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 |