Installation & example data | Phylogenetic effect | Interpreting the parameters | Adding predictors and testing for phylogenetic inertia | Continuous random predictor | Measurement variance in the ruminant neocortex example: | Estimating the intercept | Multiple optima & phylo-format | Direct effect predictors | Brownian motion | Univariate, zero-trend | Regime-dependent trends | Trend as a linear function | Measurement error and bias-correction | Grid search | References
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-4.7)slouch_2.1.5.zip(r-4.6)slouch_2.1.5.zip(r-4.5)
slouch_2.1.5.tgz(r-4.6-any)slouch_2.1.5.tgz(r-4.5-any)
slouch_2.1.5.tar.gz(r-4.7-any)slouch_2.1.5.tar.gz(r-4.6-any)
slouch_2.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
slouch/json (API)
| # 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
Datasets:
- artiodactyla - Artiodactyla Phylogeny
- neocortex - Artiodactyl brain data
Last updated from:0354962bb8. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 123 | ||
| source / vignettes | OK | 173 | ||
| linux-release-x86_64 | OK | 1511 | ||
| macos-release-arm64 | OK | 106 | ||
| macos-oldrel-arm64 | OK | 92 | ||
| windows-devel | OK | 2692 | ||
| windows-release | OK | 75 | ||
| windows-oldrel | OK | 78 | ||
| wasm-release | OK | 103 |
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 |
