Browse code

update docs;

Guangchuang Yu authored on 29/09/2022 03:42:03
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@@ -35,6 +35,7 @@ citEntry(
35 35
     number = "4",
36 36
     pages = "e56",
37 37
     doi = "10.1002/imt2.56",
38
+    url = "https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56",
38 39
     textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",
39 40
                         "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.",
40 41
                         "iMeta 2022, 4(1):e56. doi:10.1002/imt2.56")
Browse code

correct citation

Guangchuang Yu authored on 27/09/2022 02:00:01
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@@ -14,24 +14,6 @@ citEntry(
14 14
                         "Chapman and Hall/CRC. doi:10.1201/9781003279242")   
15 15
 )
16 16
 
17
-
18
-citEntry(
19
-    entry  = "article",
20
-    title = "Using ggtree to Visualize Data on Tree-Like Structures",
21
-    author = person("Guangchuang", "Yu"),
22
-    year = "2020",
23
-    journal = "Current Protocols in Bioinformatics",
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-    volume = "69",
25
-    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.",
31
-                        "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   
32
-)
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-
34
-
35 17
 citEntry(
36 18
     entry  = "article",
37 19
     title = "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data",
... ...
@@ -49,8 +31,8 @@ citEntry(
49 31
     ),
50 32
     year = "2022",
51 33
     journal = "iMeta",
52
-    volume = "4",
53
-    number = "1",
34
+    volume = "1",
35
+    number = "4",
54 36
     pages = "e56",
55 37
     doi = "10.1002/imt2.56",
56 38
     textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",
... ...
@@ -59,6 +41,23 @@ citEntry(
59 41
 )
60 42
 
61 43
 
44
+citEntry(
45
+    entry  = "article",
46
+    title = "Using ggtree to Visualize Data on Tree-Like Structures",
47
+    author = person("Guangchuang", "Yu"),
48
+    year = "2020",
49
+    journal = "Current Protocols in Bioinformatics",
50
+    volume = "69",
51
+    pages = "e96",
52
+    number = "1",
53
+    url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96",
54
+    doi = "10.1002/cpbi.96",
55
+    textVersion = paste("Guangchuang Yu.",
56
+                        "Using ggtree to visualize data on tree-like structures.",
57
+                        "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   
58
+)
59
+
60
+
62 61
 citEntry(
63 62
     entry  = "article",
64 63
     title  = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
Browse code

new citation

Guangchuang Yu authored on 26/09/2022 07:40:16
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@@ -14,6 +14,7 @@ citEntry(
14 14
                         "Chapman and Hall/CRC. doi:10.1201/9781003279242")   
15 15
 )
16 16
 
17
+
17 18
 citEntry(
18 19
     entry  = "article",
19 20
     title = "Using ggtree to Visualize Data on Tree-Like Structures",
... ...
@@ -30,6 +31,34 @@ citEntry(
30 31
                         "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   
31 32
 )
32 33
 
34
+
35
+citEntry(
36
+    entry  = "article",
37
+    title = "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data",
38
+    author = personList(
39
+        as.person("Shuangbin Xu"),
40
+        as.person("Lin Li"),
41
+        as.person("Xiao Luo"),
42
+        as.person("Meijun Chen"),
43
+        as.person("Wenli Tang"),
44
+        as.person("Li Zhan"),
45
+        as.person("Zehan Dai"),
46
+        as.person("Tommy T. Lam"),
47
+        as.person("Yi Guan"),
48
+        as.person("Guangchuang Yu")
49
+    ),
50
+    year = "2022",
51
+    journal = "iMeta",
52
+    volume = "4",
53
+    number = "1",
54
+    pages = "e56",
55
+    doi = "10.1002/imt2.56",
56
+    textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",
57
+                        "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.",
58
+                        "iMeta 2022, 4(1):e56. doi:10.1002/imt2.56")
59
+)
60
+
61
+
33 62
 citEntry(
34 63
     entry  = "article",
35 64
     title  = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
Browse code

update citation

Guangchuang Yu authored on 15/09/2022 03:05:22
Showing 1 changed files
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@@ -7,10 +7,11 @@ citEntry(
7 7
 	publisher = "Chapman and Hall/{CRC}",
8 8
     year = "2022",
9 9
 	edition = "1st edition",
10
+    doi = "10.1201/9781003279242",
10 11
     url = "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/",
11 12
     textVersion = paste("Guangchuang Yu. (2022).",
12 13
                         "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",
13
-                        "Chapman and Hall/CRC.")   
14
+                        "Chapman and Hall/CRC. doi:10.1201/9781003279242")   
14 15
 )
15 16
 
16 17
 citEntry(
Guangchuang Yu authored on 13/08/2022 09:59:31
Showing 1 changed files
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@@ -7,6 +7,7 @@ citEntry(
7 7
 	publisher = "Chapman and Hall/{CRC}",
8 8
     year = "2022",
9 9
 	edition = "1st edition",
10
+    url = "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/",
10 11
     textVersion = paste("Guangchuang Yu. (2022).",
11 12
                         "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",
12 13
                         "Chapman and Hall/CRC.")   
Browse code

update citation

Guangchuang Yu authored on 13/08/2022 09:45:00
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@@ -1,5 +1,17 @@
1 1
 citHeader("To cite ggtree in publications use:")
2 2
 
3
+citEntry(
4
+    entry  = "book",
5
+    title = "Data Integration, Manipulation and Visualization of Phylogenetic Treess",
6
+    author = person("Guangchuang", "Yu"),
7
+	publisher = "Chapman and Hall/{CRC}",
8
+    year = "2022",
9
+	edition = "1st edition",
10
+    textVersion = paste("Guangchuang Yu. (2022).",
11
+                        "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",
12
+                        "Chapman and Hall/CRC.")   
13
+)
14
+
3 15
 citEntry(
4 16
     entry  = "article",
5 17
     title = "Using ggtree to Visualize Data on Tree-Like Structures",
Browse code

update citation

Guangchuang Yu authored on 25/03/2020 13:51:45
Showing 1 changed files
... ...
@@ -60,6 +60,6 @@ citEntry(
60 60
     url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
61 61
     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
62 62
                         "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
63
-                        "Methods in Ecology and Evolution 2017, 8(1):28-36")
63
+                        "Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628")
64 64
 )
65 65
 
Browse code

new citation

Guangchuang Yu authored on 19/03/2020 13:18:33
Showing 1 changed files
... ...
@@ -2,26 +2,18 @@ citHeader("To cite ggtree in publications use:")
2 2
 
3 3
 citEntry(
4 4
     entry  = "article",
5
-    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
6
-    author = personList(
7
-        as.person("Guangchuang Yu"),
8
-        as.person("David Smith"),
9
-        as.person("Huachen Zhu"),
10
-        as.person("Yi Guan"),
11
-        as.person("Tommy Tsan-Yuk Lam")
12
-        ),
13
-    year    = "2017",
14
-    journal = "Methods in Ecology and Evolution",
15
-    volume  = "8",
16
-    issue   = "1",
17
-    number  = "",
18
-    pages   = "28-36",
19
-    doi     = "10.1111/2041-210X.12628",
20
-    PMID    = "",
21
-    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
22
-    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23
-        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
24
-        "Methods in Ecology and Evolution 2017, 8(1):28-36")
5
+    title = "Using ggtree to Visualize Data on Tree-Like Structures",
6
+    author = person("Guangchuang", "Yu"),
7
+    year = "2020",
8
+    journal = "Current Protocols in Bioinformatics",
9
+    volume = "69",
10
+    pages = "e96",
11
+    number = "1",
12
+    url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96",
13
+    doi = "10.1002/cpbi.96",
14
+    textVersion = paste("Guangchuang Yu.",
15
+                        "Using ggtree to visualize data on tree-like structures.",
16
+                        "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   
25 17
 )
26 18
 
27 19
 citEntry(
... ...
@@ -46,3 +38,28 @@ citEntry(
46 38
                         "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
47 39
                         "Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194")
48 40
 )
41
+
42
+citEntry(
43
+    entry  = "article",
44
+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
45
+    author = personList(
46
+        as.person("Guangchuang Yu"),
47
+        as.person("David Smith"),
48
+        as.person("Huachen Zhu"),
49
+        as.person("Yi Guan"),
50
+        as.person("Tommy Tsan-Yuk Lam")
51
+    ),
52
+    year    = "2017",
53
+    journal = "Methods in Ecology and Evolution",
54
+    volume  = "8",
55
+    issue   = "1",
56
+    number  = "",
57
+    pages   = "28-36",
58
+    doi     = "10.1111/2041-210X.12628",
59
+    PMID    = "",
60
+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
61
+    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
62
+                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
63
+                        "Methods in Ecology and Evolution 2017, 8(1):28-36")
64
+)
65
+
Browse code

geom_highlight

Guangchuang Yu authored on 08/01/2020 02:55:39
Showing 1 changed files
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@@ -41,7 +41,7 @@ citEntry(
41 41
     pages   = "3041-3043",
42 42
     doi     = "10.1093/molbev/msy194",
43 43
     PMID    = "",
44
-    url     = "https://doi.org/10.1093/molbev/msy194",
44
+    url     = "https://academic.oup.com/mbe/article/35/12/3041/5142656",
45 45
     textVersion = paste("Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",
46 46
                         "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
47 47
                         "Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194")
Browse code

update citation

Guangchuang Yu authored on 14/01/2019 06:41:18
Showing 1 changed files
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@@ -35,14 +35,14 @@ citEntry(
35 35
     ),
36 36
     year    = "2018",
37 37
     journal = "Molecular Biology and Evolution",
38
-    volume  = "",
39
-    issue   = "",
38
+    volume  = "35",
39
+    issue   = "2",
40 40
     number  = "",
41
-    pages   = "",
41
+    pages   = "3041-3043",
42 42
     doi     = "10.1093/molbev/msy194",
43 43
     PMID    = "",
44 44
     url     = "https://doi.org/10.1093/molbev/msy194",
45 45
     textVersion = paste("Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",
46 46
                         "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
47
-                        "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194")
47
+                        "Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194")
48 48
 )
Browse code

add citation

Guangchuang Yu authored on 24/10/2018 06:17:50
Showing 1 changed files
... ...
@@ -24,3 +24,25 @@ citEntry(
24 24
         "Methods in Ecology and Evolution 2017, 8(1):28-36")
25 25
 )
26 26
 
27
+citEntry(
28
+    entry  = "article",
29
+    title  = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
30
+    author = personList(
31
+        as.person("Guangchuang Yu"),
32
+        as.person("Tommy Tsan-Yuk Lam"),
33
+        as.person("Huachen Zhu"),
34
+        as.person("Yi Guan")
35
+    ),
36
+    year    = "2018",
37
+    journal = "Molecular Biology and Evolution",
38
+    volume  = "",
39
+    issue   = "",
40
+    number  = "",
41
+    pages   = "",
42
+    doi     = "10.1093/molbev/msy194",
43
+    PMID    = "",
44
+    url     = "https://doi.org/10.1093/molbev/msy194",
45
+    textVersion = paste("Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",
46
+                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
47
+                        "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194")
48
+)
Browse code

update citation

GuangchuangYu authored on 20/01/2017 05:21:52
Showing 1 changed files
... ...
@@ -10,17 +10,17 @@ citEntry(
10 10
         as.person("Yi Guan"),
11 11
         as.person("Tommy Tsan-Yuk Lam")
12 12
         ),
13
-    year    = "accepted",
13
+    year    = "2017",
14 14
     journal = "Methods in Ecology and Evolution",
15
-    volume  = "",
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-    issue   = "",
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+    volume  = "8",
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+    issue   = "1",
17 17
     number  = "",
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-    pages   = "",
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+    pages   = "28-36",
19 19
     doi     = "10.1111/2041-210X.12628",
20 20
     PMID    = "",
21
-    url     = "", 
21
+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", 
22 22
     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23 23
         "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
24
-        "Methods in Ecology and Evolution 2016 accepted, doi:10.1111/2041-210X.12628")
24
+        "Methods in Ecology and Evolution 2017, 8(1):28-36")
25 25
 )
26 26
 
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 1 changed files
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@@ -16,11 +16,11 @@ citEntry(
16 16
     issue   = "",
17 17
     number  = "",
18 18
     pages   = "",
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-    doi     = "",
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+    doi     = "10.1111/2041-210X.12628",
20 20
     PMID    = "",
21 21
     url     = "", 
22 22
     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23 23
         "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
24
-        "Methods in Ecology and Evolution revised")
24
+        "Methods in Ecology and Evolution 2016 accepted, doi:10.1111/2041-210X.12628")
25 25
 )
26 26
 
Browse code

update citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120063 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 12/08/2016 02:34:40
Showing 1 changed files
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@@ -10,7 +10,7 @@ citEntry(
10 10
         as.person("Yi Guan"),
11 11
         as.person("Tommy Tsan-Yuk Lam")
12 12
         ),
13
-    year    = "revised",
13
+    year    = "accepted",
14 14
     journal = "Methods in Ecology and Evolution",
15 15
     volume  = "",
16 16
     issue   = "",
Browse code

update citation info

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118925 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 24/06/2016 06:22:28
Showing 1 changed files
... ...
@@ -2,7 +2,7 @@ citHeader("To cite ggtree in publications use:")
2 2
 
3 3
 citEntry(
4 4
     entry  = "article",
5
-    title  = "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data",
5
+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
6 6
     author = personList(
7 7
         as.person("Guangchuang Yu"),
8 8
         as.person("David Smith"),
... ...
@@ -10,7 +10,7 @@ citEntry(
10 10
         as.person("Yi Guan"),
11 11
         as.person("Tommy Tsan-Yuk Lam")
12 12
         ),
13
-    year    = "submitted",
13
+    year    = "revised",
14 14
     journal = "Methods in Ecology and Evolution",
15 15
     volume  = "",
16 16
     issue   = "",
... ...
@@ -20,7 +20,7 @@ citEntry(
20 20
     PMID    = "",
21 21
     url     = "", 
22 22
     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23
-        "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.",
24
-        "Methods in Ecology and Evolution submitted")
23
+        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
24
+        "Methods in Ecology and Evolution revised")
25 25
 )
26 26
 
Browse code

update citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107495 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 17/08/2015 06:03:05
Showing 1 changed files
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@@ -2,12 +2,16 @@ citHeader("To cite ggtree in publications use:")
2 2
 
3 3
 citEntry(
4 4
     entry  = "article",
5
-    title  = "ggtree: an R package for versatile annotation and visualization of phylogenetic tree",
5
+    title  = "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data",
6 6
     author = personList(
7
-        as.person("Guangchuang Yu")
8
-    ),
9
-    year    = "2015",
10
-    journal = "in prepare",
7
+        as.person("Guangchuang Yu"),
8
+        as.person("David Smith"),
9
+        as.person("Huachen Zhu"),
10
+        as.person("Yi Guan"),
11
+        as.person("Tommy Tsan-Yuk Lam")
12
+        ),
13
+    year    = "submitted",
14
+    journal = "Methods in Ecology and Evolution",
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     volume  = "",
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     issue   = "",
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     number  = "",
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@@ -15,7 +19,8 @@ citEntry(
15 19
     doi     = "",
16 20
     PMID    = "",
17 21
     url     = "", 
18
-    textVersion =
19
-        "Guangchuang Yu. (2015) ggtree: an R package for versatile annotation and visualization of phylogenetic tree. in prepare"
22
+    textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23
+        "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.",
24
+        "Methods in Ecology and Evolution submitted")
20 25
 )
21 26
 
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: da67d3d9e80cc81a3be57a0fca3e6d329e01be0c

update citation



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@100793 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 18/03/2015 07:48:43
Showing 1 changed files
... ...
@@ -2,12 +2,12 @@ citHeader("To cite ggtree in publications use:")
2 2
 
3 3
 citEntry(
4 4
     entry  = "article",
5
-    title  = "ggtree: a phylogenetic tree viewer for different types of tree annotations",
5
+    title  = "ggtree: an R package for versatile annotation and visualization of phylogenetic tree",
6 6
     author = personList(
7 7
         as.person("Guangchuang Yu")
8 8
     ),
9 9
     year    = "2015",
10
-    journal = "submitted",
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+    journal = "in prepare",
11 11
     volume  = "",
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     issue   = "",
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     number  = "",
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@@ -16,6 +16,6 @@ citEntry(
16 16
     PMID    = "",
17 17
     url     = "", 
18 18
     textVersion =
19
-        "Guangchuang Yu. (2015) ggtree: a phylogenetic tree viewer for different types of tree annotations. submitted"
19
+        "Guangchuang Yu. (2015) ggtree: an R package for versatile annotation and visualization of phylogenetic tree. in prepare"
20 20
 )
21 21
 
Browse code

upgrade to 0.99.6

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@98386 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 16/01/2015 02:39:28
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+citHeader("To cite ggtree in publications use:")
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+
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+citEntry(
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+    entry  = "article",
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+    title  = "ggtree: a phylogenetic tree viewer for different types of tree annotations",
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+    author = personList(
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+        as.person("Guangchuang Yu")
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+    ),
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+    year    = "2015",
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+    journal = "submitted",
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+    volume  = "",
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+    issue   = "",
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+    number  = "",
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+    pages   = "",
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+    doi     = "",
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+    PMID    = "",
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+    url     = "", 
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+    textVersion =
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+        "Guangchuang Yu. (2015) ggtree: a phylogenetic tree viewer for different types of tree annotations. submitted"
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+)
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+