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rjags_models_pooled.r
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rjags_models_pooled.r
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#Note Rjags models not R code!
jcodes <- list(
"waning_none"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + study_specific_rr[ID[i]]
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(u in 1:length(uID)){
study_specific_rr[u] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
}",
"waning_linear"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + log( exp(study_specific_rr[ID[i]]) + exp(alpha)*timept[i] )
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
}",
"waning_power"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + study_specific_rr[ID[i]] + exp(alpha)*log( timept[i] )
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
}",
"waning_power_01"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + log((exp(alpha)*timept[i]^exp(beta))/(exp(study_specific_rr[ID[i]])+exp(alpha)*timept[i]^exp(beta)))
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
beta ~ dnorm(0,0.01)
}",
"waning_power2"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + study_specific_rr[ID[i]] + alpha*log(timept[i])
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
}",
"waning_power3"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + study_specific_rr[ID[i]] + alpha*timept[i]
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
}",
"waning_sigmoid"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + study_specific_rr[ID[i]] + log( 1/( 1 + exp(alpha)*exp( -exp(beta)*timept[i]) ) )
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
beta ~ dnorm(0,0.01)
}",
"waning_sigmoid_01"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + log( exp(study_specific_rr[ID[i]])/( exp(study_specific_rr[ID[i]]) + exp(alpha)*exp( -exp(beta)*timept[i]) ) )
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific RR, centered around mean RR
for(ID in 1:length(uID)){
study_specific_rr[ID] ~ dnorm(mean_rr,between_study_var)
}
#prior for mean RR and between study var
mean_rr ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
alpha ~ dnorm(0,0.01)
beta ~ dnorm(0,0.01)
}",
"waning_gamma_01"="model{
#loop through studyIDs
for (i in 1:length(ID)){
# cases poisson distributed
cases_placebo[i] ~ dpois(cases_placebo_dist[i])
cases_vaccine[i] ~ dpois(cases_vaccine_dist[i])
log(cases_placebo_dist[i]) = base_rate[i] + log(person_weeks_placebo[i])
log(cases_vaccine_dist[i]) = base_rate[i] + log(person_weeks_vaccine[i]) + log( pgamma( timept[i], exp(study_specific_alpha[ID[i]]), exp(beta) ) )
#estimate rate in each study-period
base_rate[i] ~ dnorm(0,0.01) #prior for risk in unvaccinated
}
#prior study specific mean, centered around mean
for(ID in 1:length(uID)){
study_specific_alpha[ID] ~ dnorm(alpha,between_study_var)
}
#prior for mean RR and between study var
alpha ~ dnorm(0,0.01)
between_study_var <- 1/sd^2
sd ~ dunif(0,2)
#priors for reduction in RR by time since vaccination
beta ~ dnorm(0,0.01)
}"
)