Use a size_t counter when iterating over CHOLMOD supernodes, removing a signed/unsigned comparison warning.
CRAN source builds exclude local article caches and the data downloads used only by website articles.
CAR terms now retain every node in a supplied graph even when some areas have no rows in the fitting data. Missing-response placeholder rows are no longer required for these areas; recovery and prediction retain the full graph support. This applies to proper and Leroux CAR terms, including spatially varying coefficients.
Fits now record monotonic elapsed seconds for compiled
initialization, proposal-calibration warmup, and the post-warmup MCMC
loop separately, in fit$timing$phases. Sampling time
includes all work in the loop, including repeated factorizations and any
requested in-chain latent-effect recovery.
The former timing$sampler field is renamed
timing$backend to describe its existing scope accurately:
the entire compiled call. Multi-chain fits use
backend_by_chain/backend_total and add
phases_by_chain/phases_total. The old timing
names are not aliases. Saved fits from builds without phase timing
cannot supply sampling-only timings.
Config/stLMM/Timing: phases-v1 identifies this capability
in DESCRIPTION; the package version remains 0.0.5 during
development.
Updated printed timing labels and the runtime, blocking-diagnostics, and NIMBLE-comparison articles to distinguish sampling from broader elapsed times.
CAR graph connectivity checks now preallocate their traversal queue, avoiding repeated vector copying on large graphs while preserving component labels and graph validation. This also benefits DAGAR and space-time models that use the same graph constructor.
family = "probit" for binary probit mixed models
using Albert-Chib latent-normal augmentation.joint = TRUE now defaults to
joint_method = "vecchia" instead of the dense full method.
This avoids building a dense covariance over new prediction nodes for
moderate and large prediction sets. Use
joint_method = "full" to request the previous dense
behavior for small prediction sets.stats::binomial(link = "probit") now dispatches to the
probit likelihood.stats::binomial() links such as
"cloglog" and "cauchit" now error instead of
silently using the logit/Polya-Gamma path.