# Phylogenetic Ridge Regression Methods for Comparative Studies

## Documentation for package ‘RRphylo’ version 2.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

RRphylo-package | Phylogenetic Ridge Regression Methods for Comparative Studies
angle.matrix | Ontogenetic shape vectors analysis
conv.map | Mapping morphological convergence on 3D surfaces
cutPhylo | Cut the phylogeny at a given age or node
DataApes | Example dataset
DataCetaceans | Example dataset
DataFelids | Example dataset
DataOrnithodirans | Example dataset
DataSimians | Example dataset
DataUng | Example dataset
distNodes | Finding distance between nodes and tips
evo.dir | Phylogenetic vector analysis of phenotypic change
fix.poly | Resolving polytomies to non-zero length branches
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
overfitRR | Testing RRphylo methods overfit
PGLS_fossil | Phylogenetic Generalized Least Square with fossil phylogenies
phyloclust | Test for phylogenetic clustering
plotRates | Plot RRphylo rates at a specified node
random.evolvability.test | Randomization test for phylogenetic structuring in evolvability
retrieve.angles | Extracting a user-specified subset of the evo.dir results
RRphylo | Evolutionary rates computation along phylogenies
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
StableTraitsR | Run StableTraits from within R
swap.phylo | Test the effect of phylogenetic uncertainty on rate shifts found at a particular node
swapONE | Create alternative phylogenies from a given tree
tree.merger | Fast addition of tips and clades on an existing tree