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update docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122813 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 19/10/2016 12:23:24
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 .git
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 .Rhistory
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 R/.Rhistory
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-Makefile
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 TODO.md
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 appveyor.yml
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 .travis.yml
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-README.Rmd
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 docs
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 mkdocs
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new file mode 100644
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+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
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+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
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+PKGSRC  := $(shell basename `pwd`)
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+
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+all: rd readme check clean
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+
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+alldocs: rd readme mkdocs
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+
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+rd:
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+	Rscript -e 'roxygen2::roxygenise(".")'
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+
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+readme:
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+	Rscript -e 'rmarkdown::render("README.Rmd")'
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+
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+build:
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+	cd ..;\
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+	R CMD build $(PKGSRC)
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+
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+build2:
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+	cd ..;\
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+	R CMD build --no-build-vignettes $(PKGSRC)
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+
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+install:
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+	cd ..;\
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+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
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+
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+check: build
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+	cd ..;\
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+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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+
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+check2: build
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+	cd ..;\
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+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
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+
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+bioccheck:
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+	cd ..;\
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+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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+
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+clean:
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+	cd ..;\
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+	$(RM) -r $(PKGNAME).Rcheck/
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+
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+site: mkdocs
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+
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+mkdocs: mdfiles
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+	cd mkdocs;\
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+	mkdocs build;\
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+	cd ../docs;\
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+	rm -rf fonts;\
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+	rm -rf css/font-awesome*
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+
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+mdfiles:
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+	cd mkdocs;\
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+	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
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+	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
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+	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
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+	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
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+	cd docs;\
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+	ln -f -s ../mysoftware/* ./
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+
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+
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+svnignore:
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+	svn propset svn:ignore -F .svnignore .
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+
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+svncommit:
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+	git checkout devel;\
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+	git svn rebase;\
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+	git merge master --log;\
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+	git svn dcommit;\
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+	git push -u origin devel;\
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+	git checkout master;\
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+	git merge devel
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+---
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+output:
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+  md_document:
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+    variant: markdown_github
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+html_preview: false
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+---
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+
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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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+```{r echo=FALSE, results="hide", message=FALSE}
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+library("txtplot")
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+library("ypages")
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+```
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+
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+`r badge_release("ggtree", "green")`
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+`r badge_devel("ggtree", "green")`
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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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+`r badge_download("ggtree", "total", "blue")`
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+`r badge_download("ggtree", "month", "blue")`
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+
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+
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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)
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+[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)
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+[![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+
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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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+[![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)
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+[![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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+[![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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+
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+
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+
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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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+
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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=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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+
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+-----------------------------------------------------
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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^\*^. 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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+`r badge_doi("10.1111/2041-210X.12628", "green")`
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+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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+`r badge_altmetric("10533079", "green")`
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+
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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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++ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
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++ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
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+
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+### Citation
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+
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+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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+
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+
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+```{r echo=F, comment=NA}
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+d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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+txtplot(d$year, d$cites, xlim=c(2015, 2017))
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+```
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+
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+### Download stats
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+
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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+`r badge_download("ggtree", "total", "blue")`
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+`r badge_download("ggtree", "month", "blue")`
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+
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+
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+```{r echo=F, comment=NA}
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+x <- dlstats::bioc_stats("ggtree")
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+x <- x[-nrow(x), ] # last month data is not complete
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+txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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+```
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+
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+
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+
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+
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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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 ===========================================================================================================================
3 3
 
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-[![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-1.7.0-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-15283/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)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.0-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-15413/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)
5 5
 
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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--10--18-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)
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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--10--19-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)
7 7
 
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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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@@ -17,7 +17,7 @@ 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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-[![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-195-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![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-248-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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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-15283/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)
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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-15413/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)
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          +-------------------------+------------------------+-------------------------+----------------+
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          |                                                                                         *   |