SDS.MCMC: SDS Likelihood MCMc

In 2019020826/SDSMCMC: tools::toTitleCase("SDS Epidemic")

Description

This function generates posterior samples of beta, gamma, and rho using MCMC based on SDS likelihood in subsection 4.2 This function includes an additional step for generating the initial number of susceptible n. using NegativeBinomial This function uses RAM method via adapt_S() function from ramcmc R-package

Usage

SDS.MCMC(
  data,
  Tmax,
  fitn = T,
  nrepeat = 1000,
  prior.a,
  prior.b,
  ic = c(k1, k2, k3, k4)
)

Arguments

data	input data set, must be a form of Sellke epidemic (two columns. first is infection time, second is recovery time)
Tmax	cutoff time of epidemic
fitn	if T the function estimate initial number of susceptible, if F the function does not estimate N and calculate from data, so inputted data must cover a total population
nrepeat	number of iteration of MCMC
prior.a	hyper shape parameter of gamma prior for beta, gamma, rho, hyper parameter lambda
prior.b	hyper rate parameter of gamma prior for beta, gamma, rho, hyper parameter lambda
ic	initial value of beta, gamma, rho and N

Value

returning posterior samples of beta, gamma, rho (with fitn=F) or beta, gamma, rho, and n (with fitn=T)

2019020826/SDSMCMC documentation built on March 2, 2020, 5:31 a.m.