Lean Chapter 1 fit (for comparison with Model 2a) — fit_chapter1

Fits the Chapter 1 model (model.jags) through the same lean path as run_mod_2a() and returns the raw runjags object, monitoring the nodes needed to compare against Model 2a (mu.par, prec.par). This is the same model, data, priors, and posterior as run_mod() — run_mod() simply adds post-processing on top; here we keep the MCMC in mcmc.list form so it can be compared directly with a Model 2a fit.

Unstratified only (matching the typhoid example workflow).

Usage

fit_chapter1_lean(
  data,
  file_mod = serodynamics_example("model.jags"),
  nchain = 4,
  nadapt = 1000,
  nburn = 1000,
  nmc = 1000,
  niter = 4000,
  ...
)

Arguments

data: A serocalculator case-data data.frame.
file_mod: Path to the Chapter 1 JAGS model (defaults to the packaged model.jags).
nchain, nadapt, nburn, nmc, niter: MCMC controls (as in run_mod()).
...: Prior arguments forwarded to prep_priors().

Value

A runjags object (its $mcmc is a coda::mcmc.list).