Man pages for RRphylo
Phylogenetic Ridge Regression Methods for Comparative Studies

angle.matrixOntogenetic shape vectors analysis
colorbarDraw colorbar on a plot
compRatesComparing average absolute rates between clades
conv.mapMapping morphological convergence on 3D surfaces
cutPhyloCut the phylogeny at a given age or node
DataApesExample dataset
DataCetaceansExample dataset
DataFelidsExample dataset
DataOrnithodiransExample dataset
DataSimiansExample dataset
DataUngExample dataset
distNodesFinding distance between nodes and tips
evo.dirPhylogenetic vector analysis of phenotypic change
fix.polyResolving polytomies to non-zero length branches
getGenusTaxonomic inspection of the tree at the genus level
getMommyUpward tip or node to root path
getSisGet sister clade
lollipoPlotLollipop charts
makeFossilMake fossil species on a phylogeny
makeLMatrix of branch lengths along root-to-tip paths
makeL1Matrix of branch lengths along a root-to-node path
move.lineageMove tips or clades
namesCompareChecking species names for misspelling and synonyms
node.pathsTracing nodes along paths
overfitPGLSTesting PGLS_fossil overfit
overfitRRTesting RRphylo overfit
overfitSCTesting search.conv overfit
overfitSSTesting search.shift overfit
overfitSTTesting search.trend overfit
PGLS_fossilPhylogenetic Generalized Least Square with phylogenies...
phyloclustTest for phylogenetic clustering
plotConvGraphical representation of search.conv results
plotRatesPlot RRphylo rates at a specified node
plotRRPlot the RRphylo output onto the phylogenetic tree
plotShiftGraphical representation of search.shift results
plotTrendGraphical representation of search.trend results
random.evolvability.testRandomization test for phylogenetic structuring in...
rateHistoryComputing historical rates
rate.mapMapping rate and direction of phenotypic change on 3D...
resampleTreeAltering phylogenetic trees
rescaleRRRescaling phylogenetic trees
retrieve.anglesExtracting a user-specified subset of the evo.dir results
RRphyloEvolutionary rates computation along phylogenies
RRphylo-defunctDefunct functions in Package RRphylo
RRphylo-deprecatedDeprecated functions in Package RRphylo
RRphylo-packagePhylogenetic Ridge Regression Methods for Comparative Studies
scaleTreePhylogenetic tree calibration
search.convSearching for morphological convergence among species and...
search.shiftLocating shifts in phenotypic evolutionary rates
search.trendSearching for evolutionary trends in phenotypes and rates
setBMProducing simulated phenotypes with trends
sig2BMBrownian Motion rate computation
sizedsubtreeFind a node subtending to a clade of desired size
StableTraitsRRun StableTraits from within R
swapONECreate alternative phylogenies from a given tree
tipsGet descending tips
treeCompareVisualize the difference between phylogenetic trees
treedataMatchCross-reference tree and data
tree.mergerFast construction of phylogenetic trees
RRphylo documentation built on April 3, 2025, 9:43 p.m.