treescape (version 1.8.16)

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 = NULL,
  emphasise.tips = NULL, emphasise.weight = 2,
  return.lambda.function = FALSE, save.memory = FALSE)

Value

A list of five objects:

• $centre is the "central vector", that is, the (weighted) mean of the tree vectors (which typically does not correspond to a tree itself);
• $distances gives the distance of each tree from the central vector;
• $mindist is the minimum of these distances;
• $treenumbers gives the numbers (and, if supplied, names) of the "median tree(s)", that is, the tree(s) which achieve this minimum distance to the centre;
• $trees if trees were supplied then this returns the median trees as a multiPhylo object.

If groups are provided, then one list is returned for each group. If return.lambda.function=TRUE then a function is returned that produces this list for a given value of lambda.

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))