[Vegan-commits] r240 - in pkg: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 20 11:29:52 CET 2008
Author: jarioksa
Date: 2008-02-20 11:29:52 +0100 (Wed, 20 Feb 2008)
New Revision: 240
Modified:
pkg/inst/ChangeLog
pkg/man/oecosimu.Rd
pkg/man/orditkplot.Rd
pkg/man/ordixyplot.Rd
Log:
Merged last doc fixed from vegan release 1.11-0 (submitted to CRAN today)
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2008-02-20 07:50:57 UTC (rev 239)
+++ pkg/inst/ChangeLog 2008-02-20 10:29:52 UTC (rev 240)
@@ -4,8 +4,11 @@
Version 1.12-1 (Feb 19, 2008, working...)
- * nestedtemp: returns row and column coordinates, optionally
- labels plot.
+ * nestedtemp: Detected an implementation error and made
+ .NotYetImplemented(). Returns row and column coordinates,
+ optionally labels plot.
+
+ * merged last doc fixes from branches/1.11-0/ after release.
Version 1.12-0 (Feb 15, 2008)
Modified: pkg/man/oecosimu.Rd
===================================================================
--- pkg/man/oecosimu.Rd 2008-02-20 07:50:57 UTC (rev 239)
+++ pkg/man/oecosimu.Rd 2008-02-20 10:29:52 UTC (rev 240)
@@ -14,13 +14,16 @@
\alias{plot.nestedtemp}
\title{ Nestedness and Null Models for Islands or Patches }
+
\description{
- Communities are regarded as nested if they all could be subsets of the
- same community. In general, species poor communities should be subsets
- of species rich communities, and rare species only should occur on
- species rich communities. Null models generate random communities with
- different criteria to study the significance of nestedness.
+ Patches or local communities are regarded as nested if they all could
+ be subsets of the same community. In general, species poor communities
+ should be subsets of species rich communities, and rare species should
+ only occur in species rich communities. Null models generate random
+ communities with different criteria to study the significance of
+ nestedness.
}
+
\usage{
oecosimu(comm, nestfun, method, nsimul = 99, burnin = 0, thin = 1, ...)
nestedchecker(comm)
@@ -52,16 +55,16 @@
\item{\dots}{Other arguments to functions.}
}
-\details{
+\details{
Function \code{oecosimu} is a wrapper that evaluates a nestedness
- statistic using function \code{nestfun}, and then simulates a series
- of null models using \code{commsimulator}, and evaluates the
+ statistic using function given by \code{nestfun}, and then simulates a
+ series of null models using \code{commsimulator}, and evaluates the
nestedness statistic on these null models. The \pkg{vegan} packages
contains some nestedness functions that are described below, and the
generation of null models is described towards the end of this
section.
- Function \code{netstedchecker} gives the number of checker board
+ Function \code{netstedchecker} gives the number of checkerboard
units, or 2x2 submatrices where both species occur once but on
different sites (Stone & Roberts 1990). Function \code{nestedn0}
implements nestedness measure N0 which is the number of absences
@@ -85,9 +88,9 @@
In addition to these functions provided in \pkg{vegan}, any function
can be used that takes \code{comm} as the first argument, and
returns the nestedness index in item \code{statistic}. Function
- \code{\link{chisq.test}} is one such function, and examples show how
+ \code{\link{chisq.test}} is such a function, and examples show how
to do this in general. If you write a function that may be useful
- in general, please consider submitting it to \pkg{vegan} for others
+ to others, please consider submitting it to \pkg{vegan} for others
to enjoy (you will be credited as an author of that function).
Function \code{commsimulator} implements null models for community
@@ -100,7 +103,7 @@
frequencies as probabilities, and \code{r2} uses squared column
sums. Methods \code{r1} and \code{r2} try to simulate original species
frequencies, but they are not strictly constrained. All these methods
- are surveyed by Wright et al. (1998). Method \code{c0} maintains
+ are reviewed by Wright et al. (1998). Method \code{c0} maintains
species frequencies, but does not honour site (row) frequencies (Jonsson
2001).
@@ -211,7 +214,7 @@
little, and you may need long \code{burnin} and strong
\code{thin}ning in large matrices. You should plot the simulated
values to see that they are more or less stationary and there is no
- long-term periodic variation. Method \code{quasiswap} is implemented
+ trend. Method \code{quasiswap} is implemented
in plain R, and it is very slow, and it slows down very strongly
with big matrices. In general, \code{backtrack} is faster and less
sensitive to matrix size, but it also can be very slow.
Modified: pkg/man/orditkplot.Rd
===================================================================
--- pkg/man/orditkplot.Rd 2008-02-20 07:50:57 UTC (rev 239)
+++ pkg/man/orditkplot.Rd 2008-02-20 10:29:52 UTC (rev 240)
@@ -46,30 +46,30 @@
ignored in \code{plot}, but honoured in \code{text} and \code{points}. }
}
-\details{ Function \code{orditkplot} uses \pkg{tcltk} to draw Tcl/Tk
- based ordination graphics with points and labels. The function opens
- an editable canvas with fixed points , but the labels can be moved
- with mouse to better positions. 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 faithfullness of this copy is very system
- dependent. Button \strong{Export plot} used \code{plot.orditkplot}
- function to redraw the plot into graphical files. 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 dialog box. Alternatively, the
- same dialog 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.
+\details{ Function \code{orditkplot} uses \pkg{tcltk} package to draw
+ Tcl/Tk based ordination graphics with points and labels. The function
+ opens an editable canvas with fixed points, but the labels can be
+ moved with mouse to better positions. 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 faithfullness 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 dialog box. Alternatively, the same dialog 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.
The produced plot will have equal aspect ratio. The width of the
horizontal axis is fixed, but vertical axes will be scaled to needed
@@ -105,7 +105,7 @@
\author{ Jari Oksanen }
\note{
- You need \pkg{tcltk} and \R must have been configured with
+ You need \pkg{tcltk} package and \R must have been configured with
\code{\link{capabilities}} for \code{tcltk} when building the binary.
Depending on your OS, you may need to start X11 and set the display
before loading \pkg{tcltk} and starting the function (for instance,
Modified: pkg/man/ordixyplot.Rd
===================================================================
--- pkg/man/ordixyplot.Rd 2008-02-20 07:50:57 UTC (rev 239)
+++ pkg/man/ordixyplot.Rd 2008-02-20 10:29:52 UTC (rev 240)
@@ -29,8 +29,8 @@
\item{data}{ Optional data to amend ordination results. The ordination
results are found from \code{x}, but you may give here data for other
variables needed in plots. Typically these are environmental data.}
- \item{formula}{ Formula to define the plots. This is optional in
- \code{ordisplom}, but must be given in other functions. The
+ \item{formula}{ Formula to define the plots. A default formula will be
+ used if this is omitted. The
ordination axes must be called by the same names as in the
ordination results (and these names vary among methods). In
\code{ordisplom}, special character \code{.} refers to the
@@ -60,7 +60,7 @@
function so that these graphs are extremely configurable. See
\code{\link[lattice]{Lattice}} and \code{\link[lattice]{xyplot}},
\code{\link[lattice]{splom}} and \code{\link[lattice]{cloud}} for
- details, usage and opportunities.
+ details, usage and possibilities.
The argument \code{x} must always be an ordination result. The scores
are extracted with \pkg{vegan} function \code{\link{scores}} so that
@@ -78,7 +78,7 @@
The ordination scores are found from \code{x}, and \code{data} is
optional. The \code{data} should contain other variables than
ordination scores to be used in plots. Typically, they are
- environmental variables used, such as factors to define panels or plot
+ environmental variables (typically factors) to define panels or plot
symbols.
The proper work is done by the panel function. The layout can be
@@ -102,10 +102,7 @@
\code{"trellis"}.
}
\author{Jari Oksanen }
-\note{
- These are proof-of-the-concept functions that provide only a skeleton
- at the moment. Contributions are welcome.
-}
+
\seealso{
\code{\link[lattice]{Lattice}},
\code{\link[lattice]{xyplot}},
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