Browse code

new citation

Guangchuang Yu authored on 19/03/2020 13:18:33
Showing 4 changed files

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@@ -5,6 +5,12 @@
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                   "For help: https://yulab-smu.github.io/treedata-book/", "\n\n")
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     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
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+
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+                       '\033[36m', '-', '\033[39m ',
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+                       "Guangchuang Yu. ",
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+                       "Using ggtree to visualize data on tree-like structures. ",
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+                       "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",
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+
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                        '\033[36m', '-', '\033[39m ',
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                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
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                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
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@@ -14,6 +20,7 @@
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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 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n"
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+
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                        )
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     packageStartupMessage(paste0(msg, citation))
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@@ -64,10 +64,11 @@ School of Basic Medical Sciences, Southern Medical University
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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-1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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+1. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
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+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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+3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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 visualization and annotation of phylogenetic trees with their covariates and
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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@@ -5,14 +5,14 @@
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 <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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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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-[![](https://img.shields.io/badge/release%20version-2.0.0-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/release%20version-2.0.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
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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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 [![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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 [![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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 [![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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-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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 ` r badge_devel("guangchuangyu/ggtree", "green")`
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 ` r badge_bioc_download("ggtree", "total", "blue")`
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@@ -43,14 +43,17 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in
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 published research, please cite the most appropriate paper(s) from this
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 list:
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-1.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
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+1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
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+    ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
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+    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
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+2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
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     methods for mapping and visualizing associated data on phylogeny
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     using ggtree. ***Molecular Biology and Evolution***, 2018,
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     35(2):3041-3043. doi:
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     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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       - [Source code to produce Supplementary
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         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-2.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
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+3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
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     R package for visualization and annotation of phylogenetic trees
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     with their covariates and other associated data. ***Methods in
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     Ecology and Evolution***. 2017, 8(1):28-36. doi:
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@@ -2,26 +2,18 @@ citHeader("To cite ggtree in publications use:")
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 citEntry(
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     entry  = "article",
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-    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
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-    author = personList(
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-        as.person("Guangchuang Yu"),
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-        as.person("David Smith"),
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-        as.person("Huachen Zhu"),
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-        as.person("Yi Guan"),
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-        as.person("Tommy Tsan-Yuk Lam")
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-        ),
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-    year    = "2017",
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-    journal = "Methods in Ecology and Evolution",
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-    volume  = "8",
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-    issue   = "1",
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-    number  = "",
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-    pages   = "28-36",
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-    doi     = "10.1111/2041-210X.12628",
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-    PMID    = "",
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-    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
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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 2017, 8(1):28-36")
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+    title = "Using ggtree to Visualize Data on Tree-Like Structures",
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+    author = person("Guangchuang", "Yu"),
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+    year = "2020",
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+    journal = "Current Protocols in Bioinformatics",
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+    volume = "69",
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+    pages = "e96",
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+    number = "1",
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+    url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96",
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+    doi = "10.1002/cpbi.96",
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+    textVersion = paste("Guangchuang Yu.",
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+                        "Using ggtree to visualize data on tree-like structures.",
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+                        "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   
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 )
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 citEntry(
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@@ -46,3 +38,28 @@ citEntry(
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                         "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
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                         "Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194")
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 )
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+
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+citEntry(
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+    entry  = "article",
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+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
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+    author = personList(
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+        as.person("Guangchuang Yu"),
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+        as.person("David Smith"),
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+        as.person("Huachen Zhu"),
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+        as.person("Yi Guan"),
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+        as.person("Tommy Tsan-Yuk Lam")
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+    ),
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+    year    = "2017",
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+    journal = "Methods in Ecology and Evolution",
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+    volume  = "8",
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+    issue   = "1",
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+    number  = "",
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+    pages   = "28-36",
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+    doi     = "10.1111/2041-210X.12628",
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+    PMID    = "",
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+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
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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 2017, 8(1):28-36")
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+)
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+