@@ -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: 1.15.1

+Version: 1.15.2

 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")),

@@ -220,7 +220,7 @@ importFrom(rvcheck,get_fun_from_pkg)

 importFrom(scales,alpha)

 importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

-importFrom(tidytree,as_data_frame)

+importFrom(tidytree,as_tibble)

 importFrom(tidytree,get_tree_data)

 importFrom(tidytree,groupClade)

 importFrom(tidytree,groupOTU)

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

+# ggtree 1.15.2

+

++ compatible with `tibble` v=2.0.0 (2018-11-29, Thu)

+

 # ggtree 1.15.1

 + now `revts` also reverse the `branch` column (2018-11-11, Sun)

@@ -25,8 +25,9 @@ set_branch_length <- function(tree_object, branch.length) {

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

     }

-    edge <- as_data_frame(phylo$edge)

+    edge <- phylo$edge

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

+    edge <- as_tibble(edge)

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

@@ -166,7 +167,7 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

 ## ## used by layoutEqualAngle

-## ## will change to tidytree::as_data_frame in future

+## ## will change to tidytree::as_tibble in future

 ## as.data.frame.phylo_ <- function(x, layout="rectangular",

 ##                                  branch.length="branch.length", ...) {

 ##     if (branch.length != 'none') {

@@ -4,7 +4,7 @@

 ##' @importFrom tibble data_frame

 ##' @importFrom dplyr full_join

 ##' @importFrom dplyr mutate_

-##' @importFrom tidytree as_data_frame

+##' @importFrom tidytree as_tibble

 ##' @method fortify phylo

 ##' @export

 fortify.phylo <- function(model, data,

@@ -42,7 +42,7 @@ fortify.phylo <- function(model, data,

         N <- Nnode(x, internal.only=FALSE)

         xypos <- data_frame(node=1:N, x=xpos, y=ypos)

-        df <- as_data_frame(model) %>%

+        df <- as_tibble(model) %>%

             mutate_(isTip = ~(! node %in% parent))

         res <- full_join(df, xypos, by = "node")

@@ -53,7 +53,7 @@ layoutEqualAngle <- function(model, branch.length ){

   root <- getRoot(tree)

   ## Convert Phylo tree to data.frame.

   ## df <- as.data.frame.phylo_(tree)

-  df <- as_data_frame(model) %>%

+  df <- as_tibble(model) %>%

       mutate_(isTip = ~(! node %in% parent))

     ## NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

@@ -672,13 +672,6 @@ getNodesBreadthFirst.df <- function(df){

-

-

-

-

-

-

-

 ##' convert tip or node label(s) to internal node number

 ##'

 ##'

@@ -4,12 +4,14 @@

 \alias{layoutDaylight}

 \title{Equal daylight layout method for unrooted trees.}

 \usage{

-layoutDaylight(model, branch.length)

+layoutDaylight(model, branch.length, MAX_COUNT = 5)

 }

 \arguments{

 \item{model}{tree object, e.g. phylo or treedata}

 \item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}

+

+\item{MAX_COUNT}{the maximum number of iterations to run (default 5)}

 }

 \value{

 tree as data.frame with equal angle layout.