger.md"", ""sanitization"": ""/output/sanitization_columns.json"", ""fidelity_record"": ""/output/fidelity_record.json""}, ""blockers"": [""CDC WONDER automated county outcome query did not produce a data table after accepted request form; response evidence retained."", ""Independent EPA AQS PM2.5 monitor data are not complete county coverage and only 2016 and 2020 were successfully retrieved locally."", ""The article-specified covariates (CAD, HTN, HLD, DM, obesity, smoking, income, Gini, poverty, uninsured, park access) were not reconstructed; fitting would require invented/relaxed panel coverage.""], ""fidelity_record"": {""study_id"": ""PMC11456533"", ""locked_target"": ""county-level age-65+ ischemic-stroke mortality rate, US counties, 2016-2020; PM2.5"", ""outcome_constructed"": false, ""exposure_constructed_from_independent_source"": true, ""exposure_years_available"": [2016, 2020], ""required_years"": [2016, 2017, 2018, 2019, 2020], ""covariates_constructed"": false, ""model_executed"": false, ""verdict"": ""blocked: no complete outcome/exposure/covariate panel"", ""timestamp_utc"": ""2026-09-22T15:40:14.033708+00:00""}}" |
| raw-agent-control,r3,codex-baseline-39377000-us-stroke-r3-20260922T152944Z,,39377000,completed_blocker,Compatible public age-65+ ischemic and hemorrhagic county mortality outcome for 2016-2020 was not retrieved; no proxy-outcome model was permitted.,2026-09-22T15:29:45.034879+00:00,2026-09-22T15:36:17.367977+00:00,0,0,0,1,65,"{""study_id"": ""PMID:39377000"", ""status"": ""completed_blocker"", ""target"": {""outcome"": ""County ischemic and hemorrhagic stroke mortality among adults aged 65 years or older"", ""pollutant"": ""Annual PM2.5 concentration (ug/m3)"", ""geography"": ""United States counties and county equivalents, excluding Puerto Rico, American Samoa, Guam, and US Virgin Islands"", ""period"": ""2016-2020"", ""effect_scale"": ""Linear mortality-rate difference (deaths per 100,000) per +1 ug/m3 PM2.5; published model includes stated county covariates""}, ""sources"": [{""role"": ""independent PM2.5 exposure source"", ""url"": ""https://aqs.epa.gov/aqsweb/airdata/daily_88101_2020.zip"", ""retrieved"": true, ""sha256"": ""18283fe4ffceb53e3091a7fa7de57a2d5b925ce3d56a08d3518021e00212a3ec""}, {""role"": ""public outcome release assessed but not used"", ""url"": ""https://data.cdc.gov/api/v3/views/g5fg-bgtw/export.csv?accessType=DOWNLOAD"", ""retrieved"": true, ""sha256"": ""53f17f576e01021b973e840e93f8590a212595ae848edcd210c64359471c7ee0""}, {""role"": ""exact-outcome endpoint attempt"", ""url"": ""https://wonder.cdc.gov/controller/datarequest/D176"", ""retrieved"": false, ""sha256"": null}], ""substitutions"": [{""dimension"": ""exposure"", ""published"": ""Unspecified county annual PM2.5 source/assignment"", ""reanalysis"": ""EPA AQS 2020 PM2.5 monitor-day arithmetic-mean county aggregation"", ""reason"": ""Independent public source required; this monitor-only, single-year assignment is documented but not used to fit the target model.""}], ""coverage"": {""eligible_units"": 3142, ""included_units"": 0, ""eligible_times"": 5, ""included_times"": 0, ""notes"": ""EPA monitor exposure table has 625 county FIPS for 2020, but no units/times were included in an analysis panel because a compatible target outcome was not retrieved.""}, ""effect"": null, ""artifacts"": {""code"": ""/output/code/reanalysis.py"", ""source_manifest"": ""/output/source_manifest.json"", ""exposure"": ""/output/exposure_epa_aqs_2020.csv"", ""analysis_panel"": ""/output/analysis_panel.csv"", ""model_output"": ""/output/model_output.json"", ""decision_log"": ""/output/decision_log.md"", ""fidelity_record"": ""/output/fidelity_record.json"", ""sanitization_audit"": ""/output/sanitization_audit.json"", ""blocker_ledger"": ""/output/blocker_ledger.md""}, ""blockers"": [""No compatible public county outcome for ischemic and hemorrhagic stroke mortality among adults 65+ for 2016-2020 was retrieved. CDC WONDER D176 returned HTTP 500; the alternative accessible CDC Atlas release is all-stroke, age 35+, 2018-2020 three-year age-adjusted/smoothed data and was not substituted."", ""Consequently the target outcome cannot be joined to the published covariate set and independent exposure without materially changing the scientific question; no regression was run.""]}" |
|
|
