sub-.treedata.table: Function for performing data.table operations on an object of...

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

Description

This function can be used to subset rows, select and compute on columns data.table.

Usage

## S3 method for class 'treedata.table'
x[...]

Arguments

x	An object of class treedata.table
...	Arguments in the structure of data.table used to perform changes on the treedata.table object

Value

A new object of class treedata.table with $dat and $phy corresponding with the changes set to $dat using data.table's structure.

See Also

data.table

Examples

data(anolis)
anolis2 <- anolis$phy
anolis2$tip.label[1] <- "NAA"
anolis1 <- anolis$phy
anolis1$tip.label[1] <- "NAA"
trees <- list(anolis1, anolis2)
class(trees) <- "multiPhylo"
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"

# A phylo object that fully matches the data
td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
td <- as.treedata.table(anolis$phy, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A multiphylo object that fully matches the data
td <- as.treedata.table(tree = treesFM, data = anolis$dat)
td <- as.treedata.table(treesFM, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A phylo object that partially matches the data
td <- as.treedata.table(tree = anolis1, data = anolis$dat)
td <- as.treedata.table(anolis1, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

# A multiphylo object that partially matches the data
td <- as.treedata.table(tree = trees, data = anolis$dat)
td <- as.treedata.table(trees, anolis$dat)
td[, SVL]
td[island == "Cuba" & ecomorph == "TG", .(ecomorph, island, SVL)]
td[, utils::head(.SD, 1), by = .(ecomorph, island)]

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