In ropensci/treedata.table: Manipulation of Matched Phylogenies and Data using 'data.table'

knitr::opts_chunk$set(echo = TRUE)

Working with multiphylo objects

treedata.table further allows the matching of multiple phylogenies (multiPhylo) against a single dataset (data.frame). Below, we modified the anole dataset to explain the extended functionality of treedata.table with multiPhylo objects. Note that all the trees in the multiPhylo must have exactly the same taxa.

We first load the sample dataset.

library(ape)
library(treedata.table)

# Load example data
data(anolis)
#Create treedata.table object with as.treedata.table
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)

We then create a multiPhylo object including only two phylo objects. Users can provide any number of phylo objects within the multiPhylo object. However, trees can only differ in their topology. In other words, all trees must have the same tip labels.

We also note that both the provided multiPhylo and data.frame should partially overlap

trees<-list(anolis$phy,anolis$phy)
class(trees) <- "multiPhylo"
trees

Now, we create our treedata.table object by combining the trait data (data.frame) and the newly generated multiPhylo object. Note that there is only a single character matrix.

td <- as.treedata.table(tree=trees, data=anolis$dat)

The resulting td object now returns a multiPhylo object under phy. This objectcontains only the overlapping taxa between the multiphylo objects and the input dataset.

class(td$phy);td$phy

Please note that all the basic treedata.table functions highlighted above for phylo objects are still functional when treedata.table objects include multiPhylo objects.

td[, head(.SD, 1), by = "ecomorph"]

Functions can also be run on any treedata.table object with multiphylo data. For instance, the following line will fit a phenogram for SVL on each of the trees we provided in the multiPhylo object.

tdt(td, geiger::fitContinuous(phy, extractVector(td, 'SVL'), model="BM", ncores=1))

The output is an object of class list with each element corresponding to the output function of each tree in the provided multiPhylo object.

ropensci/treedata.table documentation built on Sept. 12, 2021, 6:23 p.m.