slouch-package: SLOUCH: Stochastic Linear Ornstein Uhlenbeck Comparative...

In slouch: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses

SLOUCH: Stochastic Linear Ornstein Uhlenbeck Comparative Hypotheses

Description

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) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2307/2411186")}, Butler & King (2004) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1086/426002")}, Hansen et al. (2008) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1558-5646.2008.00412.x")}.

References

• Hansen, T. F. (1997). Stabilizing Selection and the Comparative Analysis of Adaptation. Evolution, 51(5), 1341. https://doi.org/10.2307/2411186

• Hansen, T. F., Pienaar, J., & Orzack, S. H. (2008). A comparative method for studying adaptation to a randomly evolving environment. Evolution, 62(8), 1965–1977. https://doi.org/10.1111/j.1558-5646.2008.00412.x

• Labra, A., Pienaar, J., & Hansen, T. F. (2009). Evolution of Thermal Physiology in Liolaemus Lizards: Adaptation, Phylogenetic Inertia, and Niche Tracking. The American Naturalist, 174(2), 204–220. https://doi.org/10.1086/600088

• Hansen, T. F., & Bartoszek, K. (2012). Interpreting the evolutionary regression: The interplay between observational and biological errors in phylogenetic comparative studies. Systematic Biology, 61(3), 413–425. https://doi.org/10.1093/sysbio/syr122

• Escudero, M., Hipp, A. L., Hansen, T. F., Voje, K. L., & Luceño, M. (2012). Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). New Phytologist, 195(1), 237–247. https://doi.org/10.1111/j.1469-8137.2012.04137.x

Author(s)

Maintainer: Bjørn Tore Kopperud [e-mail]

Authors:

• Jason Pienaar

• Kjetil Lysne Voje

• Steven Hecht Orzack

• Thomas F. Hansen

Other contributors:

• Mark Grabowski [contributor]

See Also

Useful links:

• https://github.com/kopperud/slouch

• Report bugs at https://github.com/kopperud/slouch/issues

slouch documentation built on May 29, 2024, 10:39 a.m.