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###################################################################################################
# trials
# difference between timepoints and times: times helps define markers
default: &default
is_ows_trial: no
case_cohort: no
hvtn705: &hvtn705
two_marker_timepoints: no
timepoints: [210]
subset_variable: None
subset_value: All
assays: [ELCZ,ELMo,ADCPgp140C97ZAfib,IgG3gp140C97ZAfibritin40delta,IgG3gp140Mos1fibritin40delta,IgG340mdw_gp120,IgG340mdw_gp140,IgG340mdw_V1V2,IgG3gp4140delta,IgG340mdw_multi,IgG340mdw_gp120_gp140_vm,mdw_xassay]
assay_labels: [IgG to VT-C (EU/ml), IgG to VT-M (EU/ml), Average phagocytosis score to gp140 C97ZA, IgG3 Net MFI to gp140 C97ZA, IgG3 Net MFI to gp140 Mosaic, IgG3 gp120 breadth (Weighted average log10 Net MFI), IgG3 gp140 breadth (Weighted average log10 Net MFI), IgG3 V1V2 breadth (Weighted average log10 Net MFI), IgG3 Net MFI to gp41, IgG3 multi-epitope breadth (Wt average log10 Net MFI), IgG3 gp120 + gp140 breadth (Wt average log10 Net MFI), Overall maximal diversity score]
primary_assays: [ELCZ,ELMo,ADCPgp140C97ZAfib,IgG3gp140C97ZAfibritin40delta]
times: [B, Day210]
time_labels: [Day 1, Day 210]
study_name: HVTN705
covariates_riskscore: ~.+ RSA + Age + BMI + Riskscore
# data_cleaned: ../vaccine/p705/correlates_temp/HVTN705_hybridrealmock_practicedata_Oct2021.csv
data_cleaned: correlates_reporting_usgcove_archive/data_clean/HVTN705_hybridrealmock_practicedata_Oct2021.csv
num_boot_replicates: 10
num_perm_replicates: 10
ows_trial: &ows_trial
forestplot_script: cor_coxph_forestplots_ows.R
is_ows_trial: yes
case_cohort: yes
moderna_trial: &moderna_trial
<<: *ows_trial
two_marker_timepoints: yes
timepoints: [29, 57]
subset_variable: None
subset_value: All
assays: [bindSpike, bindRBD, pseudoneutid50, pseudoneutid80]
assay_labels: [Binding Antibody to Spike, Binding Antibody to RBD, PsV Neutralization 50% Titer, PsV Neutralization 80% Titer]
assay_labels_short: [Anti Spike IgG (BAU/ml), Anti RBD IgG (BAU/ml), Pseudovirus-nAb cID50, Pseudovirus-nAb cID80]
times: [B, Day29, Day57, Delta29overB, Delta57overB, Delta57over29]
time_labels: [Day 1, Day 29, Day 57, D29 fold-rise over D1, D57 fold-rise over D1, D57 fold-rise over D29]
data_raw_dir: moderna
study_name_code: COVE
covariates_riskscore: ~.+ MinorityInd + HighRiskInd + risk_score
covariates_norisksco: ~.+ MinorityInd + HighRiskInd + Age
moderna_real: &moderna_real
<<: *moderna_trial
data_in_file: immune1.csv
data_cleaned: p3001/download_data/Moderna COVE mRNA 1273P301_immune_20210915/moderna_real_data_processed_with_riskscore.csv
study_name: COVE
num_boot_replicates: 1000
num_perm_replicates: 10000
moderna_mock: &moderna_mock
<<: *moderna_trial
data_in_file: COVID_VEtrial_practicedata_primarystage1.csv
study_name: MockCOVE
num_boot_replicates: 10
num_perm_replicates: 10
janssen_trial: &janssen_trial
<<: *ows_trial
two_marker_timepoints: no
timepoints: [29]
assays: [bindSpike, bindRBD]
assay_labels: [Binding Antibody to Spike, Binding Antibody to RBD]
assay_labels_short: [Anti Spike IgG (BAU/ml), Anti RBD IgG (BAU/ml)]
times: [B, Day29, Delta29overB]
time_labels: [Day 1, Day 29, D29 fold-rise over D1]
data_raw_dir: janssen
study_name_code: ENSEMBLE
janssen_trial_real: &janssen_trial_real
<<: *janssen_trial
data_in_file: COVID_ENSEMBLE_realdata.csv # ../../../mapping_immune_correlates/adata/COVID_ENSEMBLE_realdata.csv
study_name: ENSEMBLE
num_boot_replicates: 1000
num_perm_replicates: 10000
janssen_trial_mock: &janssen_trial_mock
<<: *janssen_trial
data_in_file: COVID_ENSEMBLE_practicedata.csv
study_name: MockENSEMBLE
num_boot_replicates: 10
num_perm_replicates: 10
janssen_pooled_real:
<<: *janssen_trial_real
subset_variable: None
subset_value: All
covariates_riskscore: ~.+ risk_score + as.factor(Region)
covariates_norisksco: ~.+ Age + as.factor(Region)
janssen_na_real:
<<: *janssen_trial_real
subset_variable: Region
subset_value: 0
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
janssen_la_real:
<<: *janssen_trial_real
subset_variable: Region
subset_value: 1
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
janssen_sa_real:
<<: *janssen_trial_real
subset_variable: Region
subset_value: 2
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
janssen_pooled_mock:
<<: *janssen_trial_mock
subset_variable: None
subset_value: All
covariates_riskscore: ~.+ risk_score + as.factor(Region)
covariates_norisksco: ~.+ Age + as.factor(Region)
janssen_na_mock:
<<: *janssen_trial_mock
subset_variable: Region
subset_value: 0
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
janssen_la_mock:
<<: *janssen_trial_mock
subset_variable: Region
subset_value: 1
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
janssen_sa_mock:
<<: *janssen_trial_mock
subset_variable: Region
subset_value: 2
covariates_riskscore: ~.+ risk_score
covariates_norisksco: ~.+ Age
###################################################################################################
# correlates analyses
# there are some redundancy in ph1, ph2, WtStratum, wt in that given the first three, we can compute wt
# the redundancy is not needed if we only have single time point analyses
# but for double time points analyses, we need more than one weight variable
# the reason we need WtStratum is that for bootstrapping (needed for some single time point analyses)
# primary endpoint D57 markers
D57:
ph1: ph1.D57
ph2: ph2.D57
wt: wt.D57
WtStratum: Wstratum
EventIndPrimary: EventIndPrimaryD57
EventTimePrimary: EventTimePrimaryD57
tpeak: 57
tpeaklag: 7
tfinal.tpeak: 0
txt.endpoint: COVID
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 Day 57 visit; no. cases = number of this cohort with an observed COVID endpoint.
# primary endpoint D29 markers
D29:
ph1: ph1.D29
ph2: ph2.D29
wt: wt.D29
WtStratum: Wstratum
EventIndPrimary: EventIndPrimaryD29
EventTimePrimary: EventTimePrimaryD29
tpeak: 29
tpeaklag: 7
tfinal.tpeak: 0
txt.endpoint: COVID
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 Day 29 visit; no. cases = number of this cohort with an observed COVID endpoint.
# sensitivity analyses for D29 markers, starting at 1, instead of 7, day after D29 visit
D29start1:
ph1: ph1.D29start1
ph2: ph2.D29start1
wt: wt.D29start1
WtStratum: Wstratum
EventIndPrimary: EventIndPrimaryD29
EventTimePrimary: EventTimePrimaryD29
tpeak: 29
tpeaklag: 1
tfinal.tpeak: 0
txt.endpoint: COVID
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 Day 29 visit; no. cases = number of this cohort with an observed COVID endpoint.
D210:
ph1: Ph1ptids.D210
ph2: Ph2ptids.D210
wt: wt.D210
WtStratum: Sampstratum.D210
EventIndPrimary: Delta.D210
EventTimePrimary: Ttilde.D210
tpeak: 210
tpeaklag: 1
tfinal.tpeak: 0
txt.endpoint: HIV
txt.coxph.note2: No. at-risk = estimated number in the population for analysis, i.e. per-protocol vaccine recipients not infected through 1 days post Month 7 visit; no. cases = number of this cohort with an observed endpoint.
####################
# two time points
D29D57:
tinterm: 29
tpeak: 57
tpeaklag: 7
txt.endpoint: COVID