NEWS.md

In slouch: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses

slouch 2.1.4

• Changed maintainer e-mail

slouch 2.1.3

• 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.

slouch 2.1.2

• Amended tests not to depend on set.seed(), such that it works with new sampler in R 3.6.0.

slouch 2.1.1

• Removed 'background' vignette

slouch 2.1.0

• 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

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.

slouch documentation built on Feb. 21, 2020, 5:08 p.m.