Browse code

readme

GuangchuangYu authored on 11/08/2016 10:13:34
Showing3 changed files

... ...
@@ -2,7 +2,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3
 PKGSRC  := $(shell basename `pwd`)
4 4
 
5
-all: check clean
5
+all: readme check clean
6 6
 
7 7
 docs:
8 8
 	Rscript -e 'roxygen2::roxygenise(".")'
... ...
@@ -14,7 +14,7 @@ html_preview: false
14 14
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
15 15
 
16 16
 [![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)
17
-[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)
17
+[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
18 18
 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
19 19
 [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source)
20 20
 [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) 
... ...
@@ -30,13 +30,15 @@ html_preview: false
30 30
 
31 31
 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. 
32 32
 
33
+[![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)
34
+
33 35
 -----------------------------------------------------
34 36
 
35 37
 Please cite the following article when using `ggtree`:
36 38
 
37 39
 __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_
38 40
 
39
-[![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)
41
+
40 42
 
41 43
 ----------------------------------------------------------------------------------------
42 44
 
... ...
@@ -54,6 +56,10 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
54 56
 
55 57
 ### Download stats
56 58
 
59
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
60
+[![total](https://img.shields.io/badge/downloads-`r sum(dlstats::bioc_stats("ggtree")$Nb_of_downloads)`/tatal-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/)
61
+[![month](https://img.shields.io/badge/downloads-`r x <- dlstats::bioc_stats("ggtree"); x$Nb_of_downloads[nrow(x)-1]`/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/)
62
+
57 63
 ```{r echo=F, comment=NA}
58 64
 x <- dlstats::bioc_stats("ggtree")
59 65
 x <- x[-nrow(x), ] # last month data is not complete
... ...
@@ -3,20 +3,20 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
3 3
 
4 4
 [![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)
5 5
 
6
-[![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)
6
+[![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--11-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)
7 7
 
8
-[![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/)
8
+[![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-1.5.8-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/)
9 9
 
10 10
 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.
11 11
 
12
+[![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)
13
+
12 14
 ------------------------------------------------------------------------
13 15
 
14 16
 Please cite the following article when using `ggtree`:
15 17
 
16 18
 **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*
17 19
 
18
-[![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)
19
-
20 20
 ------------------------------------------------------------------------
21 21
 
22 22
 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
... ...
@@ -32,6 +32,8 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
32 32
 
33 33
 ### Download stats
34 34
 
35
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-11940/tatal-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/)
36
+
35 37
          +---------------------------+---------------------------+----------------------------+--------+
36 38
          |                                                                                    *        |
37 39
     1200 +                                                                                             +