1. ggtree
  2. Commit 567ab02f452e2f8e9cd2fae4f54bd307ebc6592f
Browse code

citation info with doi

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120192 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 17/08/2016 05:42:13
Showing 7 changed files
DESCRIPTION
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 Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.10
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+Version: 1.5.11
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
NEWS
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+CHANGES IN VERSION 1.5.11
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+------------------------
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+ o bug fixed in geom_tiplab <2016-08-17, Wed>
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+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
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+ o update citation info, add doi. <2016-08-16, Tue>
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+
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 CHANGES IN VERSION 1.5.10
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 ------------------------
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  o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
R/geom_tiplab.R
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@@ -38,7 +38,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dott
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     if (align && (!is.na(linetype) && !is.null(linetype))) {
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         dot_mapping <- aes(xend=x+diff(range(x, na.rm=TRUE))/200, x=max(x, na.rm=TRUE), y=y, yend=y, subset=isTip)
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         if (!is.null(mapping)) {
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-            dot_mapping <- modifyList(mapping, dot_mapping)
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+            dot_mapping <- modifyList(dot_mapping, mapping)
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         }
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     }
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R/zzz.R
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new file mode 100644
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+.onAttach <- function(libname, pkgname) {
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+    ##	pkgVersion <- packageDescription(pkgname, fields="Version")
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+    msg <- paste0("If you use ggtree in published research, please cite:\n\n",
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+                  "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.\n",
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+                  "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.\n",
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+                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628\n\n")
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+    packageStartupMessage(msg)
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+}
README.md
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@@ -3,9 +3,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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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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-[![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--16-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)
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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--08--17-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)
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.16-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.10-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/)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.16-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.11-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/)
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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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 **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)
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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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 ### 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-12041/total-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/)
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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-12113/total-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/)
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+
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+    If you use ggtree in published research, please cite:
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+
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+    Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
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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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+    Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628
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          +---------------------------+---------------------------+----------------------------+--------+
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          |                                                                                    *        |
inst/CITATION
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     issue   = "",
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     number  = "",
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     pages   = "",
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-    doi     = "",
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+    doi     = "10.1111/2041-210X.12628",
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     PMID    = "",
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     url     = "",
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     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
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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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-        "Methods in Ecology and Evolution revised")
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+        "Methods in Ecology and Evolution 2016 accepted, doi:10.1111/2041-210X.12628")
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 )
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vignettes/ggtree.Rmd
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 # Citation
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 If you use `ggtree` in published research, please cite:
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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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+__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_. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)
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 # Introduction