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

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.5.4

+Version: 1.5.5

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,5 +1,12 @@

+CHANGES IN VERSION 1.5.5

+------------------------

+ o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>

+   + as.Date won't work for BCE time.

+   + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).

+ 

 CHANGES IN VERSION 1.5.4

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

+ o reroot method for raxml object <2016-05-22, Sun>

  o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>

  o bug fixed in collapse <2016-05-20, Fri>

    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly

@@ -1,3 +1,31 @@

+## not used.

+## we don't guess mrsd from tip labels

+## user should provide mrsd parameter in ggtree if they want to use time-scaled tree

+scaleX_by_time <- function(df, as.Date=FALSE) {

+    time <- with(df, gsub(".*[_/]{1}(\\d+\\.*\\d+)$", "\\1", label[isTip])) %>% as.numeric

+    latest <- which.max(time)

+

+    scaleX_by_time_from_mrsd(df, decimal2Date(time[latest]), as.Date)

+}

+

+

+scaleX_by_time_from_mrsd <- function(df, mrsd, as.Date) {

+    mrsd %<>% as.Date

+    date <- Date2decimal(mrsd)

+

+    df$x <- df$x + date - max(df$x)

+    df$branch <- (df[df$parent, "x"] + df[, "x"])/2

+

+    if (as.Date) {

+        df$x <- decimal2Date(df$x)

+        df$branch <- decimal2Date(df$branch)

+    }

+    

+    return(df)

+}

+

+

+

 ##' convert Date to decimal format, eg "2014-05-05" to "2014.34"

 ##'

 ##' 

@@ -289,17 +289,4 @@ add_pseudo_nodelabel <- function(phylo, treetext) {

 }

-##' @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]

-              

-              return(object)

-          })

-

@@ -211,26 +211,6 @@ fortify.beast <- function(model, data,

     append_extraInfo(df, model)

 }

-scaleX_by_time_from_mrsd <- function(df, mrsd) {

-    mrsd %<>% as.Date

-    date <- Date2decimal(mrsd)

-

-    df$x <- df$x + date - max(df$x)

-    df$branch <- (df[df$parent, "x"] + df[, "x"])/2

-    

-    df$x <- decimal2Date(df$x)

-    df$branch <- decimal2Date(df$branch)

-    return(df)

-

-}

-

-

-scaleX_by_time <- function(df) {

-    time <- with(df, gsub(".*[_/]{1}(\\d+\\.*\\d+)$", "\\1", label[isTip])) %>% as.numeric

-    latest <- which.max(time)

-

-    scaleX_by_time_from_mrsd(df, decimal2Date(time[latest]))

-}

 ##' @method fortify codeml

 ##' @export

@@ -499,11 +479,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

     }

     if (!is.null(mrsd)) {

-        df <- scaleX_by_time_from_mrsd(df, mrsd)

-        if (!as.Date) {

-            df$x <- Date2decimal(df$x)

-            df$branch <- Date2decimal(df$branch)

-        }

+        df <- scaleX_by_time_from_mrsd(df, mrsd, as.Date)

     }

     return(df)

 }

@@ -59,3 +59,9 @@ setMethod("get.tree", signature(object="phylip"),

           }

           )

+##' @rdname get.tree-methods

+##' @exportMethod get.tree

+setMethod("get.tree", signature(object="phylo"),

+          function(object, ...) {

+              return(object)

+          })

new file mode 100644

@@ -0,0 +1,50 @@

+

+##' @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]

+              

+              return(object)

+          })

+

+##' @rdname reroot-methods

+##' @exportMethod reroot

+setMethod("reroot", signature(object="raxml"),

+          function(object, node, ...) {

+              object@phylo <- reroot(object@phylo, node, ...)

+

+              node_map <- attr(object@phylo, "node_map")

+              idx <- match(object@bootstrap$node, node_map[,1])

+              object@bootstrap$node <- node_map[idx, 2]

+              

+              return(object)

+          })

+

+

+##' reroot a tree

+##'

+##' 

+##' @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)

+              

+              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)

+          })

+

@@ -24,6 +24,12 @@ setMethod("scale_color", signature(object="paml_rst"),

           })

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="phylo"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

 ##' add colorbar legend

deleted file mode 100644

@@ -1,42 +0,0 @@

-##' reroot a tree

-##'

-##' 

-##' @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)

-              

-              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)

-          })

-

-

-

-##' @rdname get.tree-methods

-##' @exportMethod get.tree

-setMethod("get.tree", signature(object="phylo"),

-          function(object, ...) {

-              return(object)

-          })

-

-##' @rdname scale_color-methods

-##' @exportMethod scale_color

-setMethod("scale_color", signature(object="phylo"),

-          function(object, by, ...) {

-              scale_color_(object, by, ...)

-          })

-

-

-

-

-

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/codeml_mlc.R, R/hyphy.R, R/method-get-tree.R, R/paml_rst.R, R/phangorn.R, R/phylo.R, R/r8s.R

+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/codeml_mlc.R, R/hyphy.R, R/method-get-tree.R, R/paml_rst.R, R/phangorn.R, R/r8s.R

 \docType{methods}

 \name{get.tree}

 \alias{get.tree}

@@ -38,12 +38,12 @@ get.tree(object, ...)

 \S4method{get.tree}{phylip}(object, ...)

+\S4method{get.tree}{phylo}(object, ...)

+

 \S4method{get.tree}{paml_rst}(object)

 \S4method{get.tree}{phangorn}(object, ...)

-\S4method{get.tree}{phylo}(object, ...)

-

 \S4method{get.tree}{r8s}(object, ...)

 }

 \arguments{

@@ -1,16 +1,19 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/phylo.R

+% Please edit documentation in R/AllGenerics.R, R/method-reroot.R

 \docType{methods}

 \name{reroot}

 \alias{reroot}

 \alias{reroot,beast-method}

 \alias{reroot,phylo-method}

+\alias{reroot,raxml-method}

 \title{reroot method}

 \usage{

 reroot(object, node, ...)

 \S4method{reroot}{beast}(object, node, ...)

+\S4method{reroot}{raxml}(object, node, ...)

+

 \S4method{reroot}{phylo}(object, node, ...)

 }

 \arguments{

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ape.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/method-scale-color.R, R/phangorn.R, R/phylo.R, R/r8s.R

+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ape.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/method-scale-color.R, R/phangorn.R, R/r8s.R

 \docType{methods}

 \name{scale_color}

 \alias{scale_color}

@@ -37,10 +37,10 @@ scale_color(object, by, ...)

 \S4method{scale_color}{paml_rst}(object, by, ...)

-\S4method{scale_color}{phangorn}(object, by, ...)

-

 \S4method{scale_color}{phylo}(object, by, ...)

+\S4method{scale_color}{phangorn}(object, by, ...)

+

 \S4method{scale_color}{r8s}(object, by = "bootstrap", tree = "TREE")

 }

 \arguments{