coevolve 1.2.1

coevolve 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

coevolve 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)

coevolve 1.1.0

New Features

• Allow 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)

coevolve 1.0.0

Bug Fixes

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

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)

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)

coevolve 0.1.0

Initial release version.