CompareAll: Distances between each pair of trees

In ms609/TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Distances between each pair of trees

Description

Calculate the distance between each tree in a list, and each other tree in the same list.

Usage

CompareAll(x, Func, FUN.VALUE = Func(x[[1]], x[[1]], ...), ...)

Arguments

x	List of trees, in the format expected by Func().
Func	distance function returning distance between two trees, e.g. path.dist().
FUN.VALUE	Format of output of Func(), to be passed to vapply(). If unspecified, calculated by running Func(x[[1]], x[[1]]).
...	Additional parameters to pass to Func().

Details

CompareAll() is not limited to tree comparisons: Func can be any symmetric function.

Value

CompareAll() returns a distance matrix of class dist detailing the distance between each pair of trees. Identical trees are assumed to have zero distance.

Author(s)

Martin R. Smith ([e-mail])

Examples

# Generate a list of trees to compare
library("TreeTools", quietly = TRUE)
trees <- list(bal1 = BalancedTree(1:8), 
              pec1 = PectinateTree(1:8),
              pec2 = PectinateTree(c(4:1, 5:8)))
  
# Compare each tree with each other tree
CompareAll(trees, NNIDist)
  
# Providing FUN.VALUE yields a modest speed gain:
dist <- CompareAll(trees, NNIDist, FUN.VALUE = integer(7))
  
# View distances as a matrix
as.matrix(dist$lower)

ms609/TreeDist documentation built on April 5, 2024, 12:07 a.m.