Changes in version 1.2.1                        

New Features

  - Added further documentation about repeated observations models
    (#120)
  - Added vignette "Algorithmic scaling" (#121)
  - Models with Gaussian variables and no repeated observations now use
    a conditionally non-centred parameterisation for latent terminal
    drift, i.e. the terminal drift of non-Gaussian variables and of
    missing Gaussian values. Latent drift is written as a standard
    normal innovation conditional on the observed Gaussian residuals of
    the same taxon. This is a change of variables that leaves the model,
    the posterior, and the pointwise log-likelihood unchanged, but
    removes a funnel between the drift parameters and the latent
    terminal drift that caused poor mixing in mixed Gaussian and
    non-Gaussian models. Thanks to @yuhangxoox for the diagnosis (#124)

Bug Fixes

  - Fixed the continuous time intercept term in the expected change
    along a branch, 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 deviations
  - Fixed coev_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)
  - Fixed 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)
  - Fixed the pointwise 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 observation

                        Changes in version 1.2.0                        

New Features

  - Added coev_ancestral_states() for extracting posterior estimates of
    ancestral trait values at internal phylogenetic nodes, on either the
    latent or response scale (#86)
  - Added vignette "Ancestral state reconstruction"

Bug Fixes

  - Fixed issue with plotting functions when nuts_sampler = "nutpie"
    (#114)

Other Changes

  - Updated documentation (#111)
  - Fixed cmdstanr location in documentation (#112)
  - Responded to rOpenSci package review (#113)
  - Added package citation (#116)

                        Changes in version 1.1.0                        

New Features

  - Allowed for single traits (#107)
  - Added pure JAX/NumPyro backend via nuts_sampler = "nutpie". Uses
    nutpie's Rust NUTS sampler with JAX gradients for ~5x faster
    sampling than Stan on typical models. Requires pip install jax
    numpyro nutpie (#109)

                        Changes in version 1.0.0                        

New Features

  - Added nutpie as an alternative sampler for the Stan models (#92)
  - Cached matrix computations when branch lengths are identical (#93)
  - Implemented Hilbert-space approximate Gaussian processes for spatial
    control, adding the lon_lat argument and deprecating the dist_mat
    argument in coev_fit() (#103)

Bug Fixes

  - Fixed issue with summary() when estimate_residual = FALSE (#95)

Other Changes

  - Updated license
  - Submitted to rOpenSci for package review
  - Linted package using lintr
  - Implemented srr compliance checks
  - Added continuous integration checks using GitHub Actions
  - Reduced cyclomatic complexity for some functions
  - Re-factored Stan code generation to use whisker templates (#99)
  - Implemented automatic test fixture re-generation in GitHub Actions
    (#100)

                        Changes in version 0.1.0                        

  - Initial release version.