surface (version 0.4-1)

surface-package: Fitting Hansen Models to Investigate Convergent Evolution

Description

surface provides a wrapper to the ouch package, fitting a series of Hansen multiple-peak stabilizing selection models using stepwise AIC, and identifying cases of convergence where independent lineages discovered the same adaptive peak

Details

Package:

surface

Type:

Package

Version:

0.4

Date:

2013-02-20

License:

GPL (>=2)

surface uses the Hansen model of stabilizing selection around multiple adaptive peaks to infer a macroevolutionary adaptive landscape using only trait data and a phylogenetic tree. The most important functions are surfaceForward and surfaceBackward, which carry out the two stepwise phases of the method, and runSurface, a wrapper function that carries out both phases. Results can be displayed using surfaceSummary, and visualized using surfaceTreePlot, surfaceTraitPlot, and surfaceAICPlot. Hypothesis tests, such as whether the extent of convergence exceeds the expectation under a model without true convergence, can be done with the assistance of surfaceSimulate. The vignette `surface_tutorial' demonstrates the use of the various functions included in the package

References

Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.

See Also

runSurface, surfaceForward, surfaceBackward, surfaceSimulate, surfaceSummary, surfaceTreePlot, surfaceTraitPlot, surfaceAICPlot

Examples

#executable R code and demonstrations of the key functions can be found in the tutorial
#vignette("surface_tutorial", package = "surface")