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:
surface_0.6.tar.gz
surface_0.6.zip(r-4.5)surface_0.6.zip(r-4.4)surface_0.6.zip(r-4.3)
surface_0.6.tgz(r-4.4-any)surface_0.6.tgz(r-4.3-any)
surface_0.6.tar.gz(r-4.5-noble)surface_0.6.tar.gz(r-4.4-noble)
surface_0.6.tgz(r-4.4-emscripten)surface_0.6.tgz(r-4.3-emscripten)
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')) |
- surfaceDemo - Tree and Data for Demonstrating SURFACE
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:8308983b8c. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:addRegimecollapseRegimesconvertBackconvertTreeDatagetAICgetBranchTimesnameNodesnpSurfaceouchDescendantspropRegMatchrepaintrunSurfacestartingModelsurfaceAICMultiPlotsurfaceAICPlotsurfaceBackwardsurfaceForwardsurfaceSimulatesurfaceSummarysurfaceTraitPlotsurfaceTreePlot
Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfastmatchforeachgeigergenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelouchphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fitting Hansen Models to Investigate Convergent Evolution | surface-package surface |
| Utilities for Formatting Objects for SURFACE Analysis | convertBack convertTreeData nameNodes |
| Akaike's Information Criterion for SURFACE Models | getAIC npSurface |
| Extract Branching Times from an 'ouch' Tree | getBranchTimes |
| Obtain Descendants from an 'ouch' Tree | ouchDescendants |
| Similarity of Two Hansen Models | propRegMatch |
| Paint the Branches of a Tree | repaint |
| Run All Steps of a SURFACE Analysis | runSurface |
| Create an Initial Model for a SURFACE Analysis | startingModel |
| Plot the AIC Throughout a SURFACE Analysis | surfaceAICMultiPlot surfaceAICPlot |
| Collapsing Convergent Regimes in a Hansen Model | collapseRegimes surfaceBackward |
| Tree and Data for Demonstrating SURFACE | surfaceDemo |
| Adding Regimes to a Hansen Model | addRegime surfaceForward |
| Simulate Data for SURFACE | surfaceSimulate |
| Summarize SURFACE Output | surfaceSummary |
| Visualize Results of a SURFACE Analysis | surfaceTraitPlot surfaceTreePlot |
