[Vegan-commits] r596 - in pkg/vegan: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 25 11:32:40 CET 2008
Author: jarioksa
Date: 2008-11-25 11:32:39 +0100 (Tue, 25 Nov 2008)
New Revision: 596
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/R/ordisurf.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/ordisurf.Rd
Log:
ordisurf gains argument 'bubble' to display the value of y-variate by the size of the plotting symbol
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2008-11-24 20:36:50 UTC (rev 595)
+++ pkg/vegan/DESCRIPTION 2008-11-25 10:32:39 UTC (rev 596)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 1.16-4
-Date: November 1, 2008
+Version: 1.16-5
+Date: November 25, 2008
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson,
Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
Modified: pkg/vegan/R/ordisurf.R
===================================================================
--- pkg/vegan/R/ordisurf.R 2008-11-24 20:36:50 UTC (rev 595)
+++ pkg/vegan/R/ordisurf.R 2008-11-25 10:32:39 UTC (rev 596)
@@ -1,7 +1,8 @@
"ordisurf" <-
function (x, y, choices = c(1, 2), knots = 10, family = "gaussian",
col = "red", thinplate = TRUE, add = FALSE, display = "sites",
- w = weights(x), main, nlevels = 10, levels, labcex = 0.6, ...)
+ w = weights(x), main, nlevels = 10, levels, labcex = 0.6,
+ bubble = FALSE, cex = 1, ...)
{
weights.default <- function(object, ...) NULL
GRID = 25
@@ -32,7 +33,12 @@
inpoly = as.integer(inpoly), PACKAGE="vegan")$inpoly
is.na(fit) <- inpoly == 0
if (!add) {
- plot(X, asp = 1, ...)
+ if (bubble) {
+ if (is.numeric(bubble))
+ cex <- bubble
+ cex <- (y - min(y))/diff(range(y)) * (cex-0.4) + 0.4
+ }
+ plot(X, asp = 1, cex = cex, ...)
}
if (!missing(main) || (missing(main) && !add)) {
if (missing(main))
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2008-11-24 20:36:50 UTC (rev 595)
+++ pkg/vegan/inst/ChangeLog 2008-11-25 10:32:39 UTC (rev 596)
@@ -2,21 +2,26 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 1.16-4 (opened November 1, 2008)
+Version 1.16-5
- * oecosimu: got a new control argument for quantitative null
- model analyses, and this is available if method = "permat".
- The print method and help file modified accordingly.
+ * ordisurf: gains argument 'bubble' to use bubble plots for
+ points, and 'cex' to set the symbol size (or the maximum size with
+ 'bubble = TRUE').
+
+Version 1.16-4 (closed November 25, 2008)
- * vignettes: Figures with narrower margins. Vignetted
+ * oecosimu: got a new control argument for quantitative null model
+ analyses; this is available if method = "permat". The print
+ method and help file modified accordingly.
+
+ * vignettes: Figures with narrower margins. Vignette
"diversity-vegan" adds functional diversity ('treedive'), 'beals'
and 'radfit' graphics updated to current vegan. Still missing
pieces: nestedness & null models, quantitative null models,
additive diversity partioninng, Tsallis entropy.
* radlattice: a new function to display each radfit model in a
- separate panel together with their AIC or BIC values. I wanted to
- have this for a manuscript.
+ separate panel together with their AIC or BIC values.
* plot.cca: takes care that plotted items have non-NULL names that
plot neatly. This was already take care of with formula
@@ -26,9 +31,9 @@
* permatwsap: quasiswap method is implemented for count data based
on the idea of Carsten Dormann in the bipartite::swap.web
function. This takes a random matrix first with same row and
- column sums as the original (via r2dtable), and than restores the
- original matrix fill through steps of swaping 2x2 submatrices. The
- current R code is slow.
+ column sums as the original (via r2dtable), and then restores the
+ original matrix fill through steps of swapping 2x2
+ submatrices. The current R code is slow.
* permatfull: when both cells and individuals are shuffled, the
matrix fill remains constant.
@@ -40,9 +45,9 @@
inspected. The ties are inspected only if they could change order
of columns within range of row sums (species richness). A warning
with results is only printed if there were >7 tied columns that
- could influence the statistic, because in other cases the solution
- is certainly correct. The new function may be slow, and a more
- clever solution should be found (or nesteddisc dropped from
+ could influence the statistic, because in other cases the search
+ for solution was exhaustive. The new function may be slow, and a
+ more clever solution should be found (or nesteddisc dropped from
vegan). With this code, the discrepancy statistic of the 'sipoo'
data is 50 (cf. notes on 1.16-3) instead of the original 55.
Modified: pkg/vegan/man/ordisurf.Rd
===================================================================
--- pkg/vegan/man/ordisurf.Rd 2008-11-24 20:36:50 UTC (rev 595)
+++ pkg/vegan/man/ordisurf.Rd 2008-11-25 10:32:39 UTC (rev 596)
@@ -9,7 +9,8 @@
\usage{
ordisurf(x, y, choices=c(1, 2), knots=10, family="gaussian", col="red",
thinplate = TRUE, add = FALSE, display = "sites",
- w = weights(x), main, nlevels = 10, levels, labcex = 0.6, ...)
+ w = weights(x), main, nlevels = 10, levels, labcex = 0.6,
+ bubble = FALSE, cex = 1, ...)
}
\arguments{
@@ -34,6 +35,13 @@
\code{nlevels} if \code{levels} are not supplied.}
\item{labcex}{Label size in contours. Setting this zero will suppress
labels.}
+ \item{bubble}{Use \dQuote{bubble plot} for points, or vary the point
+ diameter by the value of the plotted variable. If \code{bubble} is
+ numeric, its value is used for the maximum symbol size (as in
+ \code{cex}), or if \code{bubble = TRUE}, the value of \code{cex} gives
+ the maximum. The minimum size will always be \code{cex = 0.4}. The
+ option only has an effect if \code{add = FALSE}.}
+ \item{cex}{Character expansion of plotting symbols.}
\item{\dots}{ Other graphical parameters. }
}
\details{
@@ -89,7 +97,7 @@
library(MASS)
vare.dist <- vegdist(varespec)
vare.mds <- isoMDS(vare.dist)
-with(varechem, ordisurf(vare.mds, Baresoil))
+with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
## Cover of Cladina arbuscula
with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson))
}
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