1. ggtree
  2. Commit 5540ce8def27c2948df9ecc27ed865c2d452fb59
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update citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120063 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 12/08/2016 02:34:40
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DESCRIPTION
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 Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.8
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+Version: 1.5.9
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
NEWS
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+CHANGES IN VERSION 1.5.9
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+------------------------
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+ o update citation info <2016-08-12, Fri>
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+
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 CHANGES IN VERSION 1.5.8
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 ------------------------
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  o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
README.md
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 [![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)
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-[![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/branch/master/graph/badge.svg) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--08--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)
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+[![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--08--12-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.14-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.7-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.14-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.9-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
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+[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=https://guangchuangyu.github.io/ggtree)
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+
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 ------------------------------------------------------------------------
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 Please cite the following article when using `ggtree`:
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 **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*
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-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=https://guangchuangyu.github.io/ggtree)
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-
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 ------------------------------------------------------------------------
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 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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 -   [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
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 -   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
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-### Example
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-
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-[![](https://guangchuangyu.github.io/ggtree/featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg)](https://guangchuangyu.github.io/ggtree/featuredArticles/)
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-
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 ### Download stats
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-11940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![month](https://img.shields.io/badge/downloads-1091/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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          +---------------------------+---------------------------+----------------------------+--------+
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          |                                                                                    *        |
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     1200 +                                                                                             +
inst/CITATION
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         as.person("Yi Guan"),
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         as.person("Tommy Tsan-Yuk Lam")
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         ),
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-    year    = "revised",
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+    year    = "accepted",
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     journal = "Methods in Ecology and Evolution",
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     volume  = "",
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     issue   = "",
vignettes/ggtree.Rmd
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 # Citation
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 If you use `ggtree` in published research, please cite:
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-```
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-G Yu, D Smith, H Zhu, Y Guan, TTY Lam,
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-ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.
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-Methods in Ecology and Evolution, revised.
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-```
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+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_
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+
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 # Introduction
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