mmodely (version 0.2.5)

compare.data.gs.vs.tree.tips: Find data being dropped by mismatches to the tree

Description

This function simply lists the rows of the data that are not getting matched to tips of the tree.

Usage

compare.data.gs.vs.tree.tips(data, phylo, match.on=c('gn_sp','rownames')[1])

Value

prints rows that are not matched ot the tree tips

Arguments

data

a data frame with genus species information as row names and a column named "gn_sp"

phylo

a phylogenetic tree with labeled tip

match.on

use a character string specifiying where the 'Genus_species' vector lies

Examples

data.path <- system.file("extdata","primate-example.data.csv", package="mmodely")
data <- read.csv(data.path, row.names=1)
data$gn_sp <- rownames(data)

tree.path <- system.file("extdata","primate-springer.2012.tre", package="mmodely")
phyl <- ape::read.tree(tree.path)[[5]]


compare.data.gs.vs.tree.tips(data, phyl, match.on='rownames')