Phylogenetic Ridge Regression Methods for Comparative Studies

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Documentation for package ‘RRphylo’ version 2.8.0

• 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
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
overfitRR	Testing RRphylo methods 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.
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 addition of tips and clades on an existing tree
treeCompare	Visualize the difference between phylogenetic trees
treedataMatch	Cross-reference tree and data