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
                        fossil phylogenies
RRphylo                 Evolutionary rates computation along
                        phylogenies
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
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
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
node.paths              Tracing nodes along paths
overfitRR               Testing RRphylo methods overfit
phyloclust              Test for phylogenetic clustering
plotRates               Plot RRphylo rates at a specified node
random.evolvability.test
                        Randomization test for phylogenetic structuring
                        in evolvability
rate.map                Mapping rate and direction of phenotypic change
                        on 3D surfaces.
rescaleRR               Rescaling phylogenetic trees according to
                        RRphylo rates
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
sizedsubtree            Find a node subtending to a clade of desired
                        size
swapONE                 Create alternative phylogenies from a given
                        tree
tree.merger             Fast addition of tips and clades on an existing
                        tree
