treescape (version 1.0.0)

medTree: Geometric median tree function

Description

Finds the geometric median of a set of trees according to the Kendall Colijn metric.

Usage

medTree(x, groups = NULL, lambda = 0, weights = rep(1, length(x)),
  return.lambda.function = FALSE, save.memory = FALSE)

Value

A list with the median metric vector, distances, indices of the tree(s) that are closest to the median tree and the value of this distance or a function that produces this list for a given value of lambda. If groups are provided, then one list is returned for each group.

Examples

## EXAMPLE WITH WOODMICE DATA
data(woodmiceTrees)

## LOOKING FOR A SINGLE MEDIAN
## get median tree(s)
res <- medTree(woodmiceTrees)
res

## plot first tree
med.tree <- res$trees[[1]]
plot(med.tree)

## LOOKING FOR MEDIANS IN SEVERAL CLUSTERS
## identify 6 clusters
groves <- findGroves(woodmiceTrees, nf=3, nclust=6)

## find median trees
res.with.grp <- medTree(woodmiceTrees, groves$groups)

## there isone output per cluster
names(res.with.grp)

## get the first median of each
med.trees <- lapply(res.with.grp, function(e) ladderize(e$trees[[1]]))

## plot trees
par(mfrow=c(2,3))
for(i in 1:length(med.trees)) plot(med.trees[[i]], main=paste("cluster",i))