NEWS.md
A^-1 (exp(A t) - I) b. Since version 1.0.0 this matrix was symmetrised before being multiplied by b, which is only correct when the selection matrix A is symmetric (e.g., no cross-selection effects). Both the Stan and JAX backends now use the exact expression. In our comparisons the selection (A) and drift (Q) parameters were essentially unchanged, because b is weakly identified and absorbs most of the difference. Posterior estimates of b itself can shift; in one simulated example they moved by up to about 0.6 posterior standard deviationscoev_plot_predictive_check() when nuts_sampler = "nutpie". The JAX backend now returns yrep posterior predictions alongside the other model parameters, matching the Stan backend (#118)log_lik = TRUE is now supported with nuts_sampler = "nutpie". The JAX backend previously ignored the argument and returned no log_lik, so loo and waic could not be computed from nutpie fits (#118)prior_only = TRUE for models with Gaussian variables and no repeated observations. terminal_drift only received a prior inside the likelihood block, leaving it improper when the likelihood was skipped. Sampling failed to initialise with nuts_sampler = "nutpie" and was unreliable with nuts_sampler = "stan" (#118)log_lik and yrep for Gaussian variables with missing data. The generated quantities block used the -9999 missing value placeholder when constructing residuals, which corrupted the conditional densities of the other variables of the same observationcoev_ancestral_states() for extracting posterior estimates of ancestral trait values at internal phylogenetic nodes, on either the latent or response scale (#86)nuts_sampler = "nutpie" (#114)nutpie as an alternative sampler for the Stan models (#92)lon_lat argument and deprecating the dist_mat argument in coev_fit() (#103)