concor.node: Concordances of Trees with All Nodes of A Reference Tree
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description Usage Arguments Details Examples

concor.node analyzes and returns for each node on the ref tree the number and names of trees showing concordances.

1	concor.node(ref, trees, bp = 0, getTreeNames = FALSE, node = NULL)

`ref`	an object of class "`phylo`". A reference tree.
`trees`	a list of objects of class "`phylo`". A list of test trees such as single gene trees.
`bp`	a bootstrape value, which the concordance is counted when the corresponding node label of `trees` is higher than.
`getTreeNames`	a logical specifying whether to return the names of `trees` showing concordances for each node on `ref`. Defaults to `FALSE`.
`node`	a numeric or integer specifying the node(s) on `ref` to analyze the concordance. Defaults to `NULL` and all the nodes on `ref` are analyzed.

Concordance for a node is defined as all descendent tips of the node of ref are grouped together without other tips in trees. The main analysis of this function requires rooted trees; when the trees are not rooted, concor.node roots trees according to ref during the analysis. concor.node returns an object of class "concor" as a list of: (1) tree: the ref; (2) data: a data.frame showing the counts and percents of concordances for each node; (3) conTrees: names of trees that are concordant with ref for each node (when getTreeNames = TRUE).

## Not run: 
data(Brassidata)
trees <- Brassidata$trees
ref <- Brassidata$ref
concor.n<-concor.node(ref = ref,trees = trees, bp = c(0,30,50), getTreeNames = FALSE)

## End(Not run)