| add.ages.phylo | Adding taxa and/or node ages to a phylogeny |
| aggr.trait.map | Plot the mapping of a reconstructed trait averaging several... |
| best.leg.pos | Find best legend position in a plot |
| binarize | Binarize a vector |
| boxgroups | Multivariate and multi-subgroup boxplots |
| chardist | Get the distance matrix of string data |
| contrasting.palette | Function to give a vector of 22 contrasting colors |
| create.tree | Create a phylogenetic tree |
| densgroups | Multi-subgroup density lines |
| discrete.palette | Function to provide a user-defined discrete color palette |
| equiv.nodes | Get equivalences of nodes between phylogenies |
| extract.from.factor | Extract a vector with some levels of an initial factor vector |
| freq.cols | Get color palette depending on frequencies within data of... |
| getClade | Get the node of a given monophyletic group. |
| get.grid | Get a layout grid matrix according to desired number of plots |
| invert.dim.lists | Invert dimensions of a list of lists (with 2 or more... |
| median.tree | Get the tree with median taxa ages among a list of trees |
| morphospace | Function to create a "morphospace" |
| multkw | Multivariate Kruskal-Wallis test |
| multkw.m | Multivariate Kruskal-Wallis test with missing data |
| multkw.perm | Extended Multivariate Kruskal-Wallis test with missing data |
| param.t.test | T-test using describing parameters of data |
| phyMap3ax | Summarize three traits or axes as RGB colors and map them on... |
| plot.anc.RR | Map univariate data on phylogeny following RRphylo method. |
| plot.mapping | "Map" a trait: plot its distribution over a phylogenetic tree |
| plotPhylogram.JM | Custom phytools:::plotPhylogram function to allow vertical... |
| plot.rates.RR | Map RRphylo evolutionary rates of univariate data on... |
| print.multkw.output | Print function for results of multkw functions (multkw,... |
| reg.param.t.test | T-test of two regression slopes or intercepts |
| scale.palette | Function to provide a user-defined scaled color palette |
| shared.nodes | Getting shared nodes between several phylogenies |
| split.cols | Split character columns of a matrix/dataframe/table (or a... |
| subs.tree | Substitute a taxon of a given phylogenetic tree by another... |
| supporting.tips | Get all pairs of tips defining a node |
| swap.dim.list | Swap dimensions of a list |
| tax.arrows | Draw arrows next to phylogenetic taxa |
| thermo.var | Add "thermometers" of trait variation across reconstruction... |
| transparent.colors | Function to provide the color code of a transparent color |
