@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.15.4

+Version: 1.15.5

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

@@ -100,7 +100,6 @@ export(read.phyloT)

 export(read.r8s)

 export(read.raxml)

 export(read.tree)

-export(rescale_tree)

 export(revts)

 export(rotate)

 export(rotate_tree)

@@ -219,7 +218,6 @@ importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

 importFrom(tidytree,MRCA)

 importFrom(tidytree,as_tibble)

-importFrom(tidytree,get_tree_data)

 importFrom(tidytree,groupClade)

 importFrom(tidytree,groupOTU)

 importFrom(treeio,Nnode)

@@ -1,3 +1,7 @@

+# ggtree 1.15.5

+

++ mv `rescale_tree` to `treeio` (2019-01-11, Fri)

+

 # ggtree 1.15.4

 + reimplement `MRCA` as a method inherited from `tidytree` (2019-01-10, Thu)

@@ -1,46 +1,3 @@

-##' @importFrom tidytree get_tree_data

-set_branch_length <- function(tree_object, branch.length) {

-    if (branch.length == "branch.length") {

-        return(tree_object)

-    } else if (branch.length == "none") {

-        tree_object@phylo$edge.length <- NULL

-        return(tree_object)

-    }

-

-    if (is(tree_object, "phylo")) {

-        return(tree_object)

-    }

-

-    tree_anno <- get_tree_data(tree_object)

-    tree_anno$node <- as.integer(tree_anno$node)

-

-    phylo <- as.phylo(tree_object)

-

-    cn <- colnames(tree_anno)

-    cn <- cn[!cn %in% c('node', 'parent')]

-

-    length <- match.arg(branch.length, cn)

-

-    if (all(is.na(as.numeric(tree_anno[[length]])))) {

-        stop("branch.length should be numerical attributes...")

-    }

-

-    edge <- phylo$edge

-    colnames(edge) <- c("parent", "node")

-    edge <- as_tibble(edge)

-

-    dd <- full_join(edge, tree_anno, by = "node")

-

-    dd <- dd[match(edge[['node']], dd[['node']]),]

-    len <- unlist(dd[[length]])

-    len <- as.numeric(len)

-    len[is.na(len)] <- 0

-

-    phylo$edge.length <- len

-

-    tree_object@phylo <- phylo

-    return(tree_object)

-}

 calculate_angle <- function(data) {

deleted file mode 100644

@@ -1,13 +0,0 @@

-##' rescale branch length of tree object

-##'

-##' 

-##' @title rescale_tree

-##' @param tree_object tree object

-##' @param branch.length numerical features (e.g. dN/dS)

-##' @return update tree object

-##' @export

-##' @author Guangchuang Yu

-rescale_tree <- function(tree_object, branch.length) {

-    tree_object <- set_branch_length(tree_object, branch.length)

-    return(tree_object)

-}

@@ -6,3 +6,4 @@ drop.tip <- treeio::drop.tip

 get.fields <- treeio::get.fields

 is.tree <- treeio:::is.tree

+set_branch_length <- getFromNamespace("set_branch_length", "treeio")

deleted file mode 100644

@@ -1,22 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/rescale_tree.R

-\name{rescale_tree}

-\alias{rescale_tree}

-\title{rescale_tree}

-\usage{

-rescale_tree(tree_object, branch.length)

-}

-\arguments{

-\item{tree_object}{tree object}

-

-\item{branch.length}{numerical features (e.g. dN/dS)}

-}

-\value{

-update tree object

-}

-\description{

-rescale branch length of tree object

-}

-\author{

-Guangchuang Yu

-}