getAllCentroids {Apoderoides}

getAllCentroids

Description

Calculate all the centroids of ranks in the tree.

Usage

getAllCentroids(tree,OTUrankData=NULL,show_progress=FALSE,num_threads=1)

Arguments

tree

A phylogenetic tree to be checked. This is loaded by ape::read.tree() from a file.

OTUrankData

A list composed of two character vectors. The first vector is tips of tree. The second vector is the upper rank of the tips. When this is NULL, the function assumes that all the tree tips are expressed as Genus_species like Homo_sapience, and calculate the centroids for genera. When this is not NULL, the function returns centroids based on the upper rank in this list.

show_progress

If TRUE, calculation progress is shown on the R console.

num_threads

A positive integer to specify the number of threads to calculate the scores.

Value

A list containing vectors of integers of centroid node number(s).

Examples

data(testTree)
#calculate centroids for genus
getAllCentroids(testTree)
data(testRankList)
#calculate centroids for the rank in the list
getAllCentroids(testTree,testRankList)