surface: Fitting Hansen Models to Investigate Convergent Evolution

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SURFACE is a data-driven phylogenetic comparative method for fitting stabilizing selection models to continuous trait data, building on the ouch package. 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.

Author
Travis Ingram
Date of publication
2014-02-14 11:22:36
Maintainer
Travis Ingram <travis.ingram@otago.ac.nz>
License
GPL (>= 2)
Version
0.4-1
URLs

View on CRAN

Man pages

convertTreeData
Utilities for Formatting Objects for SURFACE Analysis
getAIC
Akaike's Information Criterion for SURFACE Models
getBranchTimes
Extract Branching Times from an 'ouch' Tree
ouchDescendants
Obtain Descendants from an 'ouch' Tree
propRegMatch
Similarity of Two Hansen Models
repaint
Paint the Branches of a Tree
runSurface
Run All Steps of a SURFACE Analysis
startingModel
Create an Initial Model for a SURFACE Analysis
surfaceAICPlot
Plot the AIC Throughout a SURFACE Analysis
surfaceBackward
Collapsing Convergent Regimes in a Hansen Model
surfaceDemo
Tree and Data for Demonstrating SURFACE
surfaceForward
Adding Regimes to a Hansen Model
surface-package
Fitting Hansen Models to Investigate Convergent Evolution
surfaceSimulate
Simulate Data for SURFACE
surfaceSummary
Summarize SURFACE Output
surfaceTreePlot
Visualize Results of a SURFACE Analysis

Files in this package

surface
surface/inst
surface/inst/CITATION
surface/inst/doc
surface/inst/doc/surface_tutorial.Rnw
surface/inst/doc/surface_tutorial.pdf
surface/inst/doc/surface_tutorial.R
surface/NAMESPACE
surface/data
surface/data/surfaceDemo.RData
surface/R
surface/R/surfaceAICMultiPlot.R
surface/R/getAIC.R
surface/R/convertBack.R
surface/R/convertTreeData.R
surface/R/getBranchTimes.R
surface/R/propRegMatch.R
surface/R/addRegime.R
surface/R/ouchDescendants.R
surface/R/runSurface.R
surface/R/surfaceTraitPlot.R
surface/R/surfaceTreePlot.R
surface/R/npSurface.R
surface/R/surfaceSummary.R
surface/R/nameNodes.R
surface/R/collapseRegimes.R
surface/R/surfaceSimulate.R
surface/R/surfaceBackward.R
surface/R/repaint.R
surface/R/surfaceForward.R
surface/R/startingModel.R
surface/R/surfaceAICPlot.R
surface/vignettes
surface/vignettes/surface_tutorial.Rnw
surface/MD5
surface/build
surface/build/vignette.rds
surface/DESCRIPTION
surface/man
surface/man/surfaceSummary.Rd
surface/man/surface-package.Rd
surface/man/surfaceTreePlot.Rd
surface/man/repaint.Rd
surface/man/surfaceSimulate.Rd
surface/man/startingModel.Rd
surface/man/getBranchTimes.Rd
surface/man/surfaceForward.Rd
surface/man/surfaceBackward.Rd
surface/man/convertTreeData.Rd
surface/man/getAIC.Rd
surface/man/ouchDescendants.Rd
surface/man/runSurface.Rd
surface/man/surfaceDemo.Rd
surface/man/propRegMatch.Rd
surface/man/surfaceAICPlot.Rd