[Vegan-commits] r2215 - in pkg/vegan: R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 13 10:54:53 CEST 2012
Author: jarioksa
Date: 2012-06-13 10:54:53 +0200 (Wed, 13 Jun 2012)
New Revision: 2215
Modified:
pkg/vegan/R/plot.envfit.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/envfit.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
plot.envfit gained argument 'bg' to set background colour of labels
Modified: pkg/vegan/R/plot.envfit.R
===================================================================
--- pkg/vegan/R/plot.envfit.R 2012-06-07 08:31:50 UTC (rev 2214)
+++ pkg/vegan/R/plot.envfit.R 2012-06-13 08:54:53 UTC (rev 2215)
@@ -1,6 +1,6 @@
`plot.envfit` <-
function (x, choices = c(1, 2), arrow.mul, at = c(0, 0),
- axis = FALSE, p.max = NULL, col = "blue", add = TRUE, ...)
+ axis = FALSE, p.max = NULL, col = "blue", bg, add = TRUE, ...)
{
formals(arrows) <- c(formals(arrows), alist(... = ))
vect <- NULL
@@ -86,11 +86,20 @@
if (!is.null(vect)) {
arrows(at[1], at[2], vect[, 1], vect[, 2], len = 0.05,
col = col)
- text(vtext, rownames(x$vectors$arrows), col = col, ...)
+ if (missing(bg))
+ text(vtext, rownames(x$vectors$arrows), col = col, ...)
+ else
+ ordilabel(vtext, labels = rownames(x$vectors$arrows),
+ col = col, fill = bg, ...)
}
if (!is.null(x$factors)) {
- text(x$factors$centroids[, choices, drop = FALSE],
- rownames(x$factors$centroids), col = col, ...)
+ if (missing(bg))
+ text(x$factors$centroids[, choices, drop = FALSE],
+ rownames(x$factors$centroids), col = col, ...)
+ else
+ ordilabel(x$factors$centroids[, choices, drop = FALSE],
+ labels = rownames(x$factors$centroids),
+ col = col, fill = bg, ...)
}
if (axis && !is.null(vect)) {
axis(3, at = ax + at[1], labels = c(maxarr, 0, maxarr),
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2012-06-07 08:31:50 UTC (rev 2214)
+++ pkg/vegan/inst/ChangeLog 2012-06-13 08:54:53 UTC (rev 2215)
@@ -4,6 +4,9 @@
Version 2.1-16 (opened May 11, 2012)
+ * envfit: plot() gained new argument 'bg' that triggers labelling
+ with ordilabel() using the colour given in 'bg' as the background.
+
* simper: added parallel processing for permutation tests in
accordance with other vegan functions and with similar user
interface. The code was developed by Eduard Szöcs in
Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd 2012-06-07 08:31:50 UTC (rev 2214)
+++ pkg/vegan/man/envfit.Rd 2012-06-13 08:54:53 UTC (rev 2215)
@@ -19,7 +19,7 @@
display = "sites", w = weights(ord), na.rm = FALSE, ...)
\method{envfit}{formula}(formula, data, ...)
\method{plot}{envfit}(x, choices = c(1,2), arrow.mul, at = c(0,0), axis = FALSE,
- p.max = NULL, col = "blue", add = TRUE, ...)
+ p.max = NULL, col = "blue", bg, add = TRUE, ...)
\method{scores}{envfit}(x, display, choices, ...)
vectorfit(X, P, permutations = 0, strata, w, ...)
factorfit(X, P, permutations = 0, strata, w, ...)
@@ -57,6 +57,9 @@
variables. You must calculate \eqn{P} values with setting
\code{permutations} to use this option. }
\item{col}{Colour in plotting.}
+ \item{bg}{Background colour for labels. If \code{bg} is set, the
+ labels are displayed with \code{\link{ordilabel}} instead of
+ \code{text}. See Examples for using semitransparent background.}
\item{add}{Results added to an existing ordination plot.}
\item{strata}{An integer vector or factor specifying the strata for
permutation. If supplied, observations are permuted only within the
@@ -196,7 +199,9 @@
fit <- envfit(ord, varechem, perm = 999, display = "lc")
plot(fit, p.max = 0.05, col = "red")
## Class variables, formula interface, and displaying the
-## inter-class variability with `ordispider'
+## inter-class variability with `ordispider', and semitransparent
+## white background for labels (semitransparent colours are not
+## supported by all graphics devices)
data(dune)
data(dune.env)
attach(dune.env)
@@ -205,7 +210,7 @@
plot(ord, type = "n")
ordispider(ord, Moisture, col="skyblue")
points(ord, display = "sites", col = as.numeric(Moisture), pch=16)
-plot(fit, cex=1.2, axis=TRUE)
+plot(fit, cex=1.2, axis=TRUE, bg = rgb(1, 1, 1, 0.5))
}
\keyword{multivariate }
\keyword{aplot}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-06-07 08:31:50 UTC (rev 2214)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-06-13 08:54:53 UTC (rev 2215)
@@ -1,8 +1,8 @@
-R version 2.15.0 (2012-03-30)
+R Under development (unstable) (2012-06-11 r59557) -- "Unsuffered Consequences"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -154,14 +154,14 @@
> plot(ef)
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-17. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x1023eddf0>
+<environment: 0x2622380>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -2552,7 +2552,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> (fit <- envfit(ord, varechem, perm = 999))
@@ -2605,7 +2605,9 @@
> fit <- envfit(ord, varechem, perm = 999, display = "lc")
> plot(fit, p.max = 0.05, col = "red")
> ## Class variables, formula interface, and displaying the
-> ## inter-class variability with `ordispider'
+> ## inter-class variability with `ordispider', and semitransparent
+> ## white background for labels (semitransparent colours are not
+> ## supported by all graphics devices)
> data(dune)
> data(dune.env)
> attach(dune.env)
@@ -2614,7 +2616,7 @@
> plot(ord, type = "n")
> ordispider(ord, Moisture, col="skyblue")
> points(ord, display = "sites", col = as.numeric(Moisture), pch=16)
-> plot(fit, cex=1.2, axis=TRUE)
+> plot(fit, cex=1.2, axis=TRUE, bg = rgb(1, 1, 1, 0.5))
>
>
>
@@ -3018,7 +3020,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> stressplot(mod)
@@ -4802,17 +4804,17 @@
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-17. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1096c3750>
+<environment: 0x912fb60>
Estimated degrees of freedom:
-6.4351 total = 7.435071
+6.4351 total = 7.43507
GCV score: 144.1236
>
@@ -4825,7 +4827,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109733fc8>
+<environment: 0x9a7e380>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4837,13 +4839,13 @@
> ## Get fitted values
> calibrate(fit)
1 2 3 4 5 6 7
-22.0644614 6.0132251 3.6350483 4.1019742 9.0030989 5.9202601 8.6399184
+22.0644615 6.0132250 3.6350484 4.1019743 9.0030990 5.9202602 8.6399182
8 9 10 11 12 13 14
-11.0719303 0.6561781 35.2282118 10.4346331 7.2900018 5.5710617 24.6503110
+11.0719302 0.6561783 35.2282116 10.4346331 7.2900019 5.5710617 24.6503109
15 16 17 18 19 20 21
-18.8754521 29.7286543 5.6158934 9.5869716 3.2876267 2.7111721 10.7832857
+18.8754520 29.7286540 5.6158934 9.5869715 3.2876268 2.7111723 10.7832857
22 23 24
- 3.0020413 9.8128952 7.3656932
+ 3.0020415 9.8128952 7.3656934
>
> ## Plot method
> plot(fit, what = "contour")
@@ -4974,14 +4976,14 @@
> ## 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 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-17. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106156f78>
+<environment: 0x978d1e0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4994,7 +4996,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109eccca0>
+<environment: 0x72ee4f8>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -5007,7 +5009,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a8d12e0>
+<environment: 0x97ecca8>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5773,8 +5775,8 @@
[2,] 0.1169579 0.9931369
Translation of averages:
- [,1] [,2]
-[1,] 3.893131e-18 -9.725997e-18
+ [,1] [,2]
+[1,] 1.79048e-17 9.246476e-19
Scaling of target:
[1] 0.6736868
@@ -7369,7 +7371,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> plot(ord, type = "t")
@@ -7539,14 +7541,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-17. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10b48ca98>
+<environment: 0x9a81d78>
Estimated degrees of freedom:
2 total = 3
@@ -8026,7 +8028,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 82.41 1.676 85.548 0 0
+Time elapsed: 25.377 0.088 25.548 0 0
> grDevices::dev.off()
null device
1
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