JAGS draw geometry and deterministic materialization

JAGS_draw_geometry() returns the retained iteration and chain geometry stored from the actual chains returned by JAGS. Geometry is independent of which coordinates are public.

JAGS_materialize_draws() reconstructs requested coordinates from the fitted parameter map. Sampled coordinates are selected from the fitted chains and structural coordinates are filled with their exact fixed_value. Internal coordinates, including a private backend anchor, are excluded by default.

JAGS_with_draws() returns a derived-draw view with supplied draws and matching geometry, plus the complete untouched fit in original_fit. Views have class BayesTools_draws_view and BayesTools_fit, with only original_fit and mcmc slots. Nonruntime analysis attributes are copied; view-local changes do not modify the original. Replacing a view retains its original fit and current local analysis attributes without nesting views. Fit-level draw metadata and stored posterior densities/ordinates are cleared; attach fresh estimates with posterior_metadata() after replacement. A view supports descriptive estimates, diagnostic plots, mixed-posterior extraction and marginal inference from its supplied draws. It does not support original-model convergence, bridge sampling or sampling extension: use fit$original_fit and regenerate the view after extending that fit. These refusals have common class BayesTools_draws_view_unavailable, with leaves BayesTools_draws_view_sampling_unavailable (also BayesTools_sampling_unavailable) and BayesTools_draws_view_inference_unavailable. Missing requested sampled coordinates signal BayesTools_draws_view_coordinate_unavailable, with a missing field. Views need not contain every original sampled coordinate; prior-draw transformations retain their existing intersection-of-columns policy. coda::as.mcmc.list() preserves chain timing. coda::as.mcmc() pools in chain-major order with indices starting at one and thinning one; pooled indices do not describe a continuous MCMC trajectory.

JAGS_draw_geometry(fit)

JAGS_draw_geometry_schema()

JAGS_materialize_draws(fit, parameters = NULL, include_internal = FALSE)

JAGS_with_draws(fit, draws)

# S3 method for class 'BayesTools_draws_view'
as.mcmc.list(x, ...)

# S3 method for class 'BayesTools_draws_view'
as.mcmc(x, ...)

# S3 method for class 'BayesTools_draws_view'
print(x, ...)

Arguments

fit

fitted object created by JAGS_fit().

parameters

optional exact vector of coordinate_name values. NULL selects every available public coordinate in map order.

include_internal

whether internal coordinates may be returned.

draws

replacement draws coercible to a coda::mcmc.list.

x

a derived-draw view.

...

additional arguments.

Value

JAGS_draw_geometry() returns a BayesTools_draw_geometry list. JAGS_draw_geometry_schema() returns field descriptions. JAGS_materialize_draws() returns a coda::mcmc.list, including a valid zero-column list when the fit has no public coordinate. JAGS_with_draws() returns a BayesTools_draws_view.