BayesRTMB 0.2.1

• Added upgrade_fit() to rebuild saved MCMC, VB, MAP, and classic fit objects with the currently loaded class definitions, optionally upgrading their embedded model objects as well.
• Improved rtmb_vector() and rtmb_array() tape construction time by automatically reusing an AD seed from model parameters when available.
• Made log_sum_exp(), softmax(), and log_softmax() work more reliably with RTMB automatic-differentiation values, including baseline-category patterns such as softmax(c(0, eta)) inside rtmb_code().
• Improved wrapper-generated model code to use AD-compatible rtmb_vector() and rtmb_array() containers in loop-filled generated quantities and generated likelihood contributions where needed.
• Improved report() handling in transformed and generated quantities, including namespaced BayesRTMB::report() calls and wrapper-generated print_code() output.
• Changed VB point estimates to use only the best variational estimate by default, aligning EAP(), MAP(), and rotation references with the selected best ELBO run while still allowing explicit chains or best_chains selection.
• Made EAP() and MAP() drop their list wrapper by default when a single parameter is requested, matching the behavior of estimate().
• Added optional taped evaluation for transformed parameters and generated quantities, with automatic fallback to R evaluation when taping is not possible.
• Improved parallel worker robustness by reducing exported globals and preserving wrapper setup environments needed by generated model code.
• Improved MCMC runtime behavior by caching metric calculations, speeding up retained draw conversion, and refining progress checks.
• Changed bootstrap progress reporting to use percentage-style progress output, consistent with other long-running workflows.
• Added diagnostic recommendations to help interpret common fitting warnings.
• Improved matrix-valued Gaussian process log-density evaluation.
• Updated MDU defaults and internals, including Euclidean distance as the default MDU distance and more explicit use of namespace-qualified factor rotations.

BayesRTMB 0.2.0

• Reworked NUTS sampling internals with Stan-style multinomial tree expansion, warmup diagnostics, Stan-window metric adaptation, and support for diagonal, dense, hybrid, and automatic metric selection.
• Improved MCMC diagnostics by reporting divergence counts and percentages, metric auto-selection details, warmup summaries, metric condition numbers, and positive-definite fallback counts.
• Added configurable progress output for MCMC and VB workflows, including streamed message-style progress for parallel workers and percentage reporting.
• Added delta-method standard errors and confidence intervals for conditional_effects() and simple_effects() with optimized and classic fits; simple_effects() for classic fits now also reports df, t value, and Pr.
• Added sd_slice and sd_multiplier controls for conditional and simple effects, including automatic SD slicing for moderators with many observed values.
• Added rhat_summary() for MCMC fits, returning a numeric R-hat vector with a compact printed summary.
• Expanded data-reshaping helpers: to_long() now supports multiple value columns, list-based column groups, and preserves input row order by default while still allowing sorted output with sort = TRUE.
• Added AD-compatible helper constructors rtmb_vector() and rtmb_array() for model code that needs mutable RTMB-compatible containers.
• Improved RTMB model setup error messages for common AD and NA/NaN failures.
• Improved wrapper behavior, including rtmb_glmer(cwc = list(ID, "all")), hierarchical lambda in rtmb_mdu(), stronger prior validation, and more robust handling of non-finite VB optimization attempts.
• Improved MDU plotting and initialization, including principal-axis reference rotation and clearer radius display controls.
• Fixed several model-specific issues, including AD-compatible negative-binomial log densities and unequal-variance JZS t-test examples.

BayesRTMB 0.1.1

• Addressed CRAN resubmission feedback by quoting ‘RTMB’ in the package title, adding method references to DESCRIPTION, and replacing \dontrun{} examples with \donttest{} where appropriate.
• Trimmed long-running examples for CRAN checks while retaining representative MCMC examples for correlation, t-test, and mixed-model workflows.
• Updated IRT post-estimation examples to use ordered response data explicitly.
• Fixed an AD-compatible negative-binomial log-density issue.
• Corrected the unequal-variance JZS t-test example and documentation.