recluster.expl.diss: Cuts a phylogenetic tree to a given series of nodes and...
In recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Description Usage Arguments Details Value Author(s) References Examples

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.

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

`tree`	A phylo tree
`dist`	A dissimilarity matrix.
`maxcl`	A custom number indicating the most external node to be cut. If NULL all the nodes are cut.
`mincl`	A custom number indicated the most internal node to be cut. If NULL the root is used
`expld`	A logical. If TRUE then the matrix for explained dissimilarity is computed.

When polytomic nodes are involved in a cut the number of clusters at that cut will increase more than one unit. Holt at al. (2013) identified levels of explained dissimilarity to be used as a reliable threshold to assess a tree cut. When cases are highly numerous maxcl can be set in order to avoid a very long computation

`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.

Leonardo Dapporto

Dapporto L., Ciolli G., Dennis R.L.H., Fox R., Shreeve, T.G. "A new procedure for extrapolating turnover regionalization at mid?small spatial scales, tested on B ritish butterflies." Methods in Ecology and Evolution (2015), 6:1287-1297.

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

Loading required package: ape
$matrix
     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A       1    2    3    3    4    5    5
B       1    2    3    3    4    4    4
lint    1    1    1    1    2    2    2
sint    2    3    4    4    5    6    6
xint    2    3    4    4    5    6    6
lA      1    1    2    2    3    3    3
lB      1    1    1    1    1    1    1
sA      2    3    4    5    6    7    8
sB      2    3    4    5    6    7    7

$expl.div
[1] 0.7100320 0.8505178 0.8862664 0.9511436 0.9670318 0.9809341 0.9920559

$nclust
[1] 2 3 4 5 6 7 8