@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 0.99.15

+Version: 0.99.16

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 0.99.16

+------------------------

+ o correct typo in vignette <2015-02-10, Tue>

+

 CHANGES IN VERSION 0.99.15

 ------------------------

  o fully support of replace operator, %<% <2015-02-09, Mon>

@@ -117,7 +117,7 @@ tree2d <- read.beast(system.file("extdata", "twoD.tree", package="ggtree"))

 ggtree(tree2d, layout="cladogram", yscale="NLGS")

 ```

-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.

+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.

 ## support multiple phylogenetic classes

@@ -125,7 +125,7 @@ In this example, y is scale by the number of N-glycosylation sites. This figure

 `r Githubpkg("GuangchuangYu/ggtree")` defined several S4 classes to store phylogenetic object and its associated annotation, including:

 + `jplace`

-+ `palm_rst`

++ `paml_rst`

 + `codeml_mlc`

 + `codeml`

 + `hyphy`

@@ -221,7 +221,7 @@ In `r Githubpkg("GuangchuangYu/ggtree")`, we implemented several functions to pa

 Classes include:

-+ _`palm_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_.

++ _`paml_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_.

 + _`codeml_mlc`_ for _`mlc`_ file obtained by _`CODEML`_.

 + _`codeml`_ for interpreting _`rst`_ and _`mlc`_ files obtained by _`CODEML`_.

 + _`hyphy`_ for [HYPHY](http://hyphy.org/w/index.php/Main_Page)[@pond_hyphy_2005] output.