recluster.cons: Consensus tree among re-sampled trees
In recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Description Usage Arguments Details Value Author(s) References Examples

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 independent of the original row order.

1 2	recluster.cons(mat, phylo = NULL, tr = 100, p = 0.5, dist = "simpson", method = "average", blenghts=TRUE, select=FALSE)

`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 indicating if non-negative least squares branch lengths should be computed.
`select`	A logical indicating if only trees having a fit higher than the median value in the least squares regression should be included in the consensus analysis.

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.

`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.

Leonardo Dapporto and Matteo Ramazzotti

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.

#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")