@@ -50,7 +50,7 @@ ByteCompile: true

 Encoding: UTF-8

 License: Artistic-2.0

 URL: https://yulab-smu.github.io/treedata-book/

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

+BugReports: https://github.com/YuLab-SMU/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization

@@ -20,23 +20,26 @@ Biocpkg <- function (pkg) {

 ```

-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-

+<a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>

+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

+[![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)

+[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

 `r badge_bioc_release("ggtree", "green")`

 `r badge_devel("guangchuangyu/ggtree", "green")`

-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

-[![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)

-[![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-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+`r badge_bioc_download_rank("ggtree")`

+`r badge_bioc_download("ggtree", "total", "blue")`

+`r badge_bioc_download("ggtree", "month", "blue")`

+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

-

-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.

+```{r comment="", echo=FALSE, results='asis'}

+cat(packageDescription('ggtree')$Description)

+```

@@ -56,8 +59,6 @@ School of Basic Medical Sciences, Southern Medical University

 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

-

-

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

 1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

@@ -69,20 +70,6 @@ other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-

-<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>

-

-

-

-`r badge_download_bioc("ggtree")`

-`r badge_bioc_download("ggtree", "total", "blue")`

-`r badge_bioc_download("ggtree", "month", "blue")`

-

-

-<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>

-

-

-

 ## :sparkling_heart: Contributing

 We welcome any contributions! By participating in this project you agree to

@@ -2,24 +2,27 @@

 # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-

-[![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](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)

-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+<a href="https://github.com/YuLab-SMU/ggtree"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

 [![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)

+[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

+[![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)

+

 [![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-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

-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.

+‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the

+grammar of graphics. ‘ggtree’ is designed for visualization and

+annotation of phylogenetic trees with their covariates and other

+associated data.

 For details, please visit <https://yulab-smu.github.io/treedata-book/>.

@@ -27,8 +30,7 @@ For details, please visit <https://yulab-smu.github.io/treedata-book/>.

 Guangchuang YU

-School of Basic Medical Sciences, Southern Medical

-University

+School of Basic Medical Sciences, Southern Medical University

 <https://guangchuangyu.github.io>

@@ -53,14 +55,6 @@ list:

     Ecology and Evolution***. 2017, 8(1):28-36. doi:

     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>

-

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-

-<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>

-

 ## :sparkling\_heart: Contributing

 We welcome any contributions\! By participating in this project you