[Vegan-commits] r2941 - in pkg/vegan: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 23 08:39:19 CET 2015
Author: jarioksa
Date: 2015-03-23 08:39:19 +0100 (Mon, 23 Mar 2015)
New Revision: 2941
Modified:
pkg/vegan/R/goodness.cca.R
pkg/vegan/R/orditkplot.R
pkg/vegan/man/goodness.cca.Rd
pkg/vegan/man/orditkplot.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local
Modified: pkg/vegan/R/goodness.cca.R
===================================================================
--- pkg/vegan/R/goodness.cca.R 2015-03-13 11:16:06 UTC (rev 2940)
+++ pkg/vegan/R/goodness.cca.R 2015-03-23 07:39:19 UTC (rev 2941)
@@ -1,7 +1,7 @@
`goodness.cca` <-
function (object, display = c("species", "sites"), choices,
model = c("CCA", "CA"), statistic = c("explained", "distance"),
- summarize = FALSE, addprevious = TRUE, ...)
+ summarize = FALSE, addprevious = FALSE, ...)
{
model <- match.arg(model)
display <- match.arg(display)
Modified: pkg/vegan/R/orditkplot.R
===================================================================
--- pkg/vegan/R/orditkplot.R 2015-03-13 11:16:06 UTC (rev 2940)
+++ pkg/vegan/R/orditkplot.R 2015-03-23 07:39:19 UTC (rev 2941)
@@ -230,6 +230,7 @@
xy <- ordDump()
ftypes <- c("eps" = "{EPS File} {.eps}",
"pdf" = "{PDF File} {.pdf}",
+ "svg" = "{SVG File} {.svg}",
"png" = "{PNG File} {.png}",
"jpg" = "{JPEG File} {.jpg .jpeg}",
"bmp" = "{BMP File} {.bmp}",
@@ -241,6 +242,8 @@
falt["png"] <- FALSE
if (!capabilities("jpeg"))
falt["jpg"] <- FALSE
+ if (!capabilities("cairo"))
+ falt["svg"] <- FALSE
## Should work also in R < 2.8.0 with no capabilities("tiff")
if (!isTRUE(unname(capabilities("tiff"))))
falt["tiff"] <- FALSE
@@ -277,6 +280,7 @@
eps = postscript(file=fname, width=xy$dim[1], height=xy$dim[2],
paper="special", horizontal = FALSE),
pdf = pdf(file=fname, width=xy$dim[1], height=xy$dim[2]),
+ svg = svg(filename=fname, width=xy$dim[1], height=xy$dim[2]),
png = png(filename=fname, width=pixdim[1], height=pixdim[2]),
jpg = jpeg(filename=fname, width=pixdim[1], height=pixdim[2],
quality = 100),
Modified: pkg/vegan/man/goodness.cca.Rd
===================================================================
--- pkg/vegan/man/goodness.cca.Rd 2015-03-13 11:16:06 UTC (rev 2940)
+++ pkg/vegan/man/goodness.cca.Rd 2015-03-23 07:39:19 UTC (rev 2941)
@@ -20,7 +20,7 @@
\usage{
\method{goodness}{cca}(object, display = c("species", "sites"), choices,
model = c("CCA", "CA"), statistic = c("explained", "distance"),
- summarize = FALSE, addprevious = TRUE, ...)
+ summarize = FALSE, addprevious = FALSE, ...)
inertcomp(object, display = c("species", "sites"),
statistic = c("explained", "distance"), proportional = FALSE)
spenvcor(object)
@@ -137,8 +137,8 @@
data(dune)
data(dune.env)
mod <- cca(dune ~ A1 + Management + Condition(Moisture), data=dune.env)
-goodness(mod)
-goodness(mod, summ = TRUE)
+goodness(mod, addprevious = TRUE)
+goodness(mod, addprevious = TRUE, summ = TRUE)
# Inertia components
inertcomp(mod, prop = TRUE)
inertcomp(mod, stat="d")
Modified: pkg/vegan/man/orditkplot.Rd
===================================================================
--- pkg/vegan/man/orditkplot.Rd 2015-03-13 11:16:06 UTC (rev 2940)
+++ pkg/vegan/man/orditkplot.Rd 2015-03-23 07:39:19 UTC (rev 2941)
@@ -69,27 +69,26 @@
passed to the new plot).
}
- In addition there are buttons
- for the following tasks: \strong{Copy to EPS} copies the current plot
- to an encapsulated postscript (eps) file using standard Tcl/Tk
- utilities. The faithfulness of this copy is system dependent. Button
- \strong{Export plot} uses \code{plot.orditkplot} function to redraw
- the plot into graphical file formats. Depending on the system, the
- following graphical formats may be available: eps, pdf, png, jpeg or
- bmp. The file type is deduced from the file suffix or the selection of
- the file type in the dialogue box. Alternatively, the same dialogue can be
- used to save the plot to an editable \code{\link{xfig}} file. Button
- \strong{Dump to R} writes the edited coordinates of labels and points
- to the \R session for further processing, and the
- \code{plot.orditkplot} function can be used to display the
- results. For faithful replication of the plot, the graph must have
- similar dimensions as the \code{orditkplot} canvas had originally. The
- \code{plot} function cannot be configured, but it uses the same
- settings as the original Tcl/Tk plot. However, \code{points} and
- \code{text} functions are fully configurable, and unaware of the
- original Tcl/Tk plot settings (probably you must set \code{cex} at
- least to get a decent plot). Finally, button \strong{Dismiss} closes
- the window.
+ In addition there are buttons for the following tasks: \strong{Copy
+ to EPS} copies the current plot to an encapsulated postscript (eps)
+ file using standard Tcl/Tk utilities. The faithfulness of this copy
+ is system dependent. Button \strong{Export plot} uses
+ \code{plot.orditkplot} function to redraw the plot into graphical
+ file formats. Depending on the system, the following graphical
+ formats may be available: eps, pdf, svg, png, jpeg, tiff, bmp or
+ xfig. Some of the output formats may be edited with external
+ software: svg files with Illustrator or Inkscape, and xfig with the
+ legacy program XFig. Button \strong{Dump to R} writes the edited
+ coordinates of labels and points to the \R session for further
+ processing, and the \code{plot.orditkplot} function can be used to
+ display the results. For faithful replication of the plot, the graph
+ must have similar dimensions as the \code{orditkplot} canvas had
+ originally. The \code{plot} function cannot be configured, but it
+ uses the same settings as the original Tcl/Tk plot. However,
+ \code{points} and \code{text} functions are fully configurable, and
+ unaware of the original Tcl/Tk plot settings (probably you must set
+ \code{cex} at least to get a decent plot). Finally, button
+ \strong{Dismiss} closes the window.
The produced plot will have equal aspect ratio. The width of the
horizontal axis is fixed, but vertical axes will be scaled to needed
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