NimbleCB.R

require(nimble)
source("simulateCB.R")
options(mc.cores = parallel::detectCores())
source('nimCB.R')

nimCBdata <- list(obs=sim$Iobs)
nimCBcon <- list(numobs=numobs,N=N,i0=i0)

nimCBinits <- list(I=sim$I,
                   effprop=effprop,
                   beta=beta,
                   reporting=reporting,
                   N0=N0
)
NimbleCB <- MCMCsuite(code=nimcode,
                   data=nimCBdata,
                   inits=nimCBinits,
                   constants=nimCBcon,
                   MCMCs=c("jags","nimble","nimble_slice"),
                   monitors=c("beta","reporting","effprop"),
                   calculateEfficiency=TRUE,
                   niter=10000,
                   makePlot=FALSE,
                   savePlot=FALSE)

print(NimbleCB$timing)
print(NimbleCB$summary)

saveRDS(NimbleCB,file="NimbleCB")