- Added rudimentary support for interaction terms between direct-effect continuous predictors, and categorical predictors. Caveat: measurement error in continuous predictor not supported for estimating interaction terms.
- Changed maintainer e-mail
- Amended tests not to depend on
set.seed(), such that it works with new sampler in R 3.6.0.
- Removed ‘background’ vignette
- Added a
NEWS.md file to track changes to the package.
- Breaking changes: several variable names in function arguments and model outputs have been changed for clarity.
- Documentation improved.
- Model summary print changed
- Draft for long-form manual/vignette begun.
slouch 2.0.0 marks a near-complete rewrite of the entire package.
New features
- Slouch now uses the phylogenetic tree format from package
ape.
- Model outputs are returned as a composite object, which consequentely is programmable.
- Implementation of explicit Brownian-motion models, including intercept-only models, regression with direct-effect covariates, random-effect (trend) covariates, regime-dependent trends and options to estimate
Ya.
- Slouch now allows estimation of parameters using numerical optimization techniques.
- Computation in general is much faster, due to better memory management and use of Cholesky decomposition in regression coefficient estimation.
- Docstrings begun.
Bug fixes
- Fixed several bugs when calculating the residual variance-covariance matrix, in particular for random-effect models with non-ultrametric trees.
- Fixed incorrect calculation of
tja and tia for non-ultrametric trees.
Scrapped features
- Fitch algorithm for ancestral state character estimation.
- The
slouchtree or ouchtree phylogeny format.