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update docs

guangchuang yu authored on 22/08/2017 06:08:09
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@@ -2,7 +2,7 @@ Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with
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     their covariates and other associated data
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-Version: 1.9.3
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+Version: 1.9.4
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 Authors@R: c(
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 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
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@@ -46,7 +46,9 @@ clean:
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 site:
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 	cd site_src;\
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+	ln -s ../../software/themes themes;\
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 	Rscript -e 'blogdown::build_site()';\
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+	rm themes;\
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 	cd ..
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 preview:
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@@ -1,3 +1,7 @@
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+CHANGES IN VERSION 1.9.4
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+------------------------
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+ o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue>
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+
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 CHANGES IN VERSION 1.9.3
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 ------------------------
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  o update to using !! in tidyr::gather for compatible with tidyr 0.7.0 <2017-08-03, Thu>
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>Documentation - ggtree</title>
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>FAQ - ggtree</title>
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>Featured Articles - ggtree</title>
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-    <meta name="generator" content="Hugo 0.21" />
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>Gallery - ggtree</title>
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>ggtree</title>
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-    <meta name="generator" content="Hugo 0.21" />
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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@@ -345,7 +345,7 @@
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 				<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-18017/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-834/month-blue.svg?style=flat" /></a></p>
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+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18100/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-834/month-blue.svg?style=flat" alt="month" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
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 <div id="authors" class="section level2">
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 <h2><i class="fa fa-user"></i> Authors</h2>
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 <div id="citation" class="section level2">
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 <h2><i class="fa fa-book"></i> Citation</h2>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-31-blue.svg?style=flat" alt="citation" /></a></p>
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+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-34-blue.svg?style=flat" alt="citation" /></a></p>
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 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
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 </div>
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 <div id="featured-articles" class="section level2">
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@@ -78,9 +78,10 @@ http://dx.doi.org/10.1111/2041-210X.12628
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       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
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       <description>Leave me a message on 
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-Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
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-&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
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-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</description>
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+The ggtree package looks like a cool way to visualize hierarchical datahttps://t.co/spsqLkqeVG pic.twitter.com/GRODlrBahW
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+&amp;mdash; lobrowR (@lobrowR) August 21, 2017 New ggtree-based visualization in R package phylofactor! Below are the top three factors (= 4 bins) of mammalian body mass. pic.twitter.com/ruT4OZF7gW
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+&amp;mdash; Alex Washburne (@alex_washburne) August 19, 2017 Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
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+&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.</description>
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     </item>
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   </channel>
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     <meta name="viewport" content="width=device-width,user-scalable=no,initial-scale=1,maximum-scale=1">
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     <meta http-equiv="X-UA-Compatible" content="IE=10" />
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     <title>Tweets - ggtree</title>
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-    <meta name="generator" content="Hugo 0.21" />
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+    <meta name="generator" content="Hugo 0.24.1" />
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     <meta name="description" content="Visualization and annotation of phylogenetic trees.">
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
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-<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Possible to combine <a href="https://twitter.com/hashtag/ggjoy?src=hash">#ggjoy</a> with <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> ? My gg-fu is weak. <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/DataViz?src=hash">#DataViz</a> <a href="https://twitter.com/hashtag/JoyPlot?src=hash">#JoyPlot</a> <a href="https://t.co/4FICfER6Oa">https://t.co/4FICfER6Oa</a></p>&mdash; Libby Megna (@LibbyMegna) <a href="https://twitter.com/LibbyMegna/status/891144389715783680">July 29, 2017</a></blockquote>
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+<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">The ggtree package looks like a cool way to visualize hierarchical data<a href="https://t.co/spsqLkqeVG">https://t.co/spsqLkqeVG</a> <a href="https://t.co/GRODlrBahW">pic.twitter.com/GRODlrBahW</a></p>&mdash; lobrowR (@lobrowR) <a href="https://twitter.com/lobrowR/status/899635001247059969">August 21, 2017</a></blockquote>
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+<script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">New ggtree-based visualization in R package phylofactor! Below are the top three factors (= 4 bins) of mammalian body mass. <a href="https://t.co/ruT4OZF7gW">pic.twitter.com/ruT4OZF7gW</a></p>&mdash; Alex Washburne (@alex_washburne) <a href="https://twitter.com/alex_washburne/status/898729425168080897">August 19, 2017</a></blockquote>
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+<script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Possible to combine <a href="https://twitter.com/hashtag/ggjoy?src=hash">#ggjoy</a> with <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> ? My gg-fu is weak. <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/DataViz?src=hash">#DataViz</a> <a href="https://twitter.com/hashtag/JoyPlot?src=hash">#JoyPlot</a> <a href="https://t.co/4FICfER6Oa">https://t.co/4FICfER6Oa</a></p>&mdash; Libby Megna (@LibbyMegna) <a href="https://twitter.com/LibbyMegna/status/891144389715783680">July 29, 2017</a></blockquote>
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 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Second post with an update on how to add tip shapes and colours to ggtree <a href="https://t.co/ezWF4TVQst">https://t.co/ezWF4TVQst</a></p>&mdash; Anthony Underwood (@bioinformAnt) <a href="https://twitter.com/bioinformAnt/status/883301626022375424">July 7, 2017</a></blockquote>
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 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Yes and no. No manual assignment =&gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</p>&mdash; Anthony Underwood (@bioinformAnt) <a href="https://twitter.com/bioinformAnt/status/883246854695256064">July 7, 2017</a></blockquote>
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 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I&#39;d use ggtree from Bioconductor as you can really tailor all the fonts etc..<a href="https://t.co/NAcbFswGYB">https://t.co/NAcbFswGYB</a></p>&mdash; Susan Holmes (@SherlockpHolmes) <a href="https://twitter.com/SherlockpHolmes/status/877576023109390336">June 21, 2017</a></blockquote>
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       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
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       <description>Leave me a message on 
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-Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
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-&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
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-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</description>
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+The ggtree package looks like a cool way to visualize hierarchical datahttps://t.co/spsqLkqeVG pic.twitter.com/GRODlrBahW
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+&amp;mdash; lobrowR (@lobrowR) August 21, 2017 New ggtree-based visualization in R package phylofactor! Below are the top three factors (= 4 bins) of mammalian body mass. pic.twitter.com/ruT4OZF7gW
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+&amp;mdash; Alex Washburne (@alex_washburne) August 19, 2017 Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
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+&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.</description>
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     </item>
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   </channel>
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 relativeurls = true
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+ignoreFiles = ["\\.Rmd$", "\\.rmd$", "\\.Rmarkdown$", "_files$", "_cache$"]
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+
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 [params]
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 	# General information
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 	author = "Guangchuang Yu"
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-18017/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-834/month-blue.svg?style=flat" /></a></p>
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+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.2-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-18100/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-834/month-blue.svg?style=flat" alt="month" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
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 <div id="authors" class="section level2">
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 <h2><i class="fa fa-user"></i> Authors</h2>
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 <div id="citation" class="section level2">
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 <h2><i class="fa fa-book"></i> Citation</h2>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-31-blue.svg?style=flat" alt="citation" /></a></p>
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+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-34-blue.svg?style=flat" alt="citation" /></a></p>
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 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
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 </div>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
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-<p>{{% tweet 891144389715783680 %}}{{% tweet 883301626022375424 %}}{{% tweet 883246854695256064 %}}{{% tweet 877576023109390336 %}}{{% tweet 875594411584782337 %}}{{% tweet 871775262152810496 %}}{{% tweet 867408666852511744 %}}{{% tweet 857665638600507393 %}}{{% tweet 840181267542994944 %}}{{% tweet 839831849736232962 %}}{{% tweet 830023569887391744 %}}{{% tweet 829398997735313408 %}}{{% tweet 824264788456984576 %}}{{% tweet 822383911258890242 %}}{{% tweet 811666431452450816 %}}{{% tweet 811661275889549312 %}}{{% tweet 797041236867686400 %}}{{% tweet 797037016403820546 %}}{{% tweet 794278716859879424 %}}{{% tweet 831952966701678592 %}}{{% tweet 788751417746059264 %}}{{% tweet 693123105707986944 %}}{{% tweet 691762302492790788 %}}{{% tweet 687933344219312128 %}}{{% tweet 684411780412526592 %}}{{% tweet 665188011047563268 %}}{{% tweet 664040586001915904 %}}{{% tweet 639507420054749184 %}}{{% tweet 671673570259509248 %}}{{% tweet 667490462693912576 %}}{{% tweet 660278158663401473 %}}{{% tweet 641251456595685376 %}}{{% tweet 559734740488818688 %}}{{% tweet 559762891478667264 %}}{{% tweet 561514846291001344 %}}{{% tweet 559542705663905793 %}}{{% tweet 561056244782227456 %}}{{% tweet 664085841766195200 %}}{{% tweet 664431087683260416 %}}{{% tweet 667706456045694976 %}}{{% tweet 663937183791759360 %}}{{% tweet 663771499589861376 %}}{{% tweet 667433534756397057 %}}{{% tweet 640573716733169664 %}}{{% tweet 664407764001779712 %}}{{% tweet 630500659960254464 %}}{{% tweet 547497335412899840 %}}{{% tweet 610364467939913728 %}}</p>
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