treescape (version 1.0.0)

multiDist: Metric function for multiPhylo input

Description

Comparison of a list of trees using the Kendall Colijn metric. Output is given as a pairwise distance matrix. This is equivalent to the $D output from treescape but may be preferable for large datasets, and when principal co-ordinate analysis is not required. It includes an option to save memory at the expense of computation time.

Usage

multiDist(trees, lambda = 0, return.lambda.function = FALSE,
  save.memory = FALSE)

Value

The distance matrix or a function that produces the distance matrix given a value for lambda.

Examples

## generate 10 random trees, each with 6 tips
trees <- rmtree(10,6)

## pairwise distance matrix when lambda=0
multiDist(trees)

## pairwise distance matrix as a function of lambda:
m <- multiDist(trees, return.lambda.function=TRUE)

## evaluate at lambda=0. Equivalent to multiDist(trees).
m0 <- m(0)

## save memory by recomputing each tree vector for each pairwise tree comparison (for fixed lambda):
m0.5 <- multiDist(trees,0.5,save.memory=TRUE)