ggvegan is a package for the R statistical software and environment. It aims to implement ggplot-based versions of the plots produced by the vegan package. Initially, ggvegan will provide fortify
and autoplot
methods for objects created in vegan, with the aim of providing full replacement plots via autoplot
. The fortify
methods allow the data contained within objects created by vegan to be converted into a format suitable for use with ggplot
directly.
ggvegan is released under the GNU General Public Licence, version 2.
ggvegan uses the roxygen2 system to document package functions alongside the code itself.
ggvegan is very much alpha code at the moment. Comments and feedback on the approach taken are welcome, as are code contributions. See Design decisions below for two important areas for consideration
The autoplot
concept is somewhat poorly defined at the moment --- at least in public. I have taken it to mean that a full ggplot object is returned, which can then be augmented with additional layers and changes to the scales etc. This means that the aesthetics for the scores are hard-coded in the autoplot
methods. If you want greater control over these aesthetics, use fortify
to return the scores in a suitable format and build the plot up yourself. I hope to include at least one example of this, where applicable, in the help pages for each autoplot
method.
fortify
methods are supposed to return a data frame but this is not necessarily the most convenient representation for vegan's ordination objects where several data frames representing the various sets of ordination scores would be more natural. Currently, ggvegan follows the existing fortify
convention of returning a single data frame so returns the ordination scores in long format with variables Score
indicating the type of score and Label
the label/rowname for each score.
The first two components of the returned data frame are always named Dim1
and Dim2
; to which ordination axes/dimensions these refer is recorded in an attribute dimlabels
, which can be accessed via
attr(fobj, "dimlabels")
where fobj
is the object returned by fortify
.
A further design decision is that ggvegan fortify
methods for ordination objects will return all possible sets of scores and the set returned can not be chosen by the user. Instead, the sets of scores to be plotted should be chosen at the autoplot
stage.
The components returned for more specialised objects will invariably not be Dim1
and Dim2
. Such fortify()
methods will return suitable components. For example, fortify.prc()
returns components Time
, Treatment
, and Response
corresponding to the two-way factors defining the experiment and the regression coefficients on RDA axis 1 respectively.
The following autoplot
methods are currently available
autoplot.cca
--- for objects of classes"cca"
and"capscale"
autoplot.rda
--- for objects of class"rda"
autoplot.metaMDS
--- for objects of class"metaMDS"
autoplot.prc
--- for objects of class"prc"
autoplot.decorana
--- for objects of class"decorana"
(AKA DCA)
The following fortify
method are currently available
fortify.cca
--- for objects of classes"cca"
,"rda"
, and"capscale"
fortify.metaMDS
--- for objects of class"metaMDS"
fortify.prc
--- for objects of class"prc"
fortify.decorana
--- for objects of class"decorana"
(AKA DCA)
No binary packages are currently available for ggvegan. If you have the correct development tools you can compile the package yourself after downloading the source code from github. Once I work out how to link git with svn I'll start a project on R-forge which will host binary packages of ggvegan.
Finally, if you use Hadley Wickham's devtools package then you can install ggvegan directly from github using functions that devtools provides. To do this, install devtools from CRAN via
install.packages("devtools")
then run
devtools::install_github("gavinsimpson/ggvegan")