phytools

Package: phytools
Version: 0.5-38
Date: 2016-6-23
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Depends: R (>= 2.10), ape (>= 3.0-10), maps
Imports: animation, clusterGeneration, graphics, grDevices, methods,
mnormt, msm, numDeriv, phangorn (>= 2.0.4), plotrix,
scatterplot3d, stats, utils
Suggests: geiger, rgl
ZipData: no
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
License: GPL (>= 2)
URL: http://github.com/liamrevell/phytools
Packaged: 2016-06-24 00:25:30 UTC; Liam
Repository: CRAN
Date/Publication: 2016-06-24 07:30:46
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'phytools' ...
** package 'phytools' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'phytools'
    finding HTML links ... done
    add.arrow                               html  
    finding level-2 HTML links ... done

    add.color.bar                           html  
    add.everywhere                          html  
    add.random                              html  
    add.simmap.legend                       html  
    add.species.to.genus                    html  
    allFurcTrees                            html  
    anc.Bayes                               html  
    anc.ML                                  html  
    anc.trend                               html  
    ancThresh                               html  
    anoletree                               html  
    applyBranchLengths                      html  
    as.multiPhylo                           html  
    ave.rates                               html  
    averageTree                             html  
    bind.tip                                html  
    bind.tree.simmap                        html  
    bmPlot                                  html  
    branching.diffusion                     html  
    brownie.lite                            html  
    brownieREML                             html  
    cladelabels                             html  
    collapse.to.star                        html  
    collapseTree                            html  
    consensus.edges                         html  
    contMap                                 html  
    cophylo                                 html  
    countSimmap                             html  
    densityMap                              html  
    densityTree                             html  
    describe.simmap                         html  
    di2multi.simmap                         html  
    dotTree                                 html  
    drop.clade                              html  
    drop.leaves                             html  
    drop.tip.contMap                        html  
    drop.tip.simmap                         html  
    edgeProbs                               html  
    estDiversity                            html  
    evol.rate.mcmc                          html  
    evol.vcv                                html  
    evolvcv.lite                            html  
    exhaustiveMP                            html  
    expm                                    html  
    export.as.xml                           html  
    fancyTree                               html  
    fastAnc                                 html  
    fastBM                                  html  
    fastMRCA                                html  
    findMRCA                                html  
    fitBayes                                html  
    fitDiversityModel                       html  
    fitMk                                   html  
    fitPagel                                html  
    gammatest                               html  
    genSeq                                  html  
    getCladesofSize                         html  
    getDescendants                          html  
    getExtant                               html  
    getSisters                              html  
    getStates                               html  
    ladderize.simmap                        html  
    lambda.transform                        html  
    likMlambda                              html  
    locate.fossil                           html  
    locate.yeti                             html  
    ls.tree                                 html  
    ltt                                     html  
    ltt95                                   html  
    make.era.map                            html  
    make.simmap                             html  
    map.overlap                             html  
    map.to.singleton                        html  
    mapped.states                           html  
    markChanges                             html  
    matchNodes                              html  
    mergeMappedStates                       html  
    midpoint.root                           html  
    minRotate                               html  
    minSplit                                html  
    mrp.supertree                           html  
    multi.mantel                            html  
    multiC                                  html  
    multiRF                                 html  
    nodeHeights                             html  
    nodelabels.cophylo                      html  
    optim.phylo.ls                          html  
    orderMappedEdge                         html  
    paintSubTree                            html  
    paste.tree                              html  
    pbtree                                  html  
    pgls.Ives                               html  
    phenogram                               html  
    phyl.RMA                                html  
    phyl.cca                                html  
    phyl.pairedttest                        html  
    phyl.pca                                html  
    phyl.resid                              html  
    phyl.vcv                                html  
    phylANOVA                               html  
    phylo.heatmap                           html  
    phylo.to.map                            html  
    phylo.toBackbone                        html  
    phyloDesign                             html  
    phylomorphospace                        html  
    phylomorphospace3d                      html  
    phylosig                                html  
    phytools-package                        html  
    plot.backbonePhylo                      html  
    plotBranchbyTrait                       html  
    plotSimmap                              html  
    plotThresh                              html  
    plotTree                                html  
    plotTree.wBars                          html  
    posterior.evolrate                      html  
    print.backbonePhylo                     html  
    ratebystate                             html  
    rateshift                               html  
    read.newick                             html  
    read.simmap                             html  
    reorder.backbonePhylo                   html  
    reorderSimmap                           html  
    rep.phylo                               html  
    reroot                                  html  
    rerootingMethod                         html  
    rescaleSimmap                           html  
    rotateNodes                             html  
    roundBranches                           html  
    roundPhylogram                          html  
    rstate                                  html  
    sampleFrom                              html  
    setMap                                  html  
    sim.corrs                               html  
    sim.history                             html  
    sim.ratebystate                         html  
    sim.rates                               html  
    skewers                                 html  
    splitEdgeColor                          html  
    splitTree                               html  
    splitplotTree                           html  
    starTree                                html  
    strahlerNumber                          html  
    threshBayes                             html  
    threshDIC                               html  
    threshState                             html  
    to.matrix                               html  
    treeSlice                               html  
    untangle                                html  
    vcvPhylo                                html  
    write.simmap                            html  
    writeAncestors                          html  
    writeNexus                              html  
** building package indices
** testing if installed package can be loaded
* DONE (phytools)
Making 'packages.html' ... done