treeDist: Calculates the distance between trees

In treenomial: Comparison of Trees using a Tree Defining Polynomial

Calculates the distance between trees

Description

Calculates the distance between two trees or a tree and a list of trees.

Usage

treeDist(
  x,
  Y,
  type = c("default", "yEvaluated", "tipLabel"),
  method = c("fraction", "logDiff", "wLogDiff", "pa", "ap"),
  y,
  numThreads = -1
)

Arguments

x	single phylo object
Y	a list of phylo objects
type	one of: “real” tree distinguishing polynomials in two variables x (columns) and y (rows) “yEvaluated” tree distinguishing polynomials with y evaluated at a specified argument “tipLabel” complex coefficient polynomial that utilize binary trait tip labels on the phylo objects
method	method to use when calculating coefficient distances: “fraction” for two coefficient matrices A and B returns sum(abs(A-B)/(A+B)), excluding elements where both A and B are zero “logDiff” for two coefficient matrices A and B returns sum(log(1+abs(A-B)) “wLogDiff” performs the “logDiff” method with weights on the rows “pa” total pairs where the coefficient is present in one matrix and absent in the other (presence-absence) “ap” opposite comparison of pa (absence-presence)
y	the y value to evaluate the polynomial at when type is “yEvaluated”, ignored otherwise
numThreads	number of threads to be used, the default (-1) will use the number of cores in the machine and numThreads = 0 will only use the main thread

Value

vector of distances

Note

• the substituted y coefficient vector only supports the “logDiff” method and the “fraction” method

• “pa” and “ap” force symmetry in the output distance matrix

Examples

library(treenomial)
library(ape)

# distance between one 10 tip tree and 100 trees with 30 tips

# generate the trees
tenTipTree <- rtree(10)
thirtyTipList <- rmtree(100, 30)

# find the distance
treeDist(tenTipTree, thirtyTipList, numThreads = 0)

treenomial documentation built on June 7, 2022, 1:08 a.m.