Package: slouch 2.1.5
slouch: 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>.
Authors:
slouch_2.1.5.tar.gz
slouch_2.1.5.zip(r-4.5)slouch_2.1.5.zip(r-4.4)slouch_2.1.5.zip(r-4.3)
slouch_2.1.5.tgz(r-4.4-any)slouch_2.1.5.tgz(r-4.3-any)
slouch_2.1.5.tar.gz(r-4.5-noble)slouch_2.1.5.tar.gz(r-4.4-noble)
slouch_2.1.5.tgz(r-4.4-emscripten)slouch_2.1.5.tgz(r-4.3-emscripten)
slouch.pdf |slouch.html✨
slouch/json (API)
NEWS
| # Install 'slouch' in R: |
| install.packages('slouch', repos = c('https://kopperud.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kopperud/slouch/issues
- artiodactyla - Artiodactyla Phylogeny
- neocortex - Artiodactyl brain data
Last updated 9 months agofrom:0354962bb8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 23 2024 |
| R-4.5-win | OK | Oct 23 2024 |
| R-4.5-linux | OK | Oct 23 2024 |
| R-4.4-win | OK | Oct 23 2024 |
| R-4.4-mac | OK | Oct 23 2024 |
| R-4.3-win | OK | Oct 23 2024 |
| R-4.3-mac | OK | Oct 23 2024 |
Exports:brown.fithillclimbplotlseqregimeplotslouch.fit
Dependencies:apecachemcrayondigestfastmaplatticememoisenlmeRcpprlang
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SLOUCH: Stochastic Linear Ornstein Uhlenbeck Comparative Hypotheses | slouch-package slouch |
| Artiodactyla Phylogeny | artiodactyla |
| Function to fit Brownian-motion models of trait evolution | brown.fit |
| Plot the hillclimber trajectory | hillclimbplot hillclimbplot.slouch |
| Extract Log-Likelihood | logLik.slouch |
| Logarithmically spaced sequence | lseq |
| Artiodactyl brain data | neocortex |
| Plot Grid Search | plot.slouch |
| Print, minimalist output | print.slouch |
| Plot the internal regimes for a given fitted model | regimeplot regimeplot.slouch |
| Function to fit Ornstein-Uhlenbeck models of trait evolution | slouch.fit |
| Model Summary | summary.slouch |
