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config.yml
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config.yml
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default: &default
placeholder: 1
moderna_boost: &moderna_boost
study_name: COVEBoost
txt.endpoint: COVID
data_cleaned: /trials/covpn/p3001/analysis/correlates/Part_C_Unblinded_Phase_Data/adata/moderna_boost_data_processed_20230912.csv
assay_metadata: assay_metadata/moderna_boost_assay_metadata.csv
sampling_scheme: case_control
covariates: ~. + MinorityInd + HighRiskInd + risk_score
multivariate_assays: [
BD1bindSpike_BA.1,
BD29bindSpike_BA.1,
BD1bindSpike_BA.1 + BD29bindSpike_BA.1,
BD1bindSpike_BA.1 * BD29bindSpike_BA.1,
BD1bindSpike + BD29bindSpike,
BD1pseudoneutid50_BA.1 + BD29pseudoneutid50_BA.1,
BD1pseudoneutid50 + BD29pseudoneutid50,
BD29pseudoneutid50_BA.1 + BD29pseudoneutid50,
BD29bindSpike_BA.1 + BD29bindSpike,
BD29pseudoneutid50_BA.1 + BD29bindSpike_BA.1,
BD29pseudoneutid50 + BD29bindSpike,
DeltaBD29overBD1pseudoneutid50_BA.1 + DeltaBD29overBD1pseudoneutid50,
DeltaBD29overBD1bindSpike_BA.1 + DeltaBD29overBD1bindSpike,
DeltaBD29overBD1pseudoneutid50_BA.1 + DeltaBD29overBD1bindSpike_BA.1,
DeltaBD29overBD1pseudoneutid50 + DeltaBD29overBD1bindSpike
]
interaction: [
BD1bindSpike_BA.1 * BD29bindSpike_BA.1,
BD1bindSpike_BA.1 * DeltaBD29overBD1bindSpike_BA.1,
BD1pseudoneutid50_BA.1 * BD29pseudoneutid50_BA.1,
BD1pseudoneutid50_BA.1 * DeltaBD29overBD1pseudoneutid50_BA.1
]
ve_ylim: [0,1]
ve_ylim_log: [0.0,0.98]
low_efficacy: no
num_boot_replicates: 1000
num_perm_replicates: 10000
ph1: [ph1.BD29]
endpoints: [EventIndOmicron]
peak_visit: BD29
txt.coxph.note2: No. at-risk = estimated number in the population for analysis, i.e. baseline negative per-protocol vaccine recipients not experiencing the COVID endpoint or infected through 6 days post BD29 visit; no. cases = number of this cohort with an observed COVID endpoint.