diff --git a/code/fit_posteriors.R b/code/fit_posteriors.R index 90075ba..6707906 100644 --- a/code/fit_posteriors.R +++ b/code/fit_posteriors.R @@ -20,7 +20,8 @@ ct_fit <- sampling(ct_model, wr_midpoint=prior_pars$wr_midpoint, sigma_prior=prior_pars$sigma_prior, lambda=prior_pars$lambda, - fpmean=prior_pars$fpmean), + fpmean=prior_pars$fpmean, + priorsd=prior_pars$priorsd), iter=1000, chains=4) # iter=2000 # , control = list(adapt_delta=0.85) # , control = list(adapt_delta=0.99) diff --git a/code/fit_posteriors.stan b/code/fit_posteriors.stan index 93fcff8..69965e6 100644 --- a/code/fit_posteriors.stan +++ b/code/fit_posteriors.stan @@ -15,8 +15,8 @@ data{ int n_id; // Number of infections real lod; // Limit of detection int id[N]; // Vector marking which datum belongs to which id - int category[n_id]; // Immune categories - int max_category; // Highest immune category + int category[n_id]; // Analysis categories + int max_category; // Highest analysis category int n_adj; // Number of adjustment variables int adjust[n_id,n_adj]; // Adjustment categories int max_adjust; // Highest adjustment category, across all adjustment variables @@ -29,6 +29,7 @@ data{ real sigma_prior[2]; // Prior observation noise Cauchy scale real lambda; // Mixture probability (~1-sensitivity) real fpmean; // False positive mean Ct + real priorsd; // Standard deviation for the lognormal priors } @@ -128,19 +129,16 @@ transformed parameters{ dp[i] = exp(log_dp_mean + log_dpadj[category[i]] + - // log_dpadj_adjust[adjust[i]] + dpadj_add + log_dp_sd*dp_raw[i])*dp_midpoint; wp[i] = exp(log_wp_mean + log_wpadj[category[i]] + - // log_wpadj_adjust[adjust[i]] + wpadj_add + log_wp_sd*wp_raw[i])*wp_midpoint; wr[i] = exp(log_wr_mean + log_wradj[category[i]] + - // log_wradj_adjust[adjust[i]] + wradj_add + log_wr_sd*wr_raw[i])*wr_midpoint; @@ -160,28 +158,27 @@ model{ tp ~ normal(tp_prior[1], tp_prior[2]); - log_dp_mean ~ normal(0, 0.25); // hierarchical mean - log_dp_sd ~ normal(0, 0.25) T[0,]; // sd of the individual-level draws - log_dpadj_cat_raw ~ normal(0, 0.25); + log_dp_mean ~ normal(0, priorsd); // hierarchical mean + log_dp_sd ~ normal(0, priorsd) T[0,]; // sd of the individual-level draws + log_dpadj_cat_raw ~ normal(0, priorsd); for(indexA in 1:(max_adjust-1)){ - log_dpadj_adjust_raw[indexA] ~ normal(0, 0.25); + log_dpadj_adjust_raw[indexA] ~ normal(0, priorsd); } - // log_dpadj_adjust_raw ~ normal(0, 0.25); dp_raw ~ std_normal(); // for generating individual-level guesses - log_wp_mean ~ normal(0, 0.25); // hierarchical mean - log_wp_sd ~ normal(0, 0.25) T[0,]; // sd of the individual-level draws - log_wpadj_cat_raw ~ normal(0, 0.25); + log_wp_mean ~ normal(0, priorsd); // hierarchical mean + log_wp_sd ~ normal(0, priorsd) T[0,]; // sd of the individual-level draws + log_wpadj_cat_raw ~ normal(0, priorsd); for(indexA in 1:(max_adjust-1)){ - log_wpadj_adjust_raw[indexA] ~ normal(0, 0.25); + log_wpadj_adjust_raw[indexA] ~ normal(0, priorsd); } wp_raw ~ std_normal(); // for generating individual-level guesses - log_wr_mean ~ normal(0, 0.25); // hierarchical mean - log_wr_sd ~ normal(0, 0.25) T[0,]; // sd of the individual-level draws - log_wradj_cat_raw ~ normal(0, 0.25); + log_wr_mean ~ normal(0, priorsd); // hierarchical mean + log_wr_sd ~ normal(0, priorsd) T[0,]; // sd of the individual-level draws + log_wradj_cat_raw ~ normal(0, priorsd); for(indexA in 1:(max_adjust-1)){ - log_wradj_adjust_raw[indexA] ~ normal(0, 0.25); + log_wradj_adjust_raw[indexA] ~ normal(0, priorsd); } wr_raw ~ std_normal(); // for generating individual-level guesses diff --git a/code/fit_posteriors_preamble.R b/code/fit_posteriors_preamble.R index d11aede..7c9f071 100644 --- a/code/fit_posteriors_preamble.R +++ b/code/fit_posteriors_preamble.R @@ -77,6 +77,7 @@ prior_pars <- list( category=catlist, max_category=max(catlist), adjust=adjmat, - max_adjust=max(max(adjmat)) + max_adjust=max(max(adjmat)), + priorsd=run_pars$priorsd ) diff --git a/code/make_inf_table.R b/code/make_inf_table.R new file mode 100644 index 0000000..75de44c --- /dev/null +++ b/code/make_inf_table.R @@ -0,0 +1,168 @@ +# FIRST INFECTION ============================================================= + +# By variant: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==1) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + group_by(LineageBroad) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + +# By variant + vax status: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==1) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + mutate(VaccinationStatus=case_when(is.na(VaccinationStatus)~"Not Reported",TRUE~VaccinationStatus)) %>% + mutate(VaccinationStatus=factor(VaccinationStatus, levels=c("Not Vaccinated","Fully Vaccinated","Not Reported"))) %>% + group_by(LineageBroad, VaccinationStatus) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + + +# By variant + boost status: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==1) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + mutate(BoosterStatus=case_when(is.na(BoosterStatus)~"Not Reported",TRUE~BoosterStatus)) %>% + mutate(BoosterStatus=factor(BoosterStatus, levels=c("Not Boosted","Boosted","Not Reported"))) %>% + group_by(LineageBroad, BoosterStatus) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + + +# By age group: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==1) %>% + group_by(AgeGrp) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + + + + + +# SECOND INFECTION =========================================================== + +# By variant: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==2) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + group_by(LineageBroad) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + +# By variant + vax status: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==2) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + mutate(VaccinationStatus=case_when(is.na(VaccinationStatus)~"Not Reported",TRUE~VaccinationStatus)) %>% + mutate(VaccinationStatus=factor(VaccinationStatus, levels=c("Not Vaccinated","Fully Vaccinated","Not Reported"))) %>% + group_by(LineageBroad, VaccinationStatus) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + + +# By variant + boost status: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==2) %>% + mutate(LineageBroad=case_when( + LineageBroad=="BA.1"~"BA.1/BA.2", + LineageBroad=="BA.2"~"BA.1/BA.2", + LineageBroad=="BA.4"~"BA.4/BA.5", + LineageBroad=="BA.5"~"BA.4/BA.5", + LineageBroad=="Other"~"Other/Unspecified", + LineageBroad=="None"~"Other/Unspecified", + TRUE~LineageBroad + )) %>% + mutate(LineageBroad=factor(LineageBroad, levels=c("Alpha","Delta","BA.1/BA.2","BA.4/BA.5","Other/Unspecified"))) %>% + mutate(BoosterStatus=case_when(is.na(BoosterStatus)~"Not Reported",TRUE~BoosterStatus)) %>% + mutate(BoosterStatus=factor(BoosterStatus, levels=c("Not Boosted","Boosted","Not Reported"))) %>% + group_by(LineageBroad, BoosterStatus) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + + +# By age group: +ct_dat_refined %>% + group_by(InfectionEvent) %>% + slice(1) %>% + filter(InfNum==2) %>% + group_by(AgeGrp) %>% + summarise(N=n()) %>% + ungroup() %>% + mutate(pct=round(100*N/sum(N),1)) %>% + print(n=Inf) + diff --git a/code/run_analysis.R b/code/run_analysis.R index a1fc5b8..c93043d 100644 --- a/code/run_analysis.R +++ b/code/run_analysis.R @@ -32,7 +32,7 @@ source("code/set_run_pars.R") # Run the analysis # ============================================================================= -for(run_pars_index in 11:11){ +for(run_pars_index in 16:17){ run_pars <- run_pars_list[[run_pars_index]] @@ -55,7 +55,7 @@ for(run_pars_index in 11:11){ # Individual-level comparisons (Spearman correlations) # ============================================================================= -for(run_pars_index in 10:10){ +for(run_pars_index in 14:14){ run_pars <- run_pars_list[[run_pars_index]] @@ -72,7 +72,7 @@ for(run_pars_index in 10:10){ # Post-hoc figure generation # ============================================================================= -for(run_pars_index in 10:10){ +for(run_pars_index in 14:14){ run_pars <- run_pars_list[[run_pars_index]] diff --git a/code/set_run_pars.R b/code/set_run_pars.R index c794a5e..42496d5 100644 --- a/code/set_run_pars.R +++ b/code/set_run_pars.R @@ -32,7 +32,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 2) Measure raw differences between variants: list(excluded_rows=(ct_dat_refined %>% @@ -73,7 +74,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 3) Measure differences in omicron trajectories by prior variant: list(excluded_rows=(ct_dat_refined %>% @@ -111,7 +113,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 4) Measure differences in 2nd omicron infections vs other omicrons: list(excluded_rows=(ct_dat_refined %>% @@ -172,7 +175,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 5) Measure differences in 2nd omicron infections vs first omicron infections in boosted and unboosted individuals (not subset to the multiply-infected individuals): list(excluded_rows=((ct_dat_refined %>% @@ -214,7 +218,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 6) Measure differences between 1st and 2nd infections, stratifying by vaccination status (first infection) or presence of an intervening vaccine dose (second infection) list(excluded_rows=(ct_dat_refined %>% @@ -255,7 +260,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 7) Measure raw differences between 1st and 2nd infections, restricting to the people with two well-documented infections list(excluded_rows=(ct_dat_refined %>% @@ -335,7 +341,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 8) Measure differences in second infection kinetics stratified by the first infection lineage, in people with two well-documented infections. list(excluded_rows=(ct_dat_refined %>% @@ -424,7 +431,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 9) Measure differences in 2nd infections by vaccination status, in people with two well-documented infections list(excluded_rows=(ct_dat_refined %>% @@ -498,7 +506,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 10) Measure raw differences between 1st and 2nd infections, restricting to the people with two well-documented infections, but allowing the others to inform the adjustment parameters list(excluded_rows=(ct_dat_refined %>% @@ -584,7 +593,8 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 ), # 11) Measure raw differences between 1st and 2nd infections, but now adjust for everything list(excluded_rows=(ct_dat_refined %>% @@ -664,7 +674,500 @@ run_pars_list <- list( wr_midpoint=12, sigma_prior=c(0,0.5), lambda=0.01, - fpmean=1/log(10) + fpmean=1/log(10), + priorsd=0.25 + ), + # 12) Measure differences in second infection kinetics stratified by the first infection lineage, in people with two well-documented infections, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum==2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter(WD2==0) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & PrevLineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & PrevLineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & PrevLineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & PrevLineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ), + # Adjust by vaccination status: + list( + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus)) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("No well-documented prior infection", "Other/None","Alpha","Delta","BA.1/BA.2"), + analysis_title="Lineage of first infection", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5"), + c("Unvaccinated/Unboosted","Unvaccinated/Unknonwn booster","Vaccinated/Unboosted","Vaccinated/Boosted","Vaccinated/Unknown booster","Not reported")), + adjustment_title=c("age group","variant","vax status"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 + ), + # 13) Measure differences in 2nd infections by vaccination status, in people with two well-documented infections, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum==2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter(WD2==0) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & (VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus))) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("Unpaired second infections", "Not vaccinated/Not boosted", "Not vaccinated/Boost unknown", "Vaccinated/Not boosted", "Vaccinated/Boosted", "Vaccinated/Boost unknown","Unknown"), + analysis_title="Vaccination status", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5") + ), + adjustment_title=c("age group","variant"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 + ), + # 14) Measure raw differences between 1st and 2nd infections, restricting to the people with two well-documented infections, but allowing the others to inform the adjustment parameters, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum<=2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter(WD2==0 & InfNum==1) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==0 & InfNum==2) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & InfNum==1) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(WD2==1 & InfNum==2) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ), + # Adjust by vaccination status: + list( + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus)) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("First Infection, baseline","Second Infection, baseline","First Infection, with two well-documented","Second Infection, with two well-documented"), + analysis_title="first vs. second infection", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5"), + c("Unvaccinated/Unboosted","Unvaccinated/Unknonwn booster","Vaccinated/Unboosted","Vaccinated/Boosted","Vaccinated/Unknown booster","Not reported")), + adjustment_title=c("age group","variant","vax status"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 + ), + # 15) Measure raw differences between 1st and 2nd infections, but now adjust for everything, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum<=2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter(InfNum==1) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(InfNum==2) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ), + # Adjust by vaccination status: + list( + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus)) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("First Infection","Second Infection"), + analysis_title="first vs. second infection, overall", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5"), + c("Unvaccinated/Unboosted","Unvaccinated/Unknonwn booster","Vaccinated/Unboosted","Vaccinated/Boosted","Vaccinated/Unknown booster","Not reported")), + adjustment_title=c("age group","variant","vax status"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 + ), + # 16) Measure differences in 2nd infections by vaccination status, in EVERYONE with two infections, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum==2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter((VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter((VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter((VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter((VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter((VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter((VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus))) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("Not vaccinated/Not boosted", "Not vaccinated/Boost unknown", "Vaccinated/Not boosted", "Vaccinated/Boosted", "Vaccinated/Boost unknown","Unknown"), + analysis_title="Vaccination status", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5") + ), + adjustment_title=c("age group","variant"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 + ), + # 17) Measure differences in second infection kinetics stratified by the first infection lineage, in EVERYONE, with wider priors + list(excluded_rows=(ct_dat_refined %>% + filter(!(InfNum==2)) %>% + pull(RowID)), + analysis_rows=list( + (ct_dat_refined %>% + filter(PrevLineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(PrevLineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(PrevLineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(PrevLineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)) + ), + adjustment_rows=list( + # Adjust by age group: + list( + (ct_dat_refined %>% + filter(AgeGrp=="[0,30)") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[30,50)" | is.na(AgeGrp)) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(AgeGrp=="[50,100)") %>% + pull(RowID)) + ), + # Adjust by variant: + list( + (ct_dat_refined %>% + filter(LineageBroad%in%c("Other","None")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Alpha") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad=="Delta") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.1","BA.2")) %>% + pull(RowID)), + (ct_dat_refined %>% + filter(LineageBroad%in%c("BA.4","BA.5")) %>% + pull(RowID)) + ), + # Adjust by vaccination status: + list( + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Boosted") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Fully Vaccinated" & BoosterStatus=="Not Reported") %>% + pull(RowID)), + (ct_dat_refined %>% + filter(VaccinationStatus=="Not Reported" | is.na(VaccinationStatus) | is.na(BoosterStatus)) %>% + pull(RowID)) + ) + ), # NULL + analysis_names=c("Other/None","Alpha","Delta","BA.1/BA.2"), + analysis_title="Lineage of first infection", + adjustment_names=list( + c("0-29","30-49","50+"), + c("Other/None","Alpha","Delta","BA.1/BA.2","BA.4/BA.5"), + c("Unvaccinated/Unboosted","Unvaccinated/Unknonwn booster","Vaccinated/Unboosted","Vaccinated/Boosted","Vaccinated/Unknown booster","Not reported")), + adjustment_title=c("age group","variant","vax status"), + tp_prior=c(0,2), + dp_midpoint=20, + wp_midpoint=5, + wr_midpoint=12, + sigma_prior=c(0,1), + lambda=0.01, + fpmean=1/log(10), + priorsd=1 ) - ) +) diff --git a/figures/run_pars_adj_12/chainplot_dpadj.pdf b/figures/run_pars_adj_12/chainplot_dpadj.pdf new file mode 100644 index 0000000..d3d0a36 Binary files /dev/null and b/figures/run_pars_adj_12/chainplot_dpadj.pdf differ diff --git a/figures/run_pars_adj_12/chainplot_dpadj.png b/figures/run_pars_adj_12/chainplot_dpadj.png new file mode 100644 index 0000000..c476be2 Binary files /dev/null and b/figures/run_pars_adj_12/chainplot_dpadj.png differ diff --git a/figures/run_pars_adj_12/chainplot_wpadj.pdf 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b/figures/run_pars_adj_12/rrhist_nolegend.pdf new file mode 100644 index 0000000..c518b27 Binary files /dev/null and b/figures/run_pars_adj_12/rrhist_nolegend.pdf differ diff --git a/figures/run_pars_adj_12/rrhist_nolegend.png b/figures/run_pars_adj_12/rrhist_nolegend.png new file mode 100644 index 0000000..9fd3db5 Binary files /dev/null and b/figures/run_pars_adj_12/rrhist_nolegend.png differ diff --git a/figures/run_pars_adj_12/summdf.csv b/figures/run_pars_adj_12/summdf.csv new file mode 100644 index 0000000..98a33b2 --- /dev/null +++ b/figures/run_pars_adj_12/summdf.csv @@ -0,0 +1,36 @@ +var,name,mean,lwr,upr,string +Peak Ct,No well-documented prior infection,26.3,21,30.7,"26.3 (21, 30.7)" +Peak Ct,Other/None,27.5,22.2,31.8,"27.5 (22.2, 31.8)" +Peak Ct,Alpha,27,21.1,31.8,"27 (21.1, 31.8)" +Peak Ct,Delta,26.9,20.9,31.7,"26.9 (20.9, 31.7)" +Peak Ct,BA.1/BA.2,27.1,20.4,31.8,"27.1 (20.4, 31.8)" +Peak GEML,No well-documented prior infection,6.5,5.2,7.9,"6.5 (5.2, 7.9)" +Peak GEML,Other/None,6.1,4.9,7.6,"6.1 (4.9, 7.6)" +Peak GEML,Alpha,6.3,4.9,7.9,"6.3 (4.9, 7.9)" +Peak GEML,Delta,6.3,5,8,"6.3 (5, 8)" +Peak GEML,BA.1/BA.2,6.2,4.9,8.1,"6.2 (4.9, 8.1)" +Proliferation time,No well-documented prior infection,5,2.4,9.2,"5 (2.4, 9.2)" +Proliferation time,Other/None,4.3,1.8,8.7,"4.3 (1.8, 8.7)" +Proliferation time,Alpha,5.7,2.3,12,"5.7 (2.3, 12)" +Proliferation time,Delta,4.3,1.7,9,"4.3 (1.7, 9)" +Proliferation time,BA.1/BA.2,4.4,1.3,10.6,"4.4 (1.3, 10.6)" +Clearance time,No well-documented prior infection,9.1,5.1,14.7,"9.1 (5.1, 14.7)" +Clearance time,Other/None,8.5,4.6,14.2,"8.5 (4.6, 14.2)" +Clearance time,Alpha,10.4,5.8,17.6,"10.4 (5.8, 17.6)" +Clearance time,Delta,8.4,4.2,14.6,"8.4 (4.2, 14.6)" +Clearance time,BA.1/BA.2,5.7,2.4,11.4,"5.7 (2.4, 11.4)" +Proliferation rate (Ct/day),No well-documented prior infection,3.1,1.3,6.6,"3.1 (1.3, 6.6)" +Proliferation rate (Ct/day),Other/None,3.5,1.2,7.5,"3.5 (1.2, 7.5)" +Proliferation rate (Ct/day),Alpha,2.8,0.9,6.3,"2.8 (0.9, 6.3)" +Proliferation rate (Ct/day),Delta,3.6,1.2,8.5,"3.6 (1.2, 8.5)" +Proliferation rate (Ct/day),BA.1/BA.2,4,1,10.9,"4 (1, 10.9)" +Clearance rate (Ct/day),No well-documented prior infection,1.6,0.8,3,"1.6 (0.8, 3)" +Clearance rate (Ct/day),Other/None,1.6,0.8,3,"1.6 (0.8, 3)" +Clearance rate (Ct/day),Alpha,1.4,0.6,2.6,"1.4 (0.6, 2.6)" +Clearance rate (Ct/day),Delta,1.7,0.8,3.5,"1.7 (0.8, 3.5)" +Clearance rate (Ct/day),BA.1/BA.2,2.7,1,5.8,"2.7 (1, 5.8)" +Symmetry (proliferation/clearance),No well-documented prior infection,0.6,0.2,1.3,"0.6 (0.2, 1.3)" +Symmetry (proliferation/clearance),Other/None,0.6,0.2,1.4,"0.6 (0.2, 1.4)" +Symmetry (proliferation/clearance),Alpha,0.6,0.2,1.5,"0.6 (0.2, 1.5)" +Symmetry (proliferation/clearance),Delta,0.6,0.2,1.5,"0.6 (0.2, 1.5)" +Symmetry (proliferation/clearance),BA.1/BA.2,0.9,0.2,3,"0.9 (0.2, 3)" diff --git a/figures/run_pars_adj_12/viztrajectories_1.pdf b/figures/run_pars_adj_12/viztrajectories_1.pdf new file 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mode 100644 index 0000000..de56c60 Binary files /dev/null and b/figures/run_pars_adj_12_lowsig/rrhist_nolegend.pdf differ diff --git a/figures/run_pars_adj_12_lowsig/rrhist_nolegend.png b/figures/run_pars_adj_12_lowsig/rrhist_nolegend.png new file mode 100644 index 0000000..0fe52f6 Binary files /dev/null and b/figures/run_pars_adj_12_lowsig/rrhist_nolegend.png differ diff --git a/figures/run_pars_adj_12_lowsig/summdf.csv b/figures/run_pars_adj_12_lowsig/summdf.csv new file mode 100644 index 0000000..8a84fa3 --- /dev/null +++ b/figures/run_pars_adj_12_lowsig/summdf.csv @@ -0,0 +1,36 @@ +var,name,mean,lwr,upr,string +Peak Ct,No well-documented prior infection,26.1,20.3,30.5,"26.1 (20.3, 30.5)" +Peak Ct,Other/None,27.3,21.5,31.6,"27.3 (21.5, 31.6)" +Peak Ct,Alpha,26.9,20.6,31.5,"26.9 (20.6, 31.5)" +Peak Ct,Delta,26.8,20.2,31.4,"26.8 (20.2, 31.4)" +Peak Ct,BA.1/BA.2,27,19.8,32.1,"27 (19.8, 32.1)" +Peak GEML,No well-documented prior infection,6.5,5.3,8.1,"6.5 (5.3, 8.1)" +Peak GEML,Other/None,6.2,5,7.8,"6.2 (5, 7.8)" +Peak GEML,Alpha,6.3,5,8,"6.3 (5, 8)" +Peak GEML,Delta,6.3,5,8.1,"6.3 (5, 8.1)" +Peak GEML,BA.1/BA.2,6.3,4.9,8.2,"6.3 (4.9, 8.2)" +Proliferation time,No well-documented prior infection,4.9,2.4,9.3,"4.9 (2.4, 9.3)" +Proliferation time,Other/None,4.1,1.8,8.4,"4.1 (1.8, 8.4)" +Proliferation time,Alpha,5.7,2.2,12.5,"5.7 (2.2, 12.5)" +Proliferation time,Delta,4.3,1.7,9.1,"4.3 (1.7, 9.1)" +Proliferation time,BA.1/BA.2,4.3,1.4,10.7,"4.3 (1.4, 10.7)" +Clearance time,No well-documented prior infection,9.3,5.4,14.5,"9.3 (5.4, 14.5)" +Clearance time,Other/None,8.7,4.9,14.1,"8.7 (4.9, 14.1)" +Clearance time,Alpha,10.7,5.6,18,"10.7 (5.6, 18)" +Clearance time,Delta,8.4,4.6,14.5,"8.4 (4.6, 14.5)" +Clearance time,BA.1/BA.2,5.7,2.4,11.3,"5.7 (2.4, 11.3)" +Proliferation rate (Ct/day),No well-documented prior infection,3.2,1.3,6.3,"3.2 (1.3, 6.3)" +Proliferation rate (Ct/day),Other/None,3.6,1.3,8,"3.6 (1.3, 8)" +Proliferation rate (Ct/day),Alpha,2.8,0.9,6.5,"2.8 (0.9, 6.5)" +Proliferation rate (Ct/day),Delta,3.7,1.3,8.6,"3.7 (1.3, 8.6)" +Proliferation rate (Ct/day),BA.1/BA.2,4,1,10.7,"4 (1, 10.7)" +Clearance rate (Ct/day),No well-documented prior infection,1.6,0.8,2.8,"1.6 (0.8, 2.8)" +Clearance rate (Ct/day),Other/None,1.6,0.8,2.9,"1.6 (0.8, 2.9)" +Clearance rate (Ct/day),Alpha,1.3,0.6,2.5,"1.3 (0.6, 2.5)" +Clearance rate (Ct/day),Delta,1.7,0.8,3.2,"1.7 (0.8, 3.2)" +Clearance rate (Ct/day),BA.1/BA.2,2.7,1,6,"2.7 (1, 6)" +Symmetry (proliferation/clearance),No well-documented prior infection,0.6,0.2,1.2,"0.6 (0.2, 1.2)" +Symmetry (proliferation/clearance),Other/None,0.5,0.2,1.2,"0.5 (0.2, 1.2)" +Symmetry (proliferation/clearance),Alpha,0.6,0.2,1.5,"0.6 (0.2, 1.5)" +Symmetry (proliferation/clearance),Delta,0.6,0.2,1.4,"0.6 (0.2, 1.4)" +Symmetry (proliferation/clearance),BA.1/BA.2,0.9,0.2,2.7,"0.9 (0.2, 2.7)" diff --git a/figures/run_pars_adj_12_lowsig/viztrajectories_1.pdf b/figures/run_pars_adj_12_lowsig/viztrajectories_1.pdf new file mode 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b/figures/run_pars_adj_13/summdf.csv @@ -0,0 +1,50 @@ +var,name,mean,lwr,upr,string +Peak Ct,Unpaired second infections,28.8,27,30.5,"28.8 (27, 30.5)" +Peak Ct,Not vaccinated/Not boosted,21.6,-35.9,38.3,"21.6 (-35.9, 38.3)" +Peak Ct,Not vaccinated/Boost unknown,28.6,20.2,34.2,"28.6 (20.2, 34.2)" +Peak Ct,Vaccinated/Not boosted,27.7,24.2,30.7,"27.7 (24.2, 30.7)" +Peak Ct,Vaccinated/Boosted,30,28,31.8,"30 (28, 31.8)" +Peak Ct,Vaccinated/Boost unknown,31.1,27.8,33.7,"31.1 (27.8, 33.7)" +Peak Ct,Unknown,28.7,25.6,31.5,"28.7 (25.6, 31.5)" +Peak GEML,Unpaired second infections,5.8,5.3,6.3,"5.8 (5.3, 6.3)" +Peak GEML,Not vaccinated/Not boosted,7.8,3.1,23.7,"7.8 (3.1, 23.7)" +Peak GEML,Not vaccinated/Boost unknown,5.8,4.3,8.2,"5.8 (4.3, 8.2)" +Peak GEML,Vaccinated/Not boosted,6.1,5.2,7,"6.1 (5.2, 7)" +Peak GEML,Vaccinated/Boosted,5.4,4.9,6,"5.4 (4.9, 6)" +Peak GEML,Vaccinated/Boost unknown,5.1,4.4,6,"5.1 (4.4, 6)" +Peak GEML,Unknown,5.8,5,6.6,"5.8 (5, 6.6)" +Proliferation time,Unpaired second infections,4.9,3,7.6,"4.9 (3, 7.6)" +Proliferation time,Not vaccinated/Not boosted,8.1,0.6,39.4,"8.1 (0.6, 39.4)" +Proliferation time,Not vaccinated/Boost unknown,6.1,1.6,18.7,"6.1 (1.6, 18.7)" +Proliferation time,Vaccinated/Not boosted,4.1,2,7.9,"4.1 (2, 7.9)" +Proliferation time,Vaccinated/Boosted,4.7,2.5,8.1,"4.7 (2.5, 8.1)" +Proliferation time,Vaccinated/Boost unknown,6.9,2.2,17.2,"6.9 (2.2, 17.2)" +Proliferation time,Unknown,4.5,2.1,8.6,"4.5 (2.1, 8.6)" +Clearance time,Unpaired second infections,5.9,4.6,7.6,"5.9 (4.6, 7.6)" +Clearance time,Not vaccinated/Not boosted,10.2,0.8,44.5,"10.2 (0.8, 44.5)" +Clearance time,Not vaccinated/Boost unknown,5.5,1.8,12.9,"5.5 (1.8, 12.9)" +Clearance time,Vaccinated/Not boosted,5.4,3.4,8.1,"5.4 (3.4, 8.1)" +Clearance time,Vaccinated/Boosted,5.9,4.3,8,"5.9 (4.3, 8)" +Clearance time,Vaccinated/Boost unknown,4.6,2.5,7.6,"4.6 (2.5, 7.6)" +Clearance time,Unknown,5.7,3.6,8.9,"5.7 (3.6, 8.9)" +Proliferation rate (Ct/day),Unpaired second infections,2.5,1.4,4,"2.5 (1.4, 4)" +Proliferation rate (Ct/day),Not vaccinated/Not boosted,6.7,0.2,36.7,"6.7 (0.2, 36.7)" +Proliferation rate (Ct/day),Not vaccinated/Boost unknown,2.9,0.5,8.7,"2.9 (0.5, 8.7)" +Proliferation rate (Ct/day),Vaccinated/Not boosted,3.3,1.4,6.7,"3.3 (1.4, 6.7)" +Proliferation rate (Ct/day),Vaccinated/Boosted,2.3,1.1,4.3,"2.3 (1.1, 4.3)" +Proliferation rate (Ct/day),Vaccinated/Boost unknown,1.7,0.4,4.3,"1.7 (0.4, 4.3)" +Proliferation rate (Ct/day),Unknown,2.9,1.1,5.9,"2.9 (1.1, 5.9)" +Clearance rate (Ct/day),Unpaired second infections,1.9,1.4,2.6,"1.9 (1.4, 2.6)" +Clearance rate (Ct/day),Not vaccinated/Not boosted,5.6,0.1,33.4,"5.6 (0.1, 33.4)" +Clearance rate (Ct/day),Not vaccinated/Boost unknown,2.7,0.7,6.8,"2.7 (0.7, 6.8)" +Clearance rate (Ct/day),Vaccinated/Not boosted,2.4,1.4,3.8,"2.4 (1.4, 3.8)" +Clearance rate (Ct/day),Vaccinated/Boosted,1.7,1.2,2.5,"1.7 (1.2, 2.5)" +Clearance rate (Ct/day),Vaccinated/Boost unknown,2.1,1.1,3.8,"2.1 (1.1, 3.8)" +Clearance rate (Ct/day),Unknown,2.1,1.1,3.3,"2.1 (1.1, 3.3)" +Symmetry (proliferation/clearance),Unpaired second infections,0.8,0.5,1.4,"0.8 (0.5, 1.4)" +Symmetry (proliferation/clearance),Not vaccinated/Not boosted,2.7,0,20.1,"2.7 (0, 20.1)" +Symmetry (proliferation/clearance),Not vaccinated/Boost unknown,1.6,0.2,7.1,"1.6 (0.2, 7.1)" +Symmetry (proliferation/clearance),Vaccinated/Not boosted,0.8,0.3,1.8,"0.8 (0.3, 1.8)" +Symmetry (proliferation/clearance),Vaccinated/Boosted,0.8,0.4,1.6,"0.8 (0.4, 1.6)" +Symmetry (proliferation/clearance),Vaccinated/Boost unknown,1.7,0.4,5,"1.7 (0.4, 5)" +Symmetry (proliferation/clearance),Unknown,0.8,0.3,1.8,"0.8 (0.3, 1.8)" diff --git a/figures/run_pars_adj_13/viztrajectories_1.pdf b/figures/run_pars_adj_13/viztrajectories_1.pdf new file mode 100644 index 0000000..34054ae Binary files /dev/null and b/figures/run_pars_adj_13/viztrajectories_1.pdf differ diff --git a/figures/run_pars_adj_13/viztrajectories_1.png 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infections,28.7,26.9,30.2,"28.7 (26.9, 30.2)" +Peak Ct,Not vaccinated/Not boosted,21.4,-42.2,38.6,"21.4 (-42.2, 38.6)" +Peak Ct,Not vaccinated/Boost unknown,28.4,20.1,34.1,"28.4 (20.1, 34.1)" +Peak Ct,Vaccinated/Not boosted,27.6,24.4,30.4,"27.6 (24.4, 30.4)" +Peak Ct,Vaccinated/Boosted,29.9,28,31.7,"29.9 (28, 31.7)" +Peak Ct,Vaccinated/Boost unknown,31,28,33.5,"31 (28, 33.5)" +Peak Ct,Unknown,28.7,25.7,31.3,"28.7 (25.7, 31.3)" +Peak GEML,Unpaired second infections,5.8,5.4,6.3,"5.8 (5.4, 6.3)" +Peak GEML,Not vaccinated/Not boosted,7.8,3.1,25.4,"7.8 (3.1, 25.4)" +Peak GEML,Not vaccinated/Boost unknown,5.9,4.3,8.2,"5.9 (4.3, 8.2)" +Peak GEML,Vaccinated/Not boosted,6.1,5.3,7,"6.1 (5.3, 7)" +Peak GEML,Vaccinated/Boosted,5.4,5,6,"5.4 (5, 6)" +Peak GEML,Vaccinated/Boost unknown,5.1,4.5,6,"5.1 (4.5, 6)" +Peak GEML,Unknown,5.8,5.1,6.6,"5.8 (5.1, 6.6)" +Proliferation time,Unpaired second infections,4.8,3,7.4,"4.8 (3, 7.4)" +Proliferation time,Not vaccinated/Not boosted,7.9,0.7,33.6,"7.9 (0.7, 33.6)" +Proliferation time,Not vaccinated/Boost unknown,5.8,1.5,17,"5.8 (1.5, 17)" +Proliferation time,Vaccinated/Not boosted,4.1,2.1,7.6,"4.1 (2.1, 7.6)" +Proliferation time,Vaccinated/Boosted,4.6,2.5,7.9,"4.6 (2.5, 7.9)" +Proliferation time,Vaccinated/Boost unknown,6.7,2.2,16.5,"6.7 (2.2, 16.5)" +Proliferation time,Unknown,4.5,2.1,8.5,"4.5 (2.1, 8.5)" +Clearance time,Unpaired second infections,5.9,4.6,7.4,"5.9 (4.6, 7.4)" +Clearance time,Not vaccinated/Not boosted,9.7,0.8,41,"9.7 (0.8, 41)" +Clearance time,Not vaccinated/Boost unknown,5.5,1.8,12.2,"5.5 (1.8, 12.2)" +Clearance time,Vaccinated/Not boosted,5.4,3.5,8.1,"5.4 (3.5, 8.1)" +Clearance time,Vaccinated/Boosted,5.8,4.1,7.9,"5.8 (4.1, 7.9)" +Clearance time,Vaccinated/Boost unknown,4.6,2.6,7.8,"4.6 (2.6, 7.8)" +Clearance time,Unknown,5.7,3.5,8.6,"5.7 (3.5, 8.6)" +Proliferation rate (Ct/day),Unpaired second infections,2.5,1.4,4,"2.5 (1.4, 4)" +Proliferation rate (Ct/day),Not vaccinated/Not boosted,7.3,0.1,45.4,"7.3 (0.1, 45.4)" +Proliferation rate (Ct/day),Not vaccinated/Boost unknown,3,0.5,8.8,"3 (0.5, 8.8)" +Proliferation rate (Ct/day),Vaccinated/Not boosted,3.4,1.5,6.5,"3.4 (1.5, 6.5)" +Proliferation rate (Ct/day),Vaccinated/Boosted,2.4,1.2,4.2,"2.4 (1.2, 4.2)" +Proliferation rate (Ct/day),Vaccinated/Boost unknown,1.8,0.5,4.5,"1.8 (0.5, 4.5)" +Proliferation rate (Ct/day),Unknown,2.9,1.2,5.9,"2.9 (1.2, 5.9)" +Clearance rate (Ct/day),Unpaired second infections,2,1.4,2.6,"2 (1.4, 2.6)" +Clearance rate (Ct/day),Not vaccinated/Not boosted,5.3,0.1,33,"5.3 (0.1, 33)" +Clearance rate (Ct/day),Not vaccinated/Boost unknown,2.6,0.7,6.7,"2.6 (0.7, 6.7)" +Clearance rate (Ct/day),Vaccinated/Not boosted,2.4,1.4,3.8,"2.4 (1.4, 3.8)" +Clearance rate (Ct/day),Vaccinated/Boosted,1.8,1.2,2.5,"1.8 (1.2, 2.5)" +Clearance rate (Ct/day),Vaccinated/Boost unknown,2.1,1.1,3.8,"2.1 (1.1, 3.8)" +Clearance rate (Ct/day),Unknown,2.1,1.2,3.5,"2.1 (1.2, 3.5)" +Symmetry (proliferation/clearance),Unpaired second infections,0.8,0.5,1.4,"0.8 (0.5, 1.4)" +Symmetry (proliferation/clearance),Not vaccinated/Not boosted,2.2,0,13.2,"2.2 (0, 13.2)" +Symmetry (proliferation/clearance),Not vaccinated/Boost unknown,1.4,0.2,5.1,"1.4 (0.2, 5.1)" +Symmetry (proliferation/clearance),Vaccinated/Not boosted,0.8,0.3,1.7,"0.8 (0.3, 1.7)" +Symmetry (proliferation/clearance),Vaccinated/Boosted,0.8,0.4,1.6,"0.8 (0.4, 1.6)" +Symmetry (proliferation/clearance),Vaccinated/Boost unknown,1.6,0.4,4.3,"1.6 (0.4, 4.3)" +Symmetry (proliferation/clearance),Unknown,0.9,0.3,1.9,"0.9 (0.3, 1.9)" diff --git a/figures/run_pars_adj_13_lowsig/viztrajectories_1.pdf b/figures/run_pars_adj_13_lowsig/viztrajectories_1.pdf new file mode 100644 index 0000000..1497611 Binary files /dev/null and b/figures/run_pars_adj_13_lowsig/viztrajectories_1.pdf differ diff --git a/figures/run_pars_adj_13_lowsig/viztrajectories_1.png b/figures/run_pars_adj_13_lowsig/viztrajectories_1.png new file mode 100644 index 0000000..2253377 Binary files /dev/null and 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time,"Second Infection, with two well-documented",6.3,5.3,7.4,"6.3 (5.3, 7.4)" +Proliferation rate (Ct/day),"First Infection, baseline",2.9,2.3,3.6,"2.9 (2.3, 3.6)" +Proliferation rate (Ct/day),"Second Infection, baseline",3.1,2.3,4.2,"3.1 (2.3, 4.2)" +Proliferation rate (Ct/day),"First Infection, with two well-documented",3.2,2.4,4.1,"3.2 (2.4, 4.1)" +Proliferation rate (Ct/day),"Second Infection, with two well-documented",3.2,2.2,4.5,"3.2 (2.2, 4.5)" +Clearance rate (Ct/day),"First Infection, baseline",1.6,1.4,1.8,"1.6 (1.4, 1.8)" +Clearance rate (Ct/day),"Second Infection, baseline",2,1.7,2.4,"2 (1.7, 2.4)" +Clearance rate (Ct/day),"First Infection, with two well-documented",1.5,1.3,1.8,"1.5 (1.3, 1.8)" +Clearance rate (Ct/day),"Second Infection, with two well-documented",2,1.6,2.5,"2 (1.6, 2.5)" +Symmetry (proliferation/clearance),"First Infection, baseline",0.5,0.4,0.7,"0.5 (0.4, 0.7)" +Symmetry (proliferation/clearance),"Second Infection, baseline",0.7,0.5,0.9,"0.7 (0.5, 0.9)" 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b/figures/run_pars_adj_16/summdf.csv @@ -0,0 +1,43 @@ +var,name,mean,lwr,upr,string +Peak Ct,Not vaccinated/Not boosted,26.4,21.1,30.8,"26.4 (21.1, 30.8)" +Peak Ct,Not vaccinated/Boost unknown,30.5,27.2,33.3,"30.5 (27.2, 33.3)" +Peak Ct,Vaccinated/Not boosted,28.8,26.5,30.9,"28.8 (26.5, 30.9)" +Peak Ct,Vaccinated/Boosted,29.2,27.2,31.1,"29.2 (27.2, 31.1)" +Peak Ct,Vaccinated/Boost unknown,28.8,26.3,31.2,"28.8 (26.3, 31.2)" +Peak Ct,Unknown,28.4,25.8,30.8,"28.4 (25.8, 30.8)" +Peak GEML,Not vaccinated/Not boosted,6.4,5.2,7.9,"6.4 (5.2, 7.9)" +Peak GEML,Not vaccinated/Boost unknown,5.3,4.5,6.2,"5.3 (4.5, 6.2)" +Peak GEML,Vaccinated/Not boosted,5.8,5.2,6.4,"5.8 (5.2, 6.4)" +Peak GEML,Vaccinated/Boosted,5.6,5.1,6.2,"5.6 (5.1, 6.2)" +Peak GEML,Vaccinated/Boost unknown,5.8,5.1,6.5,"5.8 (5.1, 6.5)" +Peak GEML,Unknown,5.9,5.2,6.6,"5.9 (5.2, 6.6)" +Proliferation time,Not vaccinated/Not boosted,4.8,2.3,9.1,"4.8 (2.3, 9.1)" +Proliferation time,Not vaccinated/Boost unknown,9,3.4,20.9,"9 (3.4, 20.9)" +Proliferation time,Vaccinated/Not boosted,3.9,2.2,6.4,"3.9 (2.2, 6.4)" +Proliferation time,Vaccinated/Boosted,5.5,3.1,8.7,"5.5 (3.1, 8.7)" +Proliferation time,Vaccinated/Boost unknown,4,2.2,6.6,"4 (2.2, 6.6)" +Proliferation time,Unknown,5.6,2.8,9.8,"5.6 (2.8, 9.8)" +Clearance time,Not vaccinated/Not boosted,9.1,5.3,14.3,"9.1 (5.3, 14.3)" +Clearance time,Not vaccinated/Boost unknown,5.5,3.3,8.8,"5.5 (3.3, 8.8)" +Clearance time,Vaccinated/Not boosted,4.8,3.5,6.4,"4.8 (3.5, 6.4)" +Clearance time,Vaccinated/Boosted,5.7,4.3,7.4,"5.7 (4.3, 7.4)" +Clearance time,Vaccinated/Boost unknown,5.3,3.8,7.1,"5.3 (3.8, 7.1)" +Clearance time,Unknown,5.8,4.1,7.9,"5.8 (4.1, 7.9)" +Proliferation rate (Ct/day),Not vaccinated/Not boosted,3.2,1.4,6.6,"3.2 (1.4, 6.6)" +Proliferation rate (Ct/day),Not vaccinated/Boost unknown,1.3,0.4,3.2,"1.3 (0.4, 3.2)" +Proliferation rate (Ct/day),Vaccinated/Not boosted,3.1,1.7,5.5,"3.1 (1.7, 5.5)" +Proliferation rate (Ct/day),Vaccinated/Boosted,2.1,1.1,3.7,"2.1 (1.1, 3.7)" +Proliferation rate (Ct/day),Vaccinated/Boost unknown,3,1.5,5.4,"3 (1.5, 5.4)" +Proliferation rate (Ct/day),Unknown,2.3,1.1,4.4,"2.3 (1.1, 4.4)" +Clearance rate (Ct/day),Not vaccinated/Not boosted,1.6,0.8,2.8,"1.6 (0.8, 2.8)" +Clearance rate (Ct/day),Not vaccinated/Boost unknown,1.8,1,3.1,"1.8 (1, 3.1)" +Clearance rate (Ct/day),Vaccinated/Not boosted,2.4,1.6,3.4,"2.4 (1.6, 3.4)" +Clearance rate (Ct/day),Vaccinated/Boosted,1.9,1.3,2.6,"1.9 (1.3, 2.6)" +Clearance rate (Ct/day),Vaccinated/Boost unknown,2.2,1.4,3.1,"2.2 (1.4, 3.1)" +Clearance rate (Ct/day),Unknown,2.1,1.4,3,"2.1 (1.4, 3)" +Symmetry (proliferation/clearance),Not vaccinated/Not boosted,0.6,0.2,1.2,"0.6 (0.2, 1.2)" +Symmetry (proliferation/clearance),Not vaccinated/Boost unknown,1.8,0.5,4.8,"1.8 (0.5, 4.8)" +Symmetry (proliferation/clearance),Vaccinated/Not boosted,0.8,0.4,1.5,"0.8 (0.4, 1.5)" +Symmetry (proliferation/clearance),Vaccinated/Boosted,1,0.5,1.8,"1 (0.5, 1.8)" +Symmetry (proliferation/clearance),Vaccinated/Boost unknown,0.8,0.4,1.4,"0.8 (0.4, 1.4)" +Symmetry (proliferation/clearance),Unknown,1,0.4,1.9,"1 (0.4, 1.9)" diff --git a/figures/run_pars_adj_16/viztrajectories_1.pdf b/figures/run_pars_adj_16/viztrajectories_1.pdf new file mode 100644 index 0000000..be598fc Binary files /dev/null and b/figures/run_pars_adj_16/viztrajectories_1.pdf differ diff --git a/figures/run_pars_adj_16/viztrajectories_1.png b/figures/run_pars_adj_16/viztrajectories_1.png new file mode 100644 index 0000000..f582c36 Binary files /dev/null and b/figures/run_pars_adj_16/viztrajectories_1.png differ diff --git a/figures/run_pars_adj_16/viztrajectories_2.pdf b/figures/run_pars_adj_16/viztrajectories_2.pdf new file mode 100644 index 0000000..1a6e1bb Binary files /dev/null and b/figures/run_pars_adj_16/viztrajectories_2.pdf differ diff --git a/figures/run_pars_adj_16/viztrajectories_2.png b/figures/run_pars_adj_16/viztrajectories_2.png new file mode 100644 index 0000000..32df061 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