surface: Fitting Hansen Models to Investigate Convergent Evolution

This data-driven phylogenetic comparative method fits stabilizing selection models to continuous trait data, building on the 'ouch' methodology of Butler and King (2004) <doi:10.1086/426002>. The main functions fit a series of Hansen models using stepwise AIC, then identify cases of convergent evolution where multiple lineages have shifted to the same adaptive peak. For more information see Ingram and Mahler (2013) <doi:10.1111/2041-210X.12034>.

Version: 0.6
Depends: R (≥ 2.6), ape, ouch, MASS, geiger
Imports: methods, phytools
Suggests: igraph
Published: 2024-08-19
DOI: 10.32614/CRAN.package.surface
Author: Travis Ingram [aut, cre]
Maintainer: Travis Ingram <travis.ingram at otago.ac.nz>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://www.otago.ac.nz/ecoevotago/research/code/index.html
NeedsCompilation: no
Citation: surface citation info
In views: Phylogenetics
CRAN checks: surface results

Documentation:

Reference manual: surface.pdf
Vignettes: Introduction to surface (source, R code)

Downloads:

Package source: surface_0.6.tar.gz
Windows binaries: r-devel: surface_0.6.zip, r-release: surface_0.6.zip, r-oldrel: surface_0.6.zip
macOS binaries: r-release (arm64): surface_0.6.tgz, r-oldrel (arm64): surface_0.6.tgz, r-release (x86_64): surface_0.6.tgz, r-oldrel (x86_64): surface_0.6.tgz
Old sources: surface archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=surface to link to this page.