[Vegan-commits] r1969 - in pkg/vegan: inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 30 19:42:19 CET 2011
Author: jarioksa
Date: 2011-10-30 19:42:19 +0100 (Sun, 30 Oct 2011)
New Revision: 1969
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/ordiplot3d.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
tell how to use xyz.convert to add points to ordiplot3d graph
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-10-30 17:52:06 UTC (rev 1968)
+++ pkg/vegan/inst/ChangeLog 2011-10-30 18:42:19 UTC (rev 1969)
@@ -4,6 +4,10 @@
Version 2.1-6 (opened October 30, 2011)
+ * ordiplot3d: expanded example to show how to use xyz.convert() to
+ add points as per
+ https://stat.ethz.ch/pipermail/r-help/2011-October/293955.html
+
* oecosimu: new proposition for implementing parallel processing.
The relevant arguments are now 'parallel = getOption("mc.cores",
1)' and 'cl'. The 'parallel' defaults to 1 (no parallel
Modified: pkg/vegan/man/ordiplot3d.Rd
===================================================================
--- pkg/vegan/man/ordiplot3d.Rd 2011-10-30 17:52:06 UTC (rev 1968)
+++ pkg/vegan/man/ordiplot3d.Rd 2011-10-30 18:42:19 UTC (rev 1969)
@@ -85,19 +85,21 @@
functions.
Function \code{ordiplot3d} plots only points. However, it returns
- invisibly an object inheriting from \code{\link{ordiplot}} so that you
- can use \code{\link{identify.ordiplot}} to identify \code{"points"} or
- \code{"arrows"}. The underlying
- \code{\link[scatterplot3d]{scatterplot3d}} function accepts \code{type
- = "n"} so that only the axes, biplot arrows and centroids of
- environmental variables will be plotted, and the ordination scores can
- be added with \code{\link{text.ordiplot}} or
- \code{\link{points.ordiplot}}. Further, you can use any functions from
- the \code{\link{ordihull}} family with the invisible result of
+ invisibly an object inheriting from \code{\link{ordiplot}} so that
+ you can use \code{\link{identify.ordiplot}} to identify
+ \code{"points"} or \code{"arrows"}. The underlying
+ \code{\link[scatterplot3d]{scatterplot3d}} function accepts
+ \code{type = "n"} so that only the axes, biplot arrows and centroids
+ of environmental variables will be plotted, and the ordination
+ scores can be added with \code{\link{text.ordiplot}} or
+ \code{\link{points.ordiplot}}. Further, you can use any functions
+ from the \code{\link{ordihull}} family with the invisible result of
\code{\link{ordiplot3d}}, but you must remember to specify the
\code{display} as \code{"points"} or \code{"arrows"}. To change the
- viewing angle, orientation etc. you must see
- \code{\link[scatterplot3d]{scatterplot3d}}.
+ viewing angle, orientation etc.{} you must see
+ \code{\link[scatterplot3d]{scatterplot3d}}. Only one kind of scores
+ will be plotted. See Examples for plotting both species and
+ site scores.
Function \code{ordigl} makes a dynamic three-dimensional graph that
can be rotated with mouse, and zoomed into with mouse buttons or wheel
@@ -121,20 +123,25 @@
\code{\link[rgl]{rgl.points}}, \code{\link[rgl]{rgl.texts}},
\code{\link[rgl]{rgl.lines}} and many others can be used.
}
- \value{
+
+\value{
+
Function \code{ordiplot3d} returns invisibly an object of class
- \code{"ordiplot3d"} inheriting from \code{\link{ordiplot}}. The return
- object will contain the coordinates projected onto two dimensions for
- \code{"points"}, and possibly for the heads of \code{"arrows"} and
- \code{"centroids"} of environmental variables. Functions like
- \code{\link{identify.ordiplot}}, \code{\link{points.ordiplot}},
- \code{\link{text.ordiplot}} can use this result, as well as
- \code{\link{ordihull}} and other functions documented with the
- latter. In addition, the result will contain the object returned by
- \code{\link[scatterplot3d]{scatterplot3d}}, including function
- \code{xyz.converter} which projects three-dimensional
- coordinates onto the plane used in the current plot.
+ \code{"ordiplot3d"} inheriting from \code{\link{ordiplot}}. The
+ return object will contain the coordinates projected onto two
+ dimensions for \code{"points"}, and possibly for the heads of
+ \code{"arrows"} and \code{"centroids"} of environmental
+ variables. Functions like \code{\link{identify.ordiplot}},
+ \code{\link{points.ordiplot}}, \code{\link{text.ordiplot}} can use
+ this result, as well as \code{\link{ordihull}} and other functions
+ documented with the latter. In addition, the result will contain the
+ object returned by \code{\link[scatterplot3d]{scatterplot3d}},
+ including function \code{xyz.convert} which projects
+ three-dimensional coordinates onto the plane used in the current
+ plot (see Examples).
+
Function \code{ordirgl} returns nothing.
+
}
\author{Jari Oksanen }
@@ -167,21 +174,24 @@
## Examples are not run, because they need non-standard packages
## 'scatterplot3d' and 'rgl' (and the latter needs user interaction).
#####
-#### Default 'ordiplot3d'
+### Default 'ordiplot3d'
\dontrun{
data(dune)
data(dune.env)
ord <- cca(dune ~ A1 + Moisture, dune.env)
ordiplot3d(ord)
-#### A boxed 'pin' version
+### A boxed 'pin' version
ordiplot3d(ord, type = "h")
-#### More user control
-pl <- ordiplot3d(ord, angle=15, type="n")
+### More user control
+pl <- ordiplot3d(ord, scaling = 3, angle=15, type="n")
points(pl, "points", pch=16, col="red", cex = 0.7)
-#### identify(pl, "arrows", col="blue") would put labels in better positions
+### identify(pl, "arrows", col="blue") would put labels in better positions
text(pl, "arrows", col="blue", pos=3)
-text(pl, "centroids", col="blue", pos=1, cex = 1.2)
-#### ordirgl
+text(pl, "centroids", col="blue", pos=1, cex = 1)
+### Add species using xyz.convert function returned by ordiplot3d
+sp <- scores(ord, choices=1:3, display="species", scaling=3)
+text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
+### ordirgl
ordirgl(ord, size=2)
ordirgl(ord, display = "species", type = "t")
rgl.quit()
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-10-30 17:52:06 UTC (rev 1968)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-10-30 18:42:19 UTC (rev 1969)
@@ -1,5 +1,5 @@
-R version 2.14.0 RC (2011-10-27 r57452)
+R version 2.14.0 RC (2011-10-29 r57474)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-5
+This is vegan 2.1-6
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -154,14 +154,14 @@
> plot(ef)
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x101fadcd0>
+<environment: 0x101faf2d8>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -4332,21 +4332,24 @@
> ## Examples are not run, because they need non-standard packages
> ## 'scatterplot3d' and 'rgl' (and the latter needs user interaction).
> #####
-> #### Default 'ordiplot3d'
+> ### Default 'ordiplot3d'
> ## Not run:
> ##D data(dune)
> ##D data(dune.env)
> ##D ord <- cca(dune ~ A1 + Moisture, dune.env)
> ##D ordiplot3d(ord)
-> ##D #### A boxed 'pin' version
+> ##D ### A boxed 'pin' version
> ##D ordiplot3d(ord, type = "h")
-> ##D #### More user control
-> ##D pl <- ordiplot3d(ord, angle=15, type="n")
+> ##D ### More user control
+> ##D pl <- ordiplot3d(ord, scaling = 3, angle=15, type="n")
> ##D points(pl, "points", pch=16, col="red", cex = 0.7)
-> ##D #### identify(pl, "arrows", col="blue") would put labels in better positions
+> ##D ### identify(pl, "arrows", col="blue") would put labels in better positions
> ##D text(pl, "arrows", col="blue", pos=3)
-> ##D text(pl, "centroids", col="blue", pos=1, cex = 1.2)
-> ##D #### ordirgl
+> ##D text(pl, "centroids", col="blue", pos=1, cex = 1)
+> ##D ### Add species using xyz.convert function returned by ordiplot3d
+> ##D sp <- scores(ord, choices=1:3, display="species", scaling=3)
+> ##D text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
+> ##D ### ordirgl
> ##D ordirgl(ord, size=2)
> ##D ordirgl(ord, display = "species", type = "t")
> ##D rgl.quit()
@@ -4685,14 +4688,14 @@
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
-This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109cec958>
+<environment: 0x10a0c9000>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4708,7 +4711,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1098eef40>
+<environment: 0x109adf6d0>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4857,14 +4860,14 @@
> ## Map of PCNMs in the sample plot
> ordisurf(mite.xy, scores(pcnm1, choi=1), bubble = 4, main = "PCNM 1")
Loading required package: mgcv
-This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x108f78578>
+<environment: 0x10692bee0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4877,7 +4880,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107654278>
+<environment: 0x1096e8098>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4890,7 +4893,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109e1a758>
+<environment: 0x10a7e9830>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -7152,14 +7155,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a9c72a8>
+<environment: 0x10952b190>
Estimated degrees of freedom:
2 total = 3
@@ -7635,7 +7638,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 90.316 1.908 92.398 0 0
+Time elapsed: 81.081 1.732 83.592 0 0
> grDevices::dev.off()
null device
1
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