Description Usage Arguments Examples
View source: R/treeplyr_functions.R
This function paints clades on the phylogeny and adds a data column that specifies to which clade each species belongs
1 2 3 4 5 6 7 8 9 | paint_clades(
tdObject,
nclades = 1,
name = "clades",
interactive = TRUE,
type = "nodes",
ids = NULL,
plot = TRUE
)
|
tdObject |
A |
nclades |
The number of clades that will be specified if used interactively |
name |
The name of the resulting data column |
interactive |
If |
type |
Either "nodes" or "branches" specifying if the ids provided specify the branch id (assuming a
post-ordered tree) or the node number. Ignored if |
ids |
A vector of node numbers of branch numbers that specify clades. Ignored if |
plot |
If |
1 2 3 4 5 6 7 8 9 | data(anolis)
td <- make.treedata(anolis$phy, anolis$dat)
td <- reorder(td, "postorder")
td.painted <- paint_clades(td, interactive=FALSE, type="nodes",
ids=c(184, 160, 135, 122), plot=TRUE)
td.painted <- group_by(td.painted, clades)
summarise(td.painted,
psig1 = phytools::phylosig(setNames(SVL, phy$tip.label), tree=phy),
meanSVL = mean(SVL))
|
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