recluster (version 2.8)

recluster.expl.diss: Cut a phylogenetic tree to a given series of nodes and computes explained dissimilarity.

Description

This function cuts a phylogenetic tree at any given series of nodes, provides membership for each element in the series of resulting clusters and computes the fraction of dissimilarity explained by each cut.

Usage

recluster.expl.diss(tree, dist, maxcl=NULL, mincl=NULL, expld=TRUE)

Arguments

tree

A phylo tree

dist

A dissimilarity matrix.

maxcl

A custom number indicated the most external node to be cutted. If NULL all the nodes are cutted.

mincl

A custom number indicated the most internal node to be cutted. If NULL the root is uded

expld

A logical. If TRUE then the matrix for explained dissimilarity is computed.

Value

• matrix
  A matrix indicating cluster membership of each site in each cut of the tree.
• expl.div
  A vector indicating the explained dissimilarity for each cut.
• nclust
  A vector indicating the number of clusters resulting from each cut.

Details

When polytomic nodes are involved in a cut the increase in the number of clusters at a given cut will be higher than one. Holt at al. (2013) discussed the level of explained dissimilarity to be used as a reliable threshold to identify a tree cut. When cases are highly numerous maxcl can be set in order to avoid a very long computation

References

Dapporto L. et al "A new procedure for extrapolating turnover regionalization at mid-small spatial scales, tested on British butterflies." submitted www.unifi.it/scibio/bioinfo/recluster.html

Examples

data(datamod)
sor_tree<- recluster.cons(datamod, dist="sorensen")
sor_diss <- recluster.dist (datamod, dist="sorensen")
expl_diss <- recluster.expl.diss (sor_tree$cons,sor_diss)
expl_diss