CompareAll function

Distances between each pair of trees

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

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().

Returns

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

Details

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

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)

Author(s)

Martin R. Smith

(martin.smith@durham.ac.uk)