clean.data: Cleaning phylogenetic data

In TGuillerme/dispRity: Measuring Disparity

Cleaning phylogenetic data

Description

Cleans a table/tree to match with a given table/tree

Usage

clean.data(data, tree, inc.nodes = FALSE)

Arguments

data	A data.frame or matrix with the elements names as row names.
tree	A phylo or multiPhylo object.
inc.nodes	Logical, whether to check if the nodes in tree are also present in data (TRUE) or not (FALSE; default).

Details

Note if inc.nodes is set to TRUE, the function outputs an error message if there is no matching.

Value

A list containing the cleaned data and tree(s) and information on the eventual dropped tips and rows.

Author(s)

Thomas Guillerme

See Also

tree.age.

Examples

##Creating a set of different trees
trees_list <- list(rtree(5, tip.label = LETTERS[1:5]), rtree(4,
     tip.label = LETTERS[1:4]), rtree(6, tip.label = LETTERS[1:6]))
class(trees_list) <- "multiPhylo"

##Creating a matrix
dummy_data <- matrix(c(rnorm(5), runif(5)), 5, 2,
    dimnames = list(LETTERS[1:5], c("var1", "var2")))

##Cleaning the trees and the data
cleaned <- clean.data(data = dummy_data, tree = trees_list)
##The taxa that where dropped (tips and rows):
c(cleaned$dropped_tips, cleaned$dropped_rows)
##The cleaned trees:
cleaned$tree
##The cleaned data set:
cleaned$data

TGuillerme/dispRity documentation built on Dec. 21, 2024, 4:05 a.m.