[Vegan-commits] r1681 - in pkg/vegan: man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 16 14:26:47 CEST 2011
Author: jarioksa
Date: 2011-07-16 14:26:47 +0200 (Sat, 16 Jul 2011)
New Revision: 1681
Added:
pkg/vegan/man/ordiarrows.Rd
Modified:
pkg/vegan/man/ordihull.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
split documentation of ordiarrows/segments/grid from ordihull/ellipse/spider/cluster
Added: pkg/vegan/man/ordiarrows.Rd
===================================================================
--- pkg/vegan/man/ordiarrows.Rd (rev 0)
+++ pkg/vegan/man/ordiarrows.Rd 2011-07-16 12:26:47 UTC (rev 1681)
@@ -0,0 +1,90 @@
+\name{ordiarrows}
+\alias{ordiarrows}
+\alias{ordisegments}
+\alias{ordigrid}
+
+\title{Add Arrows and Line Segments to Ordination Diagrams}
+
+\description{ Functions to add arrows, line segments, regular grids of
+ points. The ordination diagrams can be produced by \code{vegan}
+ \code{\link{plot.cca}}, \code{\link{plot.decorana}} or
+ \code{\link{ordiplot}}. }
+
+\usage{
+ordiarrows(ord, groups, levels, replicates, display = "sites",
+ show.groups, startmark, label = FALSE, ...)
+ordisegments(ord, groups, levels, replicates, display = "sites",
+ show.groups, label = FALSE, ...)
+ordigrid(ord, levels, replicates, display = "sites", lty = c(1,1),
+ col = c(1,1), lwd = c(1,1), ...)
+}
+
+\arguments{
+ \item{ord}{An ordination object or an \code{\link{ordiplot}} object. }
+ \item{groups}{Factor giving the groups for which the graphical item is
+ drawn. }
+ \item{levels, replicates}{Alternatively, regular
+ groups can be defined with arguments \code{levels} and
+ \code{replicates}, where \code{levels} gives the number of groups,
+ and \code{replicates} the number of successive items at the same
+ group.}
+ \item{display}{Item to displayed. }
+ \item{show.groups}{Show only given groups. This can be a vector, or
+ \code{TRUE} if you want to show items for which condition is
+ \code{TRUE}. This argument makes it possible to use different
+ colours and line types for groups. The default is to show all groups. }
+ \item{label}{Label the \code{groups} by their names. In
+ \code{ordiellipse}, \code{ordihull} and \code{ordispider} the the
+ group name is in the centroid of the object, in \code{ordiarrows}
+ in the start of the arrow, and in \code{ordisegments} at both
+ ends. \code{ordiellipse} and \code{ordihull} use standard
+ \code{\link{text}}, and others use \code{\link{ordilabel}}.}
+
+ \item{startmark}{plotting character used to mark the first item. The
+ default is to use no mark, and for instance, \code{startmark = 1}
+ will draw a circle. For other plotting characters, see \code{pch}
+ in \code{\link{points}}. }
+
+ \item{col}{Colour of lines in \code{ordigrid}. This argument is
+ also passed to other functions to change the colour of lines.}
+
+ \item{lty, lwd}{Line type, line width used for
+ \code{level}s and \code{replicate}s in \code{ordigrid}.}
+
+ \item{\dots}{Parameters passed to graphical functions such as
+ \code{\link{lines}}, \code{\link{segments}}, \code{\link{arrows}},
+ or to \code{\link{scores}} to select axes and scaling etc. }
+}
+
+\details{ Function \code{ordiarrows} draws \code{\link{arrows}} and
+ \code{ordisegments} draws line \code{\link{segments}} between
+ successive items in the groups. Function \code{ordigrid} draws line
+ \code{\link{segments}} both within the groups and for the
+ corresponding items among the groups. }
+
+\note{These functions add graphical items to ordination graph: You must
+ draw a graph first.
+ }
+\author{ Jari Oksanen }
+
+\seealso{The functions pass parameters to basic graphical functions, and
+ you may wish to change the default values in \code{\link{arrows}},
+ \code{\link{lines}} and \code{\link{segments}}. You can pass
+ parameters to \code{\link{scores}} as well.
+}
+
+\examples{
+example(pyrifos)
+mod <- rda(pyrifos)
+plot(mod, type = "n")
+## Annual succession by ditches
+ordiarrows(mod, ditch, label = TRUE)
+## Show only control and highest Pyrifos treatment
+plot(mod, type = "n")
+ordiarrows(mod, ditch, label = TRUE,
+ show.groups = c("2", "3", "5", "11"))
+ordiarrows(mod, ditch, label = TRUE, show = c("6", "9"),
+ col = 2)
+legend("topright", c("Control", "Pyrifos 44"), lty = 1, col = c(1,2))
+}
+\keyword{aplot }
Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd 2011-07-13 14:02:30 UTC (rev 1680)
+++ pkg/vegan/man/ordihull.Rd 2011-07-16 12:26:47 UTC (rev 1681)
@@ -1,8 +1,5 @@
\name{ordihull}
\alias{ordihull}
-\alias{ordiarrows}
-\alias{ordisegments}
-\alias{ordigrid}
\alias{ordispider}
\alias{ordiellipse}
\alias{ordicluster}
@@ -13,15 +10,13 @@
\alias{scores.ordihull}
\alias{summary.ordiellipse}
-\title{Add Graphical Items to Ordination Diagrams}
-\description{
- Functions to add convex hulls, arrows, line segments, regular grids of
- points, `spider' graphs, ellipses or cluster dendrogram
- to ordination diagrams. The
- ordination diagrams can be produced by \code{vegan}
- \code{\link{plot.cca}}, \code{\link{plot.decorana}} or
- \code{\link{ordiplot}}.
-}
+\title{Display Groups or Factor Levels in Ordination Diagrams}
+
+\description{ Functions to add convex hulls, `spider' graphs, ellipses
+ or cluster dendrogram to ordination diagrams. The ordination
+ diagrams can be produced by \code{vegan} \code{\link{plot.cca}},
+ \code{\link{plot.decorana}} or \code{\link{ordiplot}}. }
+
\usage{
ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"),
show.groups, label = FALSE, ...)
@@ -30,12 +25,6 @@
col = NULL, show.groups, label = FALSE, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
show.groups, label = FALSE, ...)
-ordiarrows(ord, groups, levels, replicates, display = "sites",
- show.groups, startmark, label = FALSE, ...)
-ordisegments(ord, groups, levels, replicates, display = "sites",
- show.groups, label = FALSE, ...)
-ordigrid(ord, levels, replicates, display = "sites", lty = c(1,1),
- col = c(1,1), lwd = c(1,1), ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
w = weights(ord, display), ...)
}
@@ -44,59 +33,52 @@
\item{ord}{An ordination object or an \code{\link{ordiplot}} object. }
\item{groups}{Factor giving the groups for which the graphical item is
drawn. }
- \item{levels, replicates}{Alternatively, regular
- groups can be defined with arguments \code{levels} and
- \code{replicates}, where \code{levels} gives the number of groups,
- and \code{replicates} the number of successive items at the same
- group.}
\item{display}{Item to displayed. }
- \item{draw}{Use either \code{\link{lines}} or \code{\link{polygon}} to
- draw the
- line. Graphical parameters are passed to both. The main difference
- is that \code{polygon}s may be filled and non-transparent. With \code{none}
- nothing is drawn, but the function returns the \code{\link{invisible}}
- plotting data.}
+
+ \item{draw}{Use either \code{\link{lines}} or \code{\link{polygon}}
+ to draw the lines. Graphical parameters are passed to both. The
+ main difference is that \code{polygon}s may be filled and
+ non-transparent. With \code{none} nothing is drawn, but the
+ function returns the \code{\link{invisible}} plotting data.}
+
\item{show.groups}{Show only given groups. This can be a vector, or
\code{TRUE} if you want to show items for which condition is
\code{TRUE}. This argument makes it possible to use different
colours and line types for groups. The default is to show all groups. }
- \item{label}{Label the \code{groups} by their names. In
- \code{ordiellipse}, \code{ordihull} and \code{ordispider} the the
- group name is in the centroid of the object, in \code{ordiarrows}
- in the start of the arrow, and in \code{ordisegments} at both
- ends. \code{ordiellipse} and \code{ordihull} use standard
+
+ \item{label}{Label the \code{groups} by their names in the centroid
+ of the object. \code{ordiellipse} and \code{ordihull} use standard
\code{\link{text}}, and others use \code{\link{ordilabel}}.}
- \item{startmark}{plotting character used to mark the first
- item. The default is to use no mark, and for instance,
- \code{startmark = 1} will draw a circle. For other plotting characters,
- see \code{pch} in \code{\link{points}}. }
+
\item{w}{Weights used to find the average within group. Weights are
used automatically for \code{\link{cca}}
and \code{\link{decorana}} results, unless undone by the
user. \code{w=NULL} sets equal weights to all points. }
+
\item{kind}{Whether standard deviations of points (\code{sd}) or
standard deviations of their (weighted) averages (\code{se}) are
used.}
+
\item{conf}{Confidence limit for ellipses, e.g. 0.95. If given, the
corresponding \code{sd} or \code{se} is multiplied with the
corresponding value found from the Chi-squared distribution with
2df. }
+
\item{cluster}{Result of hierarchic cluster analysis, such as
\code{\link{hclust}} or \code{\link[cluster]{agnes}}.}
- \item{col}{Colour of ellipses or ellipse fills in \code{ordiellipse}
- or lines in \code{ordigrid}. For other functions the effect depends
- on the underlining functions this argument is passed to.}
- \item{lty, lwd}{Line type, line width used for
- \code{level}s and \code{replicate}s in \code{ordigrid}.}
+
+ \item{col}{Colour of ellipses or ellipse fills in
+ \code{ordiellipse}. For other functions the effect depends on the
+ underlining functions this argument is passed to.}
+
\item{prune}{Number of upper level hierarchies removed from the
dendrogram. If \code{prune} \eqn{>0}, dendrogram will be
disconnected.}
- \item{\dots}{Parameters passed to graphical functions such
- as \code{\link{lines}}, \code{\link{segments}},
- \code{\link{arrows}}, \code{\link{polygon}} or to
- \code{\link{scores}} to select axes and
- scaling etc. }
- }
+
+ \item{\dots}{Parameters passed to graphical functions or to
+ \code{\link{scores}} to select axes and scaling etc. }
+}
+
\details{
Function \code{ordihull} draws \code{\link{lines}} or
\code{\link{polygon}}s for the convex
@@ -123,45 +105,39 @@
of the polygon. With \code{draw = "none"} only the result object is
returned and nothing is drawn.
- Function \code{ordiarrows} draws
- \code{\link{arrows}} and \code{ordisegments} draws line
- \code{\link{segments}} between successive items in the
- groups. Function \code{ordigrid} draws line
- \code{\link{segments}} both within the groups and for the
- corresponding items among the groups.
-
Function \code{ordispider} draws a `spider' diagram where each point
- is connected to the group centroid with \code{\link{segments}}.
- Weighted centroids are used in the
- correspondence analysis methods \code{\link{cca}} and
- \code{\link{decorana}} or if the user gives the weights in the
- call. If \code{ordispider} is called with \code{\link{cca}} or
- \code{\link{rda}} result without \code{groups} argument, the function
- connects each `WA' scores to the corresponding `LC' score. If the
- argument is a (\code{invisible}) \code{ordihull} object, the functin
- will connect the points of the hull to their centroid.
+ is connected to the group centroid with \code{\link{segments}}.
+ Weighted centroids are used in the correspondence analysis methods
+ \code{\link{cca}} and \code{\link{decorana}} or if the user gives
+ the weights in the call. If \code{ordispider} is called with
+ \code{\link{cca}} or \code{\link{rda}} result without \code{groups}
+ argument, the function connects each `WA' scores to the
+ corresponding `LC' score. If the argument is a (\code{invisible})
+ \code{ordihull} object, the functin will connect the points of the
+ hull to their centroid.
Function \code{ordicluster} overlays a cluster dendrogram onto
ordination. It needs the result from a hierarchic clustering such as
- \code{\link{hclust}} or \code{\link[cluster]{agnes}}, or other
- with a similar structure. Function \code{ordicluster} connects
- cluster centroids to each other with line
- \code{\link{segments}}. Function uses centroids of all points in the
- clusters, and is therefore similar to average linkage methods.
+ \code{\link{hclust}} or \code{\link[cluster]{agnes}}, or other with
+ a similar structure. Function \code{ordicluster} connects cluster
+ centroids to each other with line \code{\link{segments}}. Function
+ uses centroids of all points in the clusters, and is therefore
+ similar to average linkage methods.
}
-\note{These functions add graphical items to ordination graph: You must
- draw a graph first.
- }
+\note{These functions add graphical items to ordination graph: You
+ must draw a graph first. To draw line segments, grids or arrows, see
+ \code{\link{ordisegments}}, \code{\link{ordigrid}}
+ and\code{\link{ordiarrows}}. }
+
\author{ Jari Oksanen }
-\seealso{The functions pass parameters to basic graphical functions, and
- you may wish to change the default values in \code{\link{arrows}},
+\seealso{The functions pass parameters to basic graphical functions,
+ and you may wish to change the default values in
\code{\link{lines}}, \code{\link{segments}} and
- \code{\link{polygon}}. You can pass
- parameters to \code{\link{scores}} as well. Underlying function for
- \code{ordihull} is \code{\link{chull}}.
-}
+ \code{\link{polygon}}. You can pass parameters to
+ \code{\link{scores}} as well. Underlying function for
+ \code{ordihull} is \code{\link{chull}}. }
\examples{
data(dune)
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-07-13 14:02:30 UTC (rev 1680)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-07-16 12:26:47 UTC (rev 1681)
@@ -4001,16 +4001,52 @@
detaching ‘package:lattice’
+> nameEx("ordiarrows")
+> ### * ordiarrows
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: ordiarrows
+> ### Title: Add Arrows and Line Segments to Ordination Diagrams
+> ### Aliases: ordiarrows ordisegments ordigrid
+> ### Keywords: aplot
+>
+> ### ** Examples
+>
+> example(pyrifos)
+
+pyrifs> data(pyrifos)
+
+pyrifs> ditch <- gl(12, 1, length=132)
+
+pyrifs> week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
+
+pyrifs> dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
+> mod <- rda(pyrifos)
+> plot(mod, type = "n")
+> ## Annual succession by ditches
+> ordiarrows(mod, ditch, label = TRUE)
+> ## Show only control and highest Pyrifos treatment
+> plot(mod, type = "n")
+> ordiarrows(mod, ditch, label = TRUE,
++ show.groups = c("2", "3", "5", "11"))
+> ordiarrows(mod, ditch, label = TRUE, show = c("6", "9"),
++ col = 2)
+> legend("topright", c("Control", "Pyrifos 44"), lty = 1, col = c(1,2))
+>
+>
+>
+> cleanEx()
> nameEx("ordihull")
> ### * ordihull
>
> flush(stderr()); flush(stdout())
>
> ### Name: ordihull
-> ### Title: Add Graphical Items to Ordination Diagrams
-> ### Aliases: ordihull ordiarrows ordisegments ordigrid ordispider
-> ### ordiellipse ordicluster weights.cca weights.rda weights.decorana
-> ### summary.ordihull scores.ordihull summary.ordiellipse
+> ### Title: Display Groups or Factor Levels in Ordination Diagrams
+> ### Aliases: ordihull ordispider ordiellipse ordicluster weights.cca
+> ### weights.rda weights.decorana summary.ordihull scores.ordihull
+> ### summary.ordiellipse
> ### Keywords: aplot
>
> ### ** Examples
@@ -4613,7 +4649,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x102e8a118>
+<environment: 0x10425fa68>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4629,7 +4665,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1062d2808>
+<environment: 0x10611b910>
Estimated degrees of freedom:
6.0761 total = 7.076141
@@ -4785,7 +4821,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1071b84d8>
+<environment: 0x106481d18>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4798,7 +4834,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1068b80d8>
+<environment: 0x10702af78>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4811,7 +4847,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106b40630>
+<environment: 0x106697510>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -7004,7 +7040,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1080e5a00>
+<environment: 0x107a91898>
Estimated degrees of freedom:
2 total = 3
@@ -7469,7 +7505,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 104.018 1.278 107.134 0 0
+Time elapsed: 103.417 1.269 105.72 0 0
> grDevices::dev.off()
null device
1
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