@@ -5,6 +5,12 @@

                   "For help: https://yulab-smu.github.io/treedata-book/", "\n\n")

     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",

+

+                       '\033[36m', '-', '\033[39m ',

+                       "Guangchuang Yu. ",

+                       "Using ggtree to visualize data on tree-like structures. ",

+                       "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",

+

                        '\033[36m', '-', '\033[39m ',

                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",

                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",

@@ -14,6 +20,7 @@

                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",

                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",

                        "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n"

+

                        )

     packageStartupMessage(paste0(msg, citation))

@@ -64,10 +64,11 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-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.

+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).

+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.

 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

-2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+3. __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*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

@@ -5,14 +5,14 @@

 <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>

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

-[![](https://img.shields.io/badge/release%20version-2.0.0-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/release%20version-2.0.2-green.svg)](https://www.bioconductor.org/packages/ggtree)

 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)

 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 <!--

 [![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)

 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -43,14 +43,17 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in

 published research, please cite the most appropriate paper(s) from this

 list:

-1.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

+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).

+2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

     methods for mapping and visualizing associated data on phylogeny

     using ggtree. ***Molecular Biology and Evolution***, 2018,

     35(2):3041-3043. doi:

     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

       - [Source code to produce Supplementary

         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

-2.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an

+3.  **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***. 2017, 8(1):28-36. doi:

@@ -2,26 +2,18 @@ citHeader("To cite ggtree in publications use:")

 citEntry(

     entry  = "article",

-    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

-    author = personList(

-        as.person("Guangchuang Yu"),

-        as.person("David Smith"),

-        as.person("Huachen Zhu"),

-        as.person("Yi Guan"),

-        as.person("Tommy Tsan-Yuk Lam")

-        ),

-    year    = "2017",

-    journal = "Methods in Ecology and Evolution",

-    volume  = "8",

-    issue   = "1",

-    number  = "",

-    pages   = "28-36",

-    doi     = "10.1111/2041-210X.12628",

-    PMID    = "",

-    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 

-    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",

-        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

-        "Methods in Ecology and Evolution 2017, 8(1):28-36")

+    title = "Using ggtree to Visualize Data on Tree-Like Structures",

+    author = person("Guangchuang", "Yu"),

+    year = "2020",

+    journal = "Current Protocols in Bioinformatics",

+    volume = "69",

+    pages = "e96",

+    number = "1",

+    url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96",

+    doi = "10.1002/cpbi.96",

+    textVersion = paste("Guangchuang Yu.",

+                        "Using ggtree to visualize data on tree-like structures.",

+                        "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   

 )

 citEntry(

@@ -46,3 +38,28 @@ citEntry(

                         "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",

                         "Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194")

 )

+

+citEntry(

+    entry  = "article",

+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

+    author = personList(

+        as.person("Guangchuang Yu"),

+        as.person("David Smith"),

+        as.person("Huachen Zhu"),

+        as.person("Yi Guan"),

+        as.person("Tommy Tsan-Yuk Lam")

+    ),

+    year    = "2017",

+    journal = "Methods in Ecology and Evolution",

+    volume  = "8",

+    issue   = "1",

+    number  = "",

+    pages   = "28-36",

+    doi     = "10.1111/2041-210X.12628",

+    PMID    = "",

+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 

+    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",

+                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

+                        "Methods in Ecology and Evolution 2017, 8(1):28-36")

+)

+