recluster (version 2.8)

recluster.cons: Consensus tree among re-sampled trees

Description

This function creates a series of trees by resampling the order of sites in the original dissimilarity matrix. Then, it computes a consensus among them. The resulting tree is unaffected by original row order.

Usage

recluster.cons(mat, phylo = NULL, tr = 100, p = 0.5, 
dist = "simpson", method = "average", blenghts=TRUE, select=FALSE)

Arguments

mat

A matrix containing sites (rows) and species (columns) or any dissimilarity matrix.

phylo

An ultrametric and rooted tree for species phylogeny having the same labels as in mat columns. Only required to compute phylogenitic beta-diversity indexes.

tr

The number of trees to be used for the consensus.

p

A numeric value between 0.5 and 1 giving the proportion for a clade to be represented in the consensus tree.

dist

A beta-diversity index (the Simpson index by default) included in recluster.dist or any custom binary dissimilarity to be specified according to the syntax of designdist function of the vegan package.

method

Any clustering method allowed by hclust.

blenghts

A logical asking if non-negative least squares branch lengths should be computed.

select

A logical asking if only trees having higher than median fit in the least squares regression should be included in the consensus analysis.

Value

• cons
  The consensus tree, an object of class phylo.
• trees
  The trees used to construct the final consensus tree.
• RSS
  The Residual Sum of Squares for the trees resulting if select=TRUE.

Details

According to the primitive "consensus" function from the "ape" package, p must range between 0.5 and 1. Select = TRUE can allow lowering polytomies by removing trees with topology showing particularly low correlation with the distance matrix. Row names are required.

References

Dapporto L., Ramazzotti M., Fattorini S., Talavera G., Vila R., Dennis R. "recluster: an unbiased clustering procedure for beta-diversity turnover" Ecography (2013), 36:1070-1075. www.unifi.it/scibio/bioinfo/recluster.html

Examples

#Faunistic beta diversity
data(datamod,treemod)
tree<-recluster.cons(datamod,tr=10)
plot(tree$cons,direction="downwards")

#Phylogenetic beta diversity
tree_p<-recluster.cons(datamod,treemod,dist="phylosort",tr=10)
plot(tree_p$cons, direction="downwards")