Package: surface 0.6

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>.

Authors:Travis Ingram [aut, cre]

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surface.pdf |surface.html
surface/json (API)

# Install 'surface' in R:
install.packages('surface', repos = c('https://tingram.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.10 score 1 stars 18 scripts 224 downloads 7 mentions 21 exports 42 dependencies

Last updated 7 months agofrom:8308983b8c. Checks:9 OK. Indexed: yes.

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Doc / VignettesOKMar 30 2025
R-4.5-winOKMar 30 2025
R-4.5-macOKMar 30 2025
R-4.5-linuxOKMar 30 2025
R-4.4-winOKMar 30 2025
R-4.4-macOKMar 30 2025
R-4.4-linuxOKMar 30 2025
R-4.3-winOKMar 30 2025
R-4.3-macOKMar 30 2025

Exports:addRegimecollapseRegimesconvertBackconvertTreeDatagetAICgetBranchTimesnameNodesnpSurfaceouchDescendantspropRegMatchrepaintrunSurfacestartingModelsurfaceAICMultiPlotsurfaceAICPlotsurfaceBackwardsurfaceForwardsurfaceSimulatesurfaceSummarysurfaceTraitPlotsurfaceTreePlot

Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfastmatchforeachgeigergenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelouchphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs

Introduction to surface

Rendered fromsurface_tutorial.Rnwusingutils::Sweaveon Mar 30 2025.

Last update: 2020-12-18
Started: 2012-12-23