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

In mmodely: Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology

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])

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

Value

prints rows that are not matched ot the tree tips

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')

mmodely documentation built on May 31, 2023, 6:47 p.m.