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Adapt to risk vax burden protocol #2

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Merged
marrpesce merged 14 commits into from
Oct 8, 2026
Merged

Adapt to risk vax burden protocol #2

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8d662f4
Add flu rsv & fix covid codes
marrpesce Jul 2, 2026
c604a6c
Remove study_dates.json and replace campaign_info.json by cohort_inf…
marrpesce Jul 2, 2026
e47025c
replace milestones by cohort_end_date
marrpesce Jul 2, 2026
0376ce3
Comment covid vax product names and ckd classif (egfr)
marrpesce Jul 2, 2026
738351c
Comment out level 1 group analyses unused in the new protocol
marrpesce Jul 2, 2026
1491943
Comment rename TPP covid-19 product names
marrpesce Jul 2, 2026
6e2794c
Collapse dataset definition in 1 dataset_definition / parameter = coh…
marrpesce Jul 2, 2026
007d99e
Add disease specific vax and outputs variables / delete unused varia…
marrpesce Jul 2, 2026
90fa26d
Consolidate all data preparation in this script
marrpesce Jul 2, 2026
a281b58
Keep only one report script, based mainly on the former report_snapsh…
marrpesce Jul 2, 2026
353edcd
Add possibility of different poisson models (unujusted / sex-age)
marrpesce Jul 2, 2026
bcf4679
Create 3 action by cohort (extract, prepare and report) / new paramet…
marrpesce Jul 2, 2026
b7e07b6
remove age_date from cohort_design
marrpesce Jul 2, 2026
ce3fd60
fix bug
marrpesce Jul 3, 2026
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158 changes: 0 additions & 158 deletions analysis/0-lib/campaign_info.json
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102 changes: 102 additions & 0 deletions analysis/0-lib/cohort_info.json
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Original file line number Diff line number Diff line change
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{
"covid_2025_26": {
"cohort_id": "covid_2025_26",
"target": "COVID-19",
"cohort": "2025/26",
"cohort_start_date": "2025-09-01",
"cohort_end_date": "2026-03-31",
"age_threshold": 75,
"clinical_priority": "primis_atrisk",
"cohort_end_days": 212
},
"covid_ba1_ba2": {
"cohort_id": "covid_ba1_ba2",
"target": "COVID-19",
"cohort": "BA.1/BA.2 wave",
"cohort_start_date": "2021-12-15",
"cohort_end_date": "2022-04-29",
"age_threshold": "NA",
"clinical_priority": "primis_atrisk",
"cohort_end_days": 136
},
"covid_jn1": {
"cohort_id": "covid_jn1",
"target": "COVID-19",
"cohort": "JN.1 wave",
"cohort_start_date": "2023-12-04",
"cohort_end_date": "2024-03-31",
"age_threshold": "NA",
"clinical_priority": "primis_atrisk",
"cohort_end_days": 119
},
"covid_wave_1": {
"cohort_id": "covid_wave_1",
"target": "COVID-19",
"cohort": "Wave 1",
"cohort_start_date": "2020-03-23",
"cohort_end_date": "2020-05-30",
"age_threshold": "NA",
"clinical_priority": "primis_atrisk",
"cohort_end_days": 69
},
"flu_2023_24": {
"cohort_id": "flu_2023_24",
"target": "Influenza",
"cohort": "2023/24",
"cohort_start_date": "2023-09-01",
"cohort_end_date": "2024-03-31",
"age_threshold": 65,
"clinical_priority": "primis_atrisk",
"cohort_end_days": 213
},
"flu_2024_25": {
"cohort_id": "flu_2024_25",
"target": "Influenza",
"cohort": "2024/25",
"cohort_start_date": "2024-09-01",
"cohort_end_date": "2025-03-31",
"age_threshold": 65,
"clinical_priority": "primis_atrisk",
"cohort_end_days": 212
},
"flu_2025_26": {
"cohort_id": "flu_2025_26",
"target": "Influenza",
"cohort": "2025/26",
"cohort_start_date": "2025-09-01",
"cohort_end_date": "2026-03-31",
"age_threshold": 65,
"clinical_priority": "primis_atrisk",
"cohort_end_days": 212
},
"rsv_2023_24": {
"cohort_id": "rsv_2023_24",
"target": "RSV",
"cohort": "2023/24",
"cohort_start_date": "2023-09-01",
"cohort_end_date": "2024-03-31",
"age_threshold": "NA",
"clinical_priority": "primis_atrisk",
"cohort_end_days": 213
},
"rsv_2024_25": {
"cohort_id": "rsv_2024_25",
"target": "RSV",
"cohort": "2024/25",
"cohort_start_date": "2024-09-01",
"cohort_end_date": "2025-03-31",
"age_threshold": "NA",
"clinical_priority": "primis_atrisk",
"cohort_end_days": 212
},
"rsv_2025_26": {
"cohort_id": "rsv_2025_26",
"target": "RSV",
"cohort": "2025/26",
"cohort_start_date": "2025-09-01",
"cohort_end_date": "2026-03-31",
"age_threshold": 75,
"clinical_priority": "primis_atrisk",
"cohort_end_days": 212
}
}
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