@@ -1,8 +1,9 @@

 CHANGES IN VERSION 1.5.16

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

+ o fixed aes mapping in geom_strip <2016-10-11, Tue>

  o fixed R check <2016-10-10, Mon>

    + check.aes parameter is not available in release version of ggplot2 yet

- 

+

 CHANGES IN VERSION 1.5.15

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

  o check.aes for layers defined in ggtree <2016-10-07, Fri>

@@ -1,6 +1,6 @@

 ##' bar of range (HPD, range etc) to present uncertainty of evolutionary inference

 ##'

-##' 

+##'

 ##' @title geom_range

 ##' @param range range, e.g. "height_0.95_HPD"

 ##' @param ... additional parameter, e.g. color, size, alpha

@@ -12,12 +12,12 @@ geom_range <- function(range="height_0.95_HPD", ...) {

     position = "identity"

     show.legend = NA

     na.rm = TRUE

-    inherit.aes = FALSE    

+    inherit.aes = FALSE

     default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y)

-    

+

     mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range))

-        

+

     layer(

         stat = StatRange,

         mapping = mapping,

@@ -26,15 +26,16 @@ geom_range <- function(range="height_0.95_HPD", ...) {

         position = position,

         show.legend=show.legend,

         inherit.aes = inherit.aes,

-        params = list(na.rm = na.rm, ...)

+        params = list(na.rm = na.rm, ...),

+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

     )

-    

+

 }

 StatRange <- ggproto("StatRange", Stat,

                      compute_group = function(self, data, scales, params) {

                          ## label is actually the range

-                         

+

                          df <- data[!is.na(data[,"label"]),]

                          rr <- gsub("\\[", "", df[,"label"])

                          rr <- gsub("\\]", "", rr)

@@ -1,6 +1,6 @@

 ##' annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label

 ##'

-##' 

+##'

 ##' @title geom_strip

 ##' @param taxa1 taxa1

 ##' @param taxa2 taxa2

@@ -34,14 +34,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,

                                size=barsize, barextend=barextend,

-                               mapping=mapping, data=data, 

+                               mapping=mapping, data=data,

                                position=position, show.legend = show.legend,

                                inherit.aes = inherit.aes, na.rm=na.rm, ...)

     if (is.na(label) || is.null(label)) {

         return(layer_bar)

     }

-    

+

     if (geom == "text") {

         ## no fill parameter

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

@@ -49,7 +49,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

-        

+

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

                                     align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

@@ -57,7 +57,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     }

-    

+

     list(

         layer_bar,

         layer_text

@@ -75,13 +75,13 @@ stat_stripText <- function(mapping=NULL, data=NULL,

     } else {

         default_aes <- aes_(x=~x, y=~y, node=~node)

     }

-    

+

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

         mapping <- modifyList(mapping, default_aes)

     }

-    

+

     layer(stat=StatStripText,

           data=data,

           mapping=mapping,

@@ -100,7 +100,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       ...),

           if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

           )

-    

+

 }

 stat_stripBar <- function(mapping=NULL, data=NULL,

@@ -111,7 +111,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

     if (is.null(label) || is.na(label)) {

         default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)

     } else {

-        default_aes <- aes_(x=~x, y=~y, node=~node)

+        default_aes <- aes_(x=~x, y=~y, node=~node, xend=~x, yend=~y)

     }

     if (is.null(mapping)) {

@@ -119,7 +119,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

     } else {

         mapping <- modifyList(mapping, default_aes)

     }

-    

+

     layer(stat=StatStripBar,

           data=data,

           mapping=mapping,

@@ -150,8 +150,8 @@ StatStripText <- ggproto("StatStripText", Stat,

                          required_aes = c("x", "y", "label")

                          )

-                         

-                          

+

+

 StatStripBar <- ggproto("StatStripBar", Stat,

                         compute_group = function(self, data, scales, params,

                                                  taxa1, taxa2, offset, align, barextend) {

@@ -193,7 +193,7 @@ taxa2node <- function(data, taxa) {

     if (length(idx) == 0) {

         stop("input taxa is not valid...")

     }

-    

+

     return(data$node[idx])

 }

@@ -1,6 +1,6 @@

 ##' link between taxa

 ##'

-##' 

+##'

 ##' @title geom_taxalink

 ##' @param taxa1 taxa1, can be label or node number

 ##' @param taxa2 taxa2, can be label or node number

@@ -16,12 +16,13 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {

     position = "identity"

     show.legend = NA

     na.rm = TRUE

-    inherit.aes = FALSE    

+    inherit.aes = FALSE

     mapping <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)

     layer(stat=StatTaxalink,

           mapping=mapping,

+          data = NULL,

           geom=GeomCurve,

           position='identity',

           show.legend=show.legend,

@@ -42,12 +43,12 @@ StatTaxalink <- ggproto("StatTaxalink", Stat,

                             node2 <- taxa2node(data, taxa2)

                             x <- data$x

                             y <- data$y

-                            

+

                             data.frame(x = x[node1],

                                        xend = x[node2],

                                        y = y[node1],

                                        yend = y[node2])

-                            

+

                         },

                         required_aes = c("x", "y", "xend", "yend")

                         )

@@ -3,7 +3,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 [![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.16-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--11-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-171-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-125-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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