SpatialEpi (version 1.2.1)

MCMC_simulation: MCMC simulation to sample configurations

Description

MCMC simulation to estimate prior and posterior quantities by sampling configurations.

Usage

MCMC_simulation(n_sim, pattern, theta_init, overlap, cluster_coords, 
p_moves_orig, J, lkhd_z, lambda)

Arguments

n_sim

number of MCMC iterations

pattern

alternating pattern between unif and prop prior on single zones

theta_init

initial configuration

overlap

output of create_geo_objects: a list with two elements: 1. presence which lists for each areas all the single zones it is present in and 2. cluster_list for each single

cluster_coords

output of create_geo_objects: n.zones x 2 matrix of the centering and radial area of each single zone

p_moves_orig

probability of sampling each of the 5 possible moves to explore sample space

J

maximum number of clusters/anti-clusters to consider

lkhd_z

values associated with each single zone to use in Metropolis-Hastings ratio

lambda

lambda from definition of prior on single zones

Value

• sample
  sampled configurations
• move_trace
  trace of moves (1 = growth, 2 = trim, 3 = recenter, 4 = death, 5 = birth)
• accpt_trace
  trace of acceptance (0 = not accepted)
• ratio_trace
  trace of Metropolis-Hastings ratio

References

Wakefield J. and Kim A.Y. (2013) A Bayesian model for cluster detection. Biostatistics, 14, 752--765.

See Also

create_geo_objects, process_MCMC_sample