[Vegan-commits] r764 - in branches/1.15: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 29 09:02:25 CEST 2009
Author: jarioksa
Date: 2009-03-29 09:02:24 +0200 (Sun, 29 Mar 2009)
New Revision: 764
Modified:
branches/1.15/R/commsimulator.R
branches/1.15/R/cophenetic.spantree.R
branches/1.15/R/orditkplot.R
branches/1.15/R/plot.rad.R
branches/1.15/R/plot.spantree.R
branches/1.15/R/spantree.R
branches/1.15/inst/ChangeLog
branches/1.15/man/decorana.Rd
branches/1.15/man/decostand.Rd
branches/1.15/man/metaMDS.Rd
branches/1.15/man/radfit.Rd
branches/1.15/man/spantree.Rd
branches/1.15/man/specpool.Rd
Log:
merged some safe-looking changes to branches/1.15: r518, r538-540, r608, r676
Modified: branches/1.15/R/commsimulator.R
===================================================================
--- branches/1.15/R/commsimulator.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/commsimulator.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -94,6 +94,7 @@
out <- oldout
}
}
+ colnames(out) <- colnames(x)
+ rownames(out) <- rownames(x)
out
}
-
Modified: branches/1.15/R/cophenetic.spantree.R
===================================================================
--- branches/1.15/R/cophenetic.spantree.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/cophenetic.spantree.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -7,6 +7,6 @@
ind <- t(ind[2:1,])
mat[ind] <- x$dist
d <- as.dist(mat)
+ attr(d, "Labels") <- x$labels
stepacross(d, path = "extended", toolong=0, trace=FALSE)
}
-
Modified: branches/1.15/R/orditkplot.R
===================================================================
--- branches/1.15/R/orditkplot.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/orditkplot.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -230,6 +230,7 @@
"png" = "{PNG File} {.png}",
"jpg" = "{JPEG File} {.jpg .jpeg}",
"bmp" = "{BMP File} {.bmp}",
+ "tiff"= "{TIFF File} {.tif .tiff}",
"fig" = "{XFig File} {.fig}")
falt <- rep(TRUE, length(ftypes))
names(falt) <- names(ftypes)
@@ -237,6 +238,10 @@
falt["png"] <- FALSE
if (!capabilities("jpeg"))
falt["jpg"] <- FALSE
+ ## Should work also in R < 2.8.0 with no capabilities("tiff")
+ if (!isTRUE(unname(capabilities("tiff"))))
+ falt["tiff"] <- FALSE
+ ## bmp lives only in Windows
if (.Platform$OS.type != "windows")
falt["bmp"] <- FALSE
ftypes <- ftypes[falt]
@@ -248,6 +253,8 @@
ftype <- ftype[length(ftype)]
if (ftype == "jpeg")
ftype <- "jpg"
+ if (ftype == "tif")
+ ftype <- "tiff"
mess <- "is not a supported type: file not produced. Supported types are"
if (!(ftype %in% names(ftypes))) {
tkmessageBox(message=paste(sQuote(ftype), mess, paste(names(ftypes),
@@ -261,7 +268,8 @@
pdf = pdf(file=fname, width=xy$dim[1], height=xy$dim[2]),
png = png(file=fname, width=pixdim[1], height=pixdim[2]),
jpg = jpeg(file=fname, width=pixdim[1], height=pixdim[2],
- quality = 100),
+ quality = 100),
+ tiff = tiff(file=fname, width=pixdim[1], height=pixdim[2]),
bmp = bmp(file=fname, width=pixdim[1], height=pixdim[2]),
fig = xfig(file=fname, width=xy$dim[1], height=xy$dim[2]))
plot.orditkplot(xy)
Modified: branches/1.15/R/plot.rad.R
===================================================================
--- branches/1.15/R/plot.rad.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/plot.rad.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -1,8 +1,8 @@
"plot.rad" <-
- function(x, xlab="Rank", ylab="Abundance", ...)
+ function(x, xlab="Rank", ylab="Abundance", log = "y", ...)
{
rnk <- seq(along=x)
- plot(rnk, x, log="y", xlab=xlab, ylab=ylab, ...)
+ plot(rnk, x, log=log, xlab=xlab, ylab=ylab, ...)
out <- list(species = cbind(rnk, x))
class(out) <- "ordiplot"
invisible(out)
Modified: branches/1.15/R/plot.spantree.R
===================================================================
--- branches/1.15/R/plot.spantree.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/plot.spantree.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -26,8 +26,8 @@
points(ord, cex = cex, ...)
else if (type == "t") {
if (missing(labels))
- labels <- rownames(ord)
- text(ord, labels = labels, cex = cex, ...)
+ labels <- x$labels
+ ordilabel(ord, display = "sites", labels = labels, cex = cex, ...)
}
ord <- list(sites = ord)
class(ord) <- "ordiplot"
Modified: branches/1.15/R/spantree.R
===================================================================
--- branches/1.15/R/spantree.R 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/R/spantree.R 2009-03-29 07:02:24 UTC (rev 764)
@@ -3,11 +3,12 @@
{
dis <- as.dist(dis)
n <- attr(dis, "Size")
+ labels <- labels(dis)
dis <- .C("primtree", dist = as.double(dis), toolong = as.double(toolong),
n = as.integer(n), val = double(n + 1),
dad = integer(n + 1), NAOK = TRUE, PACKAGE = "vegan")
- out <- list(kid = dis$dad[2:n] + 1, dist = dis$val[2:n])
+ out <- list(kid = dis$dad[2:n] + 1, dist = dis$val[2:n],
+ labels = labels)
class(out) <- "spantree"
out
}
-
Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/inst/ChangeLog 2009-03-29 07:02:24 UTC (rev 764)
@@ -5,6 +5,18 @@
Version 1.15-2 (opened January 14, 2009)
+ * merged r608: plot.radfit gained argument log = "y".
+
+ * merged r538: orditkplot makes TIFF graphics.
+
+ * merged r539, 540: spantree retains names, and plot.spantree uses
+ ordilabel in plots.
+
+ * merged r676: commsimulator results retain names.
+
+ * merged r518: doubled "the" in man pages of decorana, spantree,
+ decostand, specpool and metaMDS.
+
* merged r750: better example in add1.cca.Rd.
* merged r735 & r736: stepacross fixes in metaMDSdist with
Modified: branches/1.15/man/decorana.Rd
===================================================================
--- branches/1.15/man/decorana.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/decorana.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -126,7 +126,7 @@
eigenvalues. The proper eigenvalues are estimated after extraction of
the axes and they are the ratio of biased weighted variances of site
and species scores even in detrended and rescaled solutions. The
- `decorana values' are provided only for the the compatibility with
+ `decorana values' are provided only for the compatibility with
legacy software, and they should not be used.
}
\value{
Modified: branches/1.15/man/decostand.Rd
===================================================================
--- branches/1.15/man/decostand.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/decostand.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -44,7 +44,7 @@
\item \code{chi.square}: divide by row sums and square root of
column sums, and adjust for square root of matrix total
(Legendre & Gallagher 2001). When used with the Euclidean
- distance, the distances should be similar to the the
+ distance, the distances should be similar to the
Chi-square distance used in correspondence analysis. However, the
results from \code{\link{cmdscale}} would still differ, since
CA is a weighted ordination method (default \code{MARGIN =
Modified: branches/1.15/man/metaMDS.Rd
===================================================================
--- branches/1.15/man/metaMDS.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/metaMDS.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -176,7 +176,7 @@
based on closer dissimilarities where the relation between ordination
distance and community dissimilarity is rather linear; the limit is
controlled by parameter \code{threshold}. If there are enough points
- below this threshold (controlled by the the parameter
+ below this threshold (controlled by the parameter
\code{nthreshold}), dissimilarities are regressed on distances.
The intercept of this regression is taken as the replicate
dissimilarity, and half-change is the distance where similarity
Modified: branches/1.15/man/radfit.Rd
===================================================================
--- branches/1.15/man/radfit.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/radfit.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -43,7 +43,7 @@
\method{lines}{radline}(x, ...)
\method{points}{radline}(x, ...)
as.rad(x)
-\method{plot}{rad}(x, xlab = "Rank", ylab = "Abundance", ...)
+\method{plot}{rad}(x, xlab = "Rank", ylab = "Abundance", log = "y", ...)
}
\arguments{
@@ -68,6 +68,11 @@
\item{type}{Type of the plot, \code{"b"} for plotting both observed points
and fitted lines, \code{"p"} for only points, \code{"l"} for only
fitted lines, and \code{"n"} for only setting the frame. }
+ \item{log}{Use logarithmic scale for given axis. The default
+ \code{log =" y"} gives the traditional plot in community ecology
+ where the pre-emption model is a straight line, and with
+ \code{log = "xy"} Zipf model is a straight line. With
+ \code{log = ""} both axes are in the original arithmetic scale.}
\item{\dots}{Other parameters to functions. }
}
\details{
@@ -218,7 +223,10 @@
mod
plot(mod)
mod <- radfit(BCI[1,])
+## Pre-emption model is a line
plot(mod)
+## log for both axes: Zipf model is a line
+plot(mod, log = "xy")
# Take a subset of BCI to save time and nerves
mod <- radfit(BCI[2:5,])
mod
Modified: branches/1.15/man/spantree.Rd
===================================================================
--- branches/1.15/man/spantree.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/spantree.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -35,9 +35,9 @@
by \code{\link{scores}}.}
\item{cex}{Character expansion factor.}
\item{type}{Observations are plotted as points with
- \code{type="p"} or \code{type="b"}, or as text with
+ \code{type="p"} or \code{type="b"}, or as text label with
\code{type="t"}. The tree (lines) will always be plotted.}
- \item{labels}{Text used with \code{type="t"} or row names if this is
+ \item{labels}{Text used with \code{type="t"} or node names if this is
missing.}
\item{dlim}{A ceiling value used to highest \code{cophenetic} dissimilarity.}
\item{FUN}{Ordination function to find the configuration from
@@ -60,7 +60,7 @@
the tree segments. Function \code{plot} displays the tree over a
supplied ordination configuration, and \code{lines} adds a spanning
tree to an ordination graph. If configuration is not supplied for \code{plot},
- the function ordinates the the cophenetic dissimilarities of the
+ the function ordinates the cophenetic dissimilarities of the
spanning tree and overlays the tree on this result. The default
ordination function is \code{\link[MASS]{sammon}} (package \pkg{MASS}),
because Sammon scaling emphasizes structure in the neighbourhood of
@@ -68,8 +68,7 @@
to set \code{dlim}, and sometimes the results will remain
twisted). These ordination methods do not work with disconnected
trees, but you must supply the ordination configuration. Function
- \code{lines} will overlay the tree in an existing
- plot.
+ \code{lines} will overlay the tree in an existing plot.
Function \code{spantree} uses Prim's method
implemented as priority-first search for dense graphs (Sedgewick
@@ -89,6 +88,7 @@
and tree is disconnected at the node.}
\item{dist }{Corresponding distance. If \code{kid = NA}, then
\code{dist = 0}.}
+ \item{labels }{Names of nodes as found from the input dissimilarities.}
}
\references{
Sedgewick, R. (1990). \emph{Algorithms in C}. Addison Wesley.
Modified: branches/1.15/man/specpool.Rd
===================================================================
--- branches/1.15/man/specpool.Rd 2009-03-27 07:13:56 UTC (rev 763)
+++ branches/1.15/man/specpool.Rd 2009-03-29 07:02:24 UTC (rev 764)
@@ -90,7 +90,7 @@
the number
of individuals in rare species.
- Functions estimate the the standard errors of the estimates. These
+ Functions estimate the standard errors of the estimates. These
only concern the number of added species, and assume that there is
no variance in the observed richness.
The equations of standard errors are too complicated to be reproduced in
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