Run Phylocom's bladj from R
Arguments
- tree
(character/phylo) One of: phylogeny as a newick string (will be written to a temp file) - OR path to file with a newick string - OR a an ape
phylo
object. required.- ages
(data.frame/character) ages data.frame, or path to an ages file. required.
Details
uses phylocomr::ph_bladj()
under the hood
Examples
if (FALSE) {
library("phylocomr")
# make an ages data.frame
ages_df <- data.frame(
a = c('malpighiales','eudicots','ericales_to_asterales','plantaginaceae',
'malvids', 'poales'),
b = c(81, 20, 56, 76, 47, 71)
)
# read phylogeny file as a string
phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr")
phylo_str <- readLines(phylo_file)
# Run Bladj, returns phylo object
(x <- rbladj(tree = phylo_str, ages = ages_df))
# load ape and plot tree
library(ape)
plot(x)
}