@@ -32,6 +32,7 @@ Suggests:

     scales,

     testthat

 VignetteBuilder: knitr

+ByteCompile: true

 License: Artistic-2.0

 URL: http://guangchuangyu.github.io/ggtree

 BugReports: https://github.com/GuangchuangYu/ggtree/issues

@@ -1,5 +1,7 @@

 CHANGES IN VERSION 1.5.4

 ------------------------

+ o use byte compiler <2016-05-18, Wed>

+ o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed> 

  o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106

 CHANGES IN VERSION 1.5.3

@@ -471,7 +471,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

     }

     if (! is.null(tree$edge.length)) {

-        if (any(is.na(tree$edge.length))) {

+        if (anyNA(tree$edge.length)) {

             warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...")

             tree$edge.length <- NULL

         }

@@ -16,7 +16,7 @@ reroot_node_mapping <- function(tree, tree2) {

         cc <- getChild(tree, ip)

         node2 <- node_map[cc,2]

-        if (any(is.na(node2))) {

+        if (anyNA(node2)) {

             node <- c(node, k)

             next

         }

@@ -341,7 +341,7 @@ getXcoord2 <- function(x, root, parent, child, len, start=0, rev=FALSE) {

     if (rev == TRUE) {

         direction <- -1

     }

-    while(any(is.na(x))) {

+    while(anyNA(x)) {

         idx <- which(parent %in% currentNode)

         newNode <- child[idx]

         x[newNode] <- x[parent[idx]]+len[idx] * direction

@@ -369,7 +369,7 @@ getXcoord_no_length <- function(tr) {

     child_list <- list()

     child_list[as.numeric(names(cl))] <- cl

-    while(any(is.na(x))) {

+    while(anyNA(x)) {

         idx <- match(currentNode, child)

         pNode <- parent[idx]

         ## child number table

@@ -450,7 +450,7 @@ getYcoord <- function(tr, step=1) {

     y[-tip.idx] <- NA

     currentNode <- 1:Ntip

-    while(any(is.na(y))) {

+    while(anyNA(y)) {

         pNode <- unique(parent[child %in% currentNode])

         ## piping of magrittr is slower than nested function call.

         ## pipeR is fastest, may consider to use pipeR

@@ -490,7 +490,7 @@ getYcoord_scale <- function(tr, df, yscale) {

     child <- edge[,2]

     currentNodes <- root

-    while(any(is.na(y))) {

+    while(anyNA(y)) {

         newNodes <- c()

         for (currentNode in currentNodes) {

             idx <- which(parent %in% currentNode)

@@ -564,7 +564,7 @@ getYcoord_scale2 <- function(tr, df, yscale) {

     child <- df[, "node"]

     currentNodes <- root

-    while(any(is.na(y))) {

+    while(anyNA(y)) {

         newNodes <- c()

         for (currentNode in currentNodes) {

             idx <- which(parent %in% currentNode)

@@ -594,7 +594,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {

     y <- df[, yscale]

-    if (any(is.na(y))) {

+    if (anyNA(y)) {

         warning("NA found in y scale mapping, all were setting to 0")

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

     }

@@ -674,7 +674,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {

     y <- df[, yscale]

-    if (any(is.na(y))) {

+    if (anyNA(y)) {

         warning("NA found in y scale mapping, all were setting to 0")

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

     }

@@ -753,7 +753,7 @@ set_branch_length <- function(tree_object, branch.length) {

 re_assign_ycoord_df <- function(df, currentNode) {

-    while(any(is.na(df$y))) {

+    while(anyNA(df$y)) {

         pNode <- with(df, parent[match(currentNode, node)]) %>% unique

         idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode)))

         newNode <- pNode[idx]