| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object="apeBootstrap"),
## function(object,...) {
## object@phylo
## }
## )
|
| 6f076280 |
|
| 817c093d |
## ##' get.tree method
## ##'
## ##'
## ##' @docType methods
## ##' @name get.tree
## ##' @rdname get.tree-methods
## ##' @aliases get.tree,beast
## ##' @exportMethod get.tree
## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
## ##' @usage get.tree(object, ...)
## setMethod("get.tree", signature(object="beast"),
## function(object,...) {
## object@phylo
## }
## )
|
| 6f076280 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## ##' @param by one of rst or mlc
## setMethod("get.tree", signature(object="codeml"),
## function(object, by="rst", ...) {
## if (by == "rst") {
## return(object@rst@phylo)
## } else {
## return(object@mlc@phylo)
## }
## })
|
| 6f076280 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object="jplace"),
## function(object) {
## object@phylo
## })
|
| 6f076280 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object = "nhx"),
## function(object) {
## object@phylo
## }
## )
|
| 6f076280 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object="phylip"),
## function(object,...) {
## object@phylo
## }
## )
|
| 6f076280 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object="phylo"),
## function(object, ...) {
## return(object)
## })
|
| 1a0e6ac4 |
|
| 817c093d |
## ##' @rdname get.tree-methods
## ##' @exportMethod get.tree
## setMethod("get.tree", signature(object="data.frame"),
## function(object, ...) {
## edge <- object[, c("parent", "node")]
## i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
## edge <- edge[i, ]
## edge.length <- object[i, "branch.length"]
## tip.label <- object[object[, "isTip"], "label"]
## phylo <- list(edge = as.matrix(edge),
## edge.length = edge.length,
## tip.label = tip.label)
|
| e0430f69 |
|
| 817c093d |
## node.label <- object[!object[, "isTip"], "label"]
## if (!all(is.na(node.label))) {
## phylo$node.label <- node.label
## }
## phylo$Nnode <- sum(!object[, "isTip"])
## class(phylo) <- "phylo"
## return(phylo)
## })
|
| 8d41c5d9 |
|
