Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses

An implementation of a phylogenetic comparative method. It can fit univariate among-species Ornstein-Uhlenbeck models of phenotypic trait evolution, where the trait evolves towards a primary optimum. The optimum can be modelled as a single parameter, as multiple discrete regimes on the phylogenetic tree, and/or with continuous covariates. See also Hansen (1997) doi:10.2307/2411186, Butler & King (2004) doi:10.1086/426002, Hansen et al. (2008) doi:10.1111/j.1558-5646.2008.00412.x.


News

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.

Reference manual

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install.packages("slouch")

2.1.1 by Bjørn Tore Kopperud, a month ago


http://github.com/kopperud/slouch


Report a bug at http://github.com/kopperud/slouch/issues


Browse source code at https://github.com/cran/slouch


Authors: Bjørn Tore Kopperud [aut, cre] , Jason Pienaar [aut] , Kjetil Lysne Voje [aut] , Steven Hecht Orzack [aut] , Thomas F. Hansen [aut] , Mark Grabowski [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports parallel, ape, memoise

Depends on base, stats

Suggests knitr, rmarkdown, bookdown, testthat


See at CRAN