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update docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119974 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 09/08/2016 12:43:33
Showing 5 changed files

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@@ -4,3 +4,5 @@ appveyor.yml
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 .gitignore
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 .svnignore
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 Makefile
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+^appveyor\.yml$
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+README.Rmd
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@@ -5,3 +5,5 @@ Makefile
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 TODO.md
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 README.md
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 appveyor.yml
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+.travis.yml
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+README.Rmd
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@@ -1,34 +1,38 @@
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 ## reference: http://docs.travis-ci.com/user/languages/r/
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 language: r
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+r:
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+  - devel
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+  - bioc-devel
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+  
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+cache: packages
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 bioc_required: true
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+os:
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+  - linux
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+  - osx
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+
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+
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 apt_packages:
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   - libfftw3-dev
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-r_packages:
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-  - ape
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-  - phylobase
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-  - colorspace
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-  - grid
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-  - ggplot2
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-  - gridExtra
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-  - jsonlite
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-  - magrittr
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-  - reshape2
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-  - rmarkdown
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-  - testthat
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-  - knitr
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-bioc_packages:
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-  - Biostrings
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-  - EBImage
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-  - BiocStyle
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+env:
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+  global:
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+    - _R_CHECK_FORCE_SUGGESTS_=False
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+    - R_LIBS="http://cran.rstudio.com"
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+
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 after_failure:
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   - ./travis-tool.sh dump_logs
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-notifications:
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-  email:
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-    on_success: change
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-    on_failure: change
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+r_github_packages:
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+  - jimhester/covr
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+
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+after_success:
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+- Rscript -e 'library(covr); codecov()'
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+
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+## notifications:
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+##   email:
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+##     on_success: change
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+##     on_failure: change
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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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+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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+===========================================================================================================================
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-<!--[![Build Status](https://travis-ci.org/GuangchuangYu/ggtree.svg?branch=master)](https://travis-ci.org/GuangchuangYu/ggtree)
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-[![Build Status](https://ci.appveyor.com/api/projects/status/github/GuangchuangYu/ggtree?svg=true)](https://ci.appveyor.com/project/GuangchuangYu/ggtree/branch/master)-->
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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)
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-[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
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-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-[![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/)
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-[![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source)
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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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)
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+[![packageversion](https://img.shields.io/badge/Package%20version-1.5.7-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree/blob/master/DESCRIPTION) [![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/) [![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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-The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. 
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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--09-yellowgreen.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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-`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. 
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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`.
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+`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
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+
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+Please cite the following article when using `ggtree`:
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+
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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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+
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+------------------------------------------------------------------------
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 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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+
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+-   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
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+-   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
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+-   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
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+-   [Example](https://guangchuangyu.github.io/ggtree/featuredArticles/)
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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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@@ -1,29 +1,43 @@
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-environment:
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-  R_CHECK_ARGS: --no-manual
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+# DO NOT CHANGE the "init" and "install" sections below
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+# Download script file from GitHub
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 init:
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   ps: |
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         $ErrorActionPreference = "Stop"
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         Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
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         Import-Module '..\appveyor-tool.ps1'
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-  
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 install:
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   ps: Bootstrap
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+# Adapt as necessary starting from here
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+
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 build_script:
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+  - travis-tool.sh install_bioc BiocStyle Biostrings  
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   - travis-tool.sh install_deps
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-  - travis-tool.sh install_bioc BiocStyle Biostrings EBImage
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-##  - travis-tool.sh install_bioc_deps
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-  
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+
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 test_script:
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   - travis-tool.sh run_tests
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 on_failure:
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-  - travis-tool.sh dump_logs
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+  - 7z a failure.zip *.Rcheck\*
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+  - appveyor PushArtifact failure.zip
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+
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+artifacts:
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+  - path: '*.Rcheck\**\*.log'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.out'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.fail'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.Rout'
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+    name: Logs
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-notifications:
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-  email:
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-    on_success: change
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-    on_failure: change
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+  - path: '\*_*.tar.gz'
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+    name: Linux Package
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+  - path: '\*_*.zip'
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+    name: Windows Package