update to latest roxygen; use export not method and s3method; add som…

…e imports from ggplot2; rebuild documentation
gavinsimpson · Feb 25, 2015 · 0688ce2 · 0688ce2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ggvegan
 Type: Package
 Title: ggplot2 plots for vegan functions
-Version: 0.0-1
-Date: 20 April 2013
+Version: 0.0-2
+Date: 24 February 2015
 Depends:
     vegan,
     ggplot2

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,11 +1,20 @@
+# Generated by roxygen2 (4.1.0): do not edit by hand
+
 S3method(autoplot,cca)
 S3method(autoplot,metaMDS)
 S3method(autoplot,prc)
 S3method(fortify,cca)
 S3method(fortify,metaMDS)
 S3method(fortify,prc)
 importFrom(ggplot2,autoplot)
+importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,fortify)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
 importFrom(grid,arrow)
 importFrom(grid,unit)
 importFrom(reshape2,melt)

diff --git a/R/autoplot.cca.R b/R/autoplot.cca.R
@@ -33,11 +33,10 @@ if(getRversion() >= "2.15.1") {
 ##' @return Returns a ggplot object.
 ##' @author Gavin L. Simpson
 ##'
-##' @method autoplot cca
-##' @S3method autoplot cca
+##' @export
 ##'
 ##' @importFrom grid arrow unit
-##' @importFrom ggplot2 autoplot
+##' @importFrom ggplot2 autoplot ggplot geom_point geom_text geom_segment xlab ylab coord_fixed aes
 ##'
 ##' @examples
 ##' data(dune)

diff --git a/R/autoplot.metaMDS.R b/R/autoplot.metaMDS.R
@@ -31,8 +31,7 @@ if(getRversion() >= "2.15.1") {
 ##'
 ##' @author Gavin L. Simpson
 ##'
-##' @method autoplot metaMDS
-##' @S3method autoplot metaMDS
+##' @export
 ##'
 ##' @importFrom grid arrow unit
 ##' @importFrom ggplot2 autoplot

diff --git a/R/autoplot.prc.R b/R/autoplot.prc.R
@@ -33,8 +33,7 @@ if(getRversion() >= "2.15.1") {
 ##'
 ##' @author Gavin L. Simpson
 ##'
-##' @method autoplot prc
-##' @S3method autoplot prc
+##' @export
 ##'
 ##' @examples
 ##' data(pyrifos)

diff --git a/R/fortify.cca.R b/R/fortify.cca.R
@@ -17,8 +17,7 @@
 ##' The first two components are the axis scores.
 ##' @author Gavin L. Simpson
 ##'
-##' @method fortify cca
-##' @S3method fortify cca
+##' @export
 ##'
 ##' @importFrom ggplot2 fortify
 ##' @importFrom vegan scores

diff --git a/R/fortify.metaMDS.R b/R/fortify.metaMDS.R
@@ -17,8 +17,7 @@
 ##' The first two components are the axis scores.
 ##' @author Gavin L. Simpson
 ##'
-##' @method fortify metaMDS
-##' @S3method fortify metaMDS
+##' @export
 ##'
 ##' @importFrom ggplot2 fortify
 ##' @importFrom vegan scores

diff --git a/R/fortify.prc.R b/R/fortify.prc.R
@@ -23,8 +23,7 @@
 ##' in plotting.
 ##' @author Gavin L. Simpson
 ##'
-##' @method fortify prc
-##' @S3method fortify prc
+##' @export
 ##'
 ##' @importFrom ggplot2 fortify
 ##' @importFrom reshape2 melt

diff --git a/man/autoplot.cca.Rd b/man/autoplot.cca.Rd
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/autoplot.cca.R
 \name{autoplot.cca}
 \alias{autoplot.cca}
 \title{ggplot-based plot for objects of class \code{"cca"}}
@@ -7,34 +9,32 @@
   ...)
 }
 \arguments{
-  \item{object}{an object of class \code{"cca"}, the result
-  of a call to \code{\link[vegan]{cca}}.}
+\item{object}{an object of class \code{"cca"}, the result of a call
+to \code{\link[vegan]{cca}}.}
 
-  \item{geom}{character; which geoms to use for the layers.
-  Can be a vector of length equal to
-  \code{length(display)}, in which case the \emph{i}th
-  element of \code{type} refers to the \emph{i}th element
-  of \code{display}.}
+\item{geom}{character; which geoms to use for the layers. Can be a
+vector of length equal to \code{length(display)}, in which case the
+\emph{i}th element of \code{type} refers to the \emph{i}th element
+of \code{display}.}
 
-  \item{layers}{character; which scores to plot as layers}
+\item{layers}{character; which scores to plot as layers}
 
-  \item{xlab}{character; label for the x-axis}
+\item{ylab}{character; label for the y-axis}
 
-  \item{ylab}{character; label for the y-axis}
+\item{xlab}{character; label for the x-axis}
 
-  \item{const}{General scaling constant to \code{rda}
-  scores. See \code{\link[vegan]{plot.cca}} for details.}
+\item{const}{General scaling constant to \code{rda} scores. See
+\code{\link[vegan]{plot.cca}} for details.}
 
-  \item{...}{Additional arguments passed to
-  \code{\link{fortify.cca}}.}
+\item{...}{Additional arguments passed to \code{\link{fortify.cca}}.}
 }
 \value{
 Returns a ggplot object.
 }
 \description{
-Produces a multi-layer ggplot object representing the
-output of objects produced by \code{\link[vegan]{cca}},
-\code{\link[vegan]{rda}}, or \code{\link[vegan]{capscale}}.
+Produces a multi-layer ggplot object representing the output of
+objects produced by \code{\link[vegan]{cca}}, \code{\link[vegan]{rda}},
+or \code{\link[vegan]{capscale}}.
 }
 \details{
 TODO

diff --git a/man/autoplot.metaMDS.Rd b/man/autoplot.metaMDS.Rd
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/autoplot.metaMDS.R
 \name{autoplot.metaMDS}
 \alias{autoplot.metaMDS}
 \title{ggplot-based plot for objects of class \code{"metaMDS"}}
@@ -6,30 +8,28 @@
   layers = c("species", "sites"), ylab, xlab, ...)
 }
 \arguments{
-  \item{object}{an object of class \code{"metaMDS"}, the
-  result of a call to \code{\link[vegan]{metaMDS}}.}
+\item{object}{an object of class \code{"metaMDS"}, the result of a call
+to \code{\link[vegan]{metaMDS}}.}
 
-  \item{geom}{character; which geoms to use for the layers.
-  Can be a vector of length equal to
-  \code{length(display)}, in which case the \emph{i}th
-  element of \code{type} refers to the \emph{i}th element
-  of \code{display}.}
+\item{geom}{character; which geoms to use for the layers. Can be a
+vector of length equal to \code{length(display)}, in which case the
+\emph{i}th element of \code{type} refers to the \emph{i}th element
+of \code{display}.}
 
-  \item{layers}{character; which scores to plot as layers}
+\item{layers}{character; which scores to plot as layers}
 
-  \item{xlab}{character; label for the x-axis}
+\item{ylab}{character; label for the y-axis}
 
-  \item{ylab}{character; label for the y-axis}
+\item{xlab}{character; label for the x-axis}
 
-  \item{...}{Additional arguments passed to
-  \code{\link{fortify.metaMDS}}.}
+\item{...}{Additional arguments passed to \code{\link{fortify.metaMDS}}.}
 }
 \value{
 Returns a ggplot object.
 }
 \description{
-Produces a multi-layer ggplot object representing the
-output of objects produced by \code{\link[vegan]{metaMDS}}.
+Produces a multi-layer ggplot object representing the output of
+objects produced by \code{\link[vegan]{metaMDS}}.
 }
 \details{
 TODO

diff --git a/man/autoplot.prc.Rd b/man/autoplot.prc.Rd
@@ -1,37 +1,36 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/autoplot.prc.R
 \name{autoplot.prc}
 \alias{autoplot.prc}
 \title{ggplot-based plot for objects of class \code{"prc"}}
 \usage{
 \method{autoplot}{prc}(object, select, xlab, ylab, leg.pos = "top", ...)
 }
 \arguments{
-  \item{object}{an object inheriting from class
-  \code{"prc"}, the result of a call to
-  \code{\link[vegan]{prc}}.}
+\item{object}{an object inheriting from class \code{"prc"}, the
+result of a call to \code{\link[vegan]{prc}}.}
 
-  \item{select}{a logical vector where \code{TRUE} selects
-  and \code{FALSE} deselects species. Alternatively a
-  numeric vector that contains the indices selecting
-  species. Note that these are with respect to the original
-  species matrix, \strong{not} the fortified object.}
+\item{select}{a logical vector where \code{TRUE} selects and
+\code{FALSE} deselects species. Alternatively a numeric vector that
+contains the indices selecting species. Note that these are with
+respect to the original species matrix, \strong{not} the fortified
+object.}
 
-  \item{xlab}{character; label for the x-axis}
+\item{xlab}{character; label for the x-axis}
 
-  \item{ylab}{character; label for the y-axis}
+\item{ylab}{character; label for the y-axis}
 
-  \item{leg.pos}{character; position for the legend grob.
-  See argument \code{legend.position} in function
-  \code{\link[ggplot2]{theme}}.}
+\item{leg.pos}{character; position for the legend grob. See argument
+\code{legend.position} in function \code{\link[ggplot2]{theme}}.}
 
-  \item{...}{Additional arguments passed to
-  \code{\link{fortify.prc}}.}
+\item{...}{Additional arguments passed to \code{\link{fortify.prc}}.}
 }
 \value{
 Returns a ggplot object.
 }
 \description{
-Produces a multi-layer ggplot object representing the
-output of objects produced by \code{\link[vegan]{prc}}.
+Produces a multi-layer ggplot object representing the output of
+objects produced by \code{\link[vegan]{prc}}.
 }
 \details{
 TODO

diff --git a/man/fortify.cca.Rd b/man/fortify.cca.Rd
@@ -1,28 +1,28 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fortify.cca.R
 \name{fortify.cca}
 \alias{fortify.cca}
 \title{Fortify a \code{"cca"} object.}
 \usage{
 \method{fortify}{cca}(model, data, ...)
 }
 \arguments{
-  \item{model}{an object of class \code{"cca"}, the result
-  of a call to \code{\link[vegan]{cca}},
-  \code{\link[vegan]{rda}}, or
-  \code{\link[vegan]{capscale}}.}
+\item{model}{an object of class \code{"cca"}, the result of a call to
+\code{\link[vegan]{cca}}, \code{\link[vegan]{rda}}, or
+\code{\link[vegan]{capscale}}.}
 
-  \item{data}{currently ignored.}
+\item{data}{currently ignored.}
 
-  \item{...}{additional arguments passed to
-  \code{\link[vegan]{scores.cca}}.}
+\item{...}{additional arguments passed to \code{\link[vegan]{scores.cca}}.}
 }
 \value{
-A data frame in long format containing the ordination
-scores. The first two components are the axis scores.
+A data frame in long format containing the ordination scores.
+The first two components are the axis scores.
 }
 \description{
-Fortifies an object of class \code{"cca"} to produce a data
-frame of the selected axis scores in long format, suitable
-for plotting with \code{\link[ggplot2]{ggplot}}.
+Fortifies an object of class \code{"cca"} to produce a
+data frame of the selected axis scores in long format, suitable for
+plotting with \code{\link[ggplot2]{ggplot}}.
 }
 \details{
 TODO

diff --git a/man/fortify.metaMDS.Rd b/man/fortify.metaMDS.Rd
@@ -1,27 +1,28 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fortify.metaMDS.R
 \name{fortify.metaMDS}
 \alias{fortify.metaMDS}
 \title{Fortify a \code{"mataMDS"} object.}
 \usage{
 \method{fortify}{metaMDS}(model, data, ...)
 }
 \arguments{
-  \item{model}{an object of class \code{"metaMDS"}, the
-  result of a call to \code{\link[vegan]{metaMDS}}.}
+\item{model}{an object of class \code{"metaMDS"}, the result of a call
+to \code{\link[vegan]{metaMDS}}.}
 
-  \item{data}{currently ignored.}
+\item{data}{currently ignored.}
 
-  \item{...}{additional arguments passed to
-  \code{\link[vegan]{scores.metaMDS}}. Note you can't use
-  \code{display}.}
+\item{...}{additional arguments passed to
+\code{\link[vegan]{scores.metaMDS}}. Note you can't use \code{display}.}
 }
 \value{
-A data frame in long format containing the ordination
-scores. The first two components are the axis scores.
+A data frame in long format containing the ordination scores.
+The first two components are the axis scores.
 }
 \description{
 Fortifies an object of class \code{"metaMDS"} to produce a
-data frame of the selected axis scores in long format,
-suitable for plotting with \code{\link[ggplot2]{ggplot}}.
+data frame of the selected axis scores in long format, suitable for
+plotting with \code{\link[ggplot2]{ggplot}}.
 }
 \details{
 TODO

diff --git a/man/fortify.prc.Rd b/man/fortify.prc.Rd
@@ -1,36 +1,36 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fortify.prc.R
 \name{fortify.prc}
 \alias{fortify.prc}
 \title{Fortify a \code{"prc"} object}
 \usage{
 \method{fortify}{prc}(model, data, scaling = 3, axis = 1, ...)
 }
 \arguments{
-  \item{model}{an object of class \code{"prc"}, the result
-  of a call to \code{\link[vegan]{prc}}.}
+\item{model}{an object of class \code{"prc"}, the result of a call to
+\code{\link[vegan]{prc}}.}
 
-  \item{data}{currently ignored.}
+\item{data}{currently ignored.}
 
-  \item{scaling}{the desired scaling. See
-  \code{\link{scores.cca}} for details.}
+\item{scaling}{the desired scaling. See \code{\link{scores.cca}} for
+details.}
 
-  \item{axis}{numeric; which PRC axis to extract. Default
-  is \code{axis = 1}, which is the most generally useful
-  choice.}
+\item{axis}{numeric; which PRC axis to extract. Default is
+\code{axis = 1}, which is the most generally useful choice.}
 
-  \item{...}{additional arguments currently ignored.}
+\item{...}{additional arguments currently ignored.}
 }
 \value{
-A data frame in long format containing the ordination
-scores. The first three components are the \code{Time},
-\code{Treatment}, and associated \code{Response}. The last
-two components, \code{Score} and \code{Label} are an
-indictor factor and a label for the rows for use in
-plotting.
+A data frame in long format containing the ordination scores.
+The first three components are the \code{Time}, \code{Treatment}, and
+associated \code{Response}. The last two components, \code{Score} and
+\code{Label} are an indictor factor and a label for the rows for use
+in plotting.
 }
 \description{
-Fortifies an object of class \code{"prc"} to produce a data
-frame of the selected axis scores in long format, suitable
-for plotting with \code{\link[ggplot2]{ggplot}}.
+Fortifies an object of class \code{"prc"} to produce a
+data frame of the selected axis scores in long format, suitable for
+plotting with \code{\link[ggplot2]{ggplot}}.
 }
 \details{
 TODO