DataApes                Example dataset
DataCetaceans           Example dataset
DataFelids              Example dataset
DataOrnithodirans       Example dataset
DataSimians             Example dataset
DataUng                 Example dataset
PGLS_fossil             Phylogenetic Generalized Least Square with
                        phylogenies including fossils
RRphylo                 Evolutionary rates computation along
                        phylogenies
RRphylo-defunct         Defunct functions in Package RRphylo
RRphylo-deprecated      Deprecated functions in Package RRphylo
RRphylo-package         Phylogenetic Ridge Regression Methods for
                        Comparative Studies
StableTraitsR           Run StableTraits from within R
angle.matrix            Ontogenetic shape vectors analysis
colorbar                Draw colorbar on a plot
compRates               Comparing average absolute rates between clades
conv.map                Mapping morphological convergence on 3D
                        surfaces
cutPhylo                Cut the phylogeny at a given age or node
distNodes               Finding distance between nodes and tips
evo.dir                 Phylogenetic vector analysis of phenotypic
                        change
fix.poly                Resolving polytomies to non-zero length
                        branches
getGenus                Taxonomic inspection of the tree at the genus
                        level
getMommy                Upward tip or node to root path
getSis                  Get sister clade
lollipoPlot             Lollipop charts
makeFossil              Make fossil species on a phylogeny
makeL                   Matrix of branch lengths along root-to-tip
                        paths
makeL1                  Matrix of branch lengths along a root-to-node
                        path
move.lineage            Move tips or clades
namesCompare            Checking species names for misspelling and
                        synonyms
node.paths              Tracing nodes along paths
overfitPGLS             Testing PGLS_fossil overfit
overfitRR               Testing RRphylo overfit
overfitSC               Testing search.conv overfit
overfitSS               Testing search.shift overfit
overfitST               Testing search.trend overfit
phyloclust              Test for phylogenetic clustering
plotConv                Graphical representation of search.conv results
plotRR                  Plot the RRphylo output onto the phylogenetic
                        tree
plotRates               Plot RRphylo rates at a specified node
plotShift               Graphical representation of search.shift
                        results
plotTrend               Graphical representation of search.trend
                        results
random.evolvability.test
                        Randomization test for phylogenetic structuring
                        in evolvability
rate.map                Mapping rate and direction of phenotypic change
                        on 3D surfaces.
rateHistory             Computing historical rates
resampleTree            Altering phylogenetic trees
rescaleRR               Rescaling phylogenetic trees
retrieve.angles         Extracting a user-specified subset of the
                        evo.dir results
scaleTree               Phylogenetic tree calibration
search.conv             Searching for morphological convergence among
                        species and clades
search.shift            Locating shifts in phenotypic evolutionary
                        rates
search.trend            Searching for evolutionary trends in phenotypes
                        and rates
setBM                   Producing simulated phenotypes with trends
sig2BM                  Brownian Motion rate computation
sizedsubtree            Find a node subtending to a clade of desired
                        size
swapONE                 Create alternative phylogenies from a given
                        tree
tips                    Get descending tips
tree.merger             Fast construction of phylogenetic trees
treeCompare             Visualize the difference between phylogenetic
                        trees
treedataMatch           Cross-reference tree and data
