R/jags.R

In Freshwater-Fish-Ecology-Laboratory/detrange: Estimate Detection Range from Passive Acoustic Telemetry

run_jags <- function(template, data, monitor, inits, niters, nchains, nthin, quiet, seed) {

  rjags::load.module('glm', quiet = TRUE)
  rng <- list(.RNG.name = "base::Wichmann-Hill",
              .RNG.seed = seed)
  model <- rjags::jags.model(textConnection(template), data,
                             inits = c(inits, rng),
                             n.adapt = 0, quiet = quiet, n.chains = nchains)

  progress_bar <- if(quiet) "none" else "text"

  niters <- niters * nthin
  adapted <- rjags::adapt(model, n.iter = floor(niters / 2),
                          progress.bar = progress_bar,
                          end.adaptation = TRUE)

  # if (!adapted) warning("incomplete adaptation")

  update(model, n.iter = floor(niters / 2),
         progress.bar = progress_bar)

  monitor <- monitor[monitor %in% stats::variable.names(model)]

  samples <- rjags::jags.samples(model = model, variable.names = monitor,
                                 n.iter = niters, thin = nthin,
                                 progress.bar = progress_bar)
  samples <- mcmcr::as.mcmcr(samples)
  # converged <- mcmcr::converged(samples)
  # if(!converged) warning("model did not converge")
  list(model = model, samples = samples)
}