Phylogenetic Ridge Regression Methods for Comparative Studies

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Documentation for package ‘RRphylo’ version 2.7.0

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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
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
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
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