Changelog

Source: NEWS.md

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

  • 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)

coevolve 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)

coevolve 0.1.0

  • Initial release version.