Sero_Gibbs_MCMC_parameter_step: MCMC parameter step for Sero

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

Description

MCMC parameter step for Sero

Usage

Sero_Gibbs_MCMC_parameter_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)

Arguments

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)

Value

next step in the metropolis-within-gibbs for the parameters (param, like, prior, accept)

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