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##' @rdname reroot-methods
##' @exportMethod reroot
setMethod("reroot", signature(object="beast"),
function(object, node, ...) {
object@phylo <- reroot(object@phylo, node, ...)
node_map <- attr(object@phylo, "node_map")
idx <- match(object@stats$node, node_map[,1])
object@stats$node <- node_map[idx, 2]
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| 905d1116 |
|
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return(object)
})
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| 905d1116 |
## ##' @rdname reroot-methods
## ##' @exportMethod reroot
## setMethod("reroot", signature(object="raxml"),
## function(object, node, ...) {
## object@phylo <- reroot(object@phylo, node, ...)
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| 85777d7b |
|
| 905d1116 |
## node_map <- attr(object@phylo, "node_map")
## idx <- match(object@bootstrap$node, node_map[,1])
## object@bootstrap$node <- node_map[idx, 2]
## return(object)
## })
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| 85777d7b |
##' reroot a tree
##'
|
| 905d1116 |
##'
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| 85777d7b |
##' @rdname reroot-methods
##' @exportMethod reroot
setMethod("reroot", signature(object="phylo"),
function(object, node, ...) {
pos <- 0.5* object$edge.length[which(object$edge[,2] == node)]
## @importFrom phytools reroot
phytools <- "phytools"
require(phytools, character.only = TRUE)
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| 905d1116 |
|
| 85777d7b |
phytools_reroot <- eval(parse(text="phytools::reroot"))
tree <- phytools_reroot(object, node, pos)
attr(tree, "reroot") <- TRUE
node_map <- reroot_node_mapping(object, tree)
attr(tree, "node_map") <- node_map
return(tree)
})
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