Package: extendedSurface 0.1.0

Nicolas Mongiardino Koch

extendedSurface: Fit Complex Multi-OU Models by Extending SURFACE and Providing an Interface with OUwie

Multi Ornstein Uhlenbeck (OUM) models are routinely employed to describe the phenotypic evolution of clades across a macroevolutionary adaptive landscape. Multiple implementations exist, including those that require an a priori assigment of lineages to adaptive regimes (e.g., OUwie), and those that infer the location of such regimes shifts (e.g., SURFACE). However, SURFACE has been found to favor overly complex models, which is likely a consequence of fixing a single rate of evolution and force of attraction for the entire tree. Although these parameters can be optimized for each regime by using the SURFACE output as the set of regime shifts required by OUwie, such complex models often fail to be optimized. extendedSurface provides a solution by continuing the backwards phase of SURFACE, merging regimes and generating simpler (yet suboptimal) multiOU models. These are then fed to OUwie, where parameters for each regime can be independetly optimized. Using simpler OUM models as starting points improves the probability of successful model fitting. The resulting models are more realistic, and have been found to be favored over others using empirical comparative datasets. The package allows the user to decide which models should be fit (OUMA, OUMV, OUMVA, with and without stationary root state), and plots the fit of these against those explored by SURFACE to easily compare model fit. Additionally, several approaches to record and plot the evolutionary dynamics of discrete traits through time are also implemented.

Authors:Nicolas Mongiardino Koch [aut, cre]

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Peer review:

Bug tracker:https://github.com/mongiardino/extendedsurface/issues

On CRAN:

4 exports 4 stars 0.61 score 93 dependencies

Last updated 3 years agofrom:de922e5de5. Checks:ERROR: 1 WARNING: 6. Indexed: no.

Exports:extended_surfaceAICPlotplot_tttsurfaceExtendedtransitions_through_time

Dependencies:apebitopscliclusterGenerationcodacodetoolscolorspacecombinatcorHMMcorpcorcowplotcpp11data.tabledeldirDEoptimdeSolvedigestdoParalleldplyrexpmfansifarverfastmatchforeachfuturefuture.applygeigergenericsGenSAggplot2ggseqlogoglobalsgluegmpgridExtragtableigraphinterpisobanditeratorsjsonlitelabelinglatticelhslifecyclelistenvmagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenloptrnnetnumDerivoptimParallelouchOUwiepaleotreeparallellyphangornphylolmphytoolspillarpkgconfigplyrpngquadprogR6RColorBrewerRcppRcppEigenRCurlreshape2rlangRmpfrscalesscatterplot3dstringistringrsubplexsurfacetibbletidyselectutf8vctrsviridisviridisLitewithr