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Commit id: 56b987ad918722a45f128d44c0da1bbeb3b86419

fixed typo

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-10 10:34:50 +0800
Author date: 2015-02-10 10:34:50 +0800


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@99299 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 10/02/2015 02:35:12
Showing 3 changed files

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@@ -1,7 +1,7 @@
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 Package: ggtree
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 Type: Package
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 Title: a phylogenetic tree viewer for different types of tree annotations
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-Version: 0.99.15
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+Version: 0.99.16
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 Author: Guangchuang Yu
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: ggtree extends the ggplot2 plotting system which implemented the
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@@ -1,3 +1,7 @@
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+CHANGES IN VERSION 0.99.16
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+------------------------
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+ o correct typo in vignette <2015-02-10, Tue>
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+
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 CHANGES IN VERSION 0.99.15
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 ------------------------
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  o fully support of replace operator, %<% <2015-02-09, Mon>
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@@ -117,7 +117,7 @@ tree2d <- read.beast(system.file("extdata", "twoD.tree", package="ggtree"))
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 ggtree(tree2d, layout="cladogram", yscale="NLGS")
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 ```
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-In this example, y is scale by the number of N-glycosylation sites. This figure demonstrates the number of N-glycosylation sites increase along the trunk. User can highlight the trunk with different line size or color.
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+In this example, y is scale by the number of N-glycosylation sites. This figure demonstrates the quantity of y increase along the trunk. User can highlight the trunk with different line size or color using the functions we described below.
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 ## support multiple phylogenetic classes
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@@ -125,7 +125,7 @@ In this example, y is scale by the number of N-glycosylation sites. This figure
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 `r Githubpkg("GuangchuangYu/ggtree")` defined several S4 classes to store phylogenetic object and its associated annotation, including:
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 + `jplace`
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-+ `palm_rst`
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++ `paml_rst`
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 + `codeml_mlc`
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 + `codeml`
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 + `hyphy`
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@@ -221,7 +221,7 @@ In `r Githubpkg("GuangchuangYu/ggtree")`, we implemented several functions to pa
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 Classes include:
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-+ _`palm_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_.
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++ _`paml_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_.
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 + _`codeml_mlc`_ for _`mlc`_ file obtained by _`CODEML`_.
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 + _`codeml`_ for interpreting _`rst`_ and _`mlc`_ files obtained by _`CODEML`_.
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 + _`hyphy`_ for [HYPHY](http://hyphy.org/w/index.php/Main_Page)[@pond_hyphy_2005] output.