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| RRphylo-package | Phylogenetic Ridge Regression Methods for Comparative Studies |
| angle.matrix | Ontogenetic shape vectors analysis |
| DataApes | Example dataset |
| DataCetaceans | Example dataset |
| DataFelids | Example dataset |
| DataOrnithodirans | Example dataset |
| DataUng | Example dataset |
| distNodes | Finding distance between nodes and tips |
| evo.dir | Phylogenetic vector analysis of phenotypic change |
| 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 |
| PGLS_fossil | Phylogenetic Generalized Least Square with fossil phylogenies |
| plotRates | Plot RRphylo rates at a specified node |
| RBC | Rate By Clade |
| retrieve.angles | Extracting a user-specified subset of the evo.dir results |
| RRphylo | Evolutionary rates computation along phylogenies |
| 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 desidered size |
| swap.phylo | Test the effect of phylogenetic uncertainty on rate shifts found at a particular node |
| swapONE | Create alternative phylogenies from a given tree |