checkTreeValidity: Check Validity of an RDP-Based Taxonomic Tree

In HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Description

This function goes through every node in the tree and for each node it checks that the sum of that nodes children are less than or equal to the value of that node.

Usage

checkTreeValidity(data, samples = NULL, epsilon = 0.0001, split = ".")

Arguments

data	A data frame in which each column contains the rdp read counts for every taxa given in the row names.
samples	Deprecated. Only send the columns in data to create.
epsilon	This value allows for rounding problems or other such small errors in the data such that the (parent + epsilon > sum(children)).
split	This is the character that separates the taxa levels in the row names.

Value

A boolean vector that indicates the validity of every tree tested.

Author(s)

Berkley Shands, Patricio S. La Rosa, Elena Deych, William D. Shannon

Examples

	data(saliva) 
	
	validTree <- checkTreeValidity(saliva[,1, drop=FALSE])
	validTree

HMPTrees documentation built on May 2, 2019, 4:02 p.m.