Sero_Gibbs_MCMC: MCMC for Sero

In mrc-ide/YFestimation: Estimate ecological niche and two transmission models for yellow fever in Africa.

Description

MCMC for Sero

Usage

Sero_Gibbs_MCMC(pars_ini, seroout, foi_const_surv, vc_agg3d, pop_agg3d,
  pop_moments_agg, dim_year, dim_age, p_at_survey, P_tot_survey,
  inc_v3d_agg, model_type, parameter_type, prob_Foi,
  posterior_distributions, ign, name_dir, Niter, run_id = 1)

Arguments

pars_ini	vector of initial parameters for seroprevalence
seroout	processed serological 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)
model_type	either "R0" or "Foi"
parameter_type	indexing for the different types of parameters
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)
name_dir	where to save the output
Niter	number of mcmc iterations
run_id	for parallel running- differentiates the different chains. Default = 1

Value

saves the output in name_dir

mrc-ide/YFestimation documentation built on March 13, 2021, 1:40 p.m.