# Phylogenetic Ridge Regression Methods for Comparative Studies

## Documentation for package ‘RRphylo’ version 3.0.0

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

## Help Pages

RRphylo-package | Phylogenetic Ridge Regression Methods for Comparative Studies
addShift | Graphical representation of search.shift results
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
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
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
PGLS_fossil | Phylogenetic Generalized Least Square with phylogenies including fossils
phyloclust | Test for phylogenetic clustering
plotConv | Graphical representation of search.conv results
plotRates | Plot RRphylo rates at a specified node
plotRR | Plot the RRphylo output onto the phylogenetic tree
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
RRphylo | Evolutionary rates computation along phylogenies
RRphylo-defunct | Defunct functions in Package RRphylo
RRphylo-deprecated | Deprecated functions in Package RRphylo
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
StableTraitsR | Run StableTraits from within R
swap.phylo | Defunct functions in Package RRphylo
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