Description Usage Arguments Value
View source: R/SERO_productspace_mcmc_functions.R
MCMC model step for Sero
1 2 3 4 | Sero_Gibbs_MCMC_model_step(param, seroout, foi_const_surv, vc_agg3d,
pop_agg3d, pop_moments_agg, dim_year, dim_age, p_at_survey, P_tot_survey,
inc_v3d_agg, chain_cov, adapt, model_type, parameter_type, accCurrent,
prob_Foi, posterior_distributions, ign, like, prior)
|
param |
vector of parameters for seroprevalence |
seroout |
processed serology data |
foi_const_surv |
vector of additional foi for each survey (R0 model) |
vc_agg3d |
aggregated vaccination array |
pop_agg3d |
aggregated population array |
pop_moments_agg |
population moments aggregated |
dim_year |
years of interest |
dim_age |
ages of interest |
p_at_survey |
population proportion at time of serological survey |
P_tot_survey |
total population at time of serological survey |
inc_v3d_agg |
the incidence of vaccination (aggregated) |
chain_cov |
covariance of chain up to now |
adapt |
whether to use the chain covariance to adapt the proposal distribution is 0 or 1 |
model_type |
either "R0" or "Foi" |
parameter_type |
indexing for the different types of parameters |
accCurrent |
current posterior probability |
prob_Foi |
log of the model prior for Foi model |
posterior_distributions |
distribution parameters for each model pseudo priors |
ign |
sero surveys to ignore (good for bug hunting) |
like |
value of the likelihood from the Sero_Gibbs_MCMC_parameter_step |
prior |
value of the prior from the Sero_Gibbs_MCMC_parameter_step |
next step in the metropolis-within-gibbs for the model type (param, model_type, accCurrent, accept)
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