[Vegan-commits] r237 - in branches/1.11-0: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 20 08:12:53 CET 2008
Author: jarioksa
Date: 2008-02-20 08:12:53 +0100 (Wed, 20 Feb 2008)
New Revision: 237
Modified:
branches/1.11-0/inst/ChangeLog
branches/1.11-0/inst/NEWS
branches/1.11-0/man/oecosimu.Rd
branches/1.11-0/man/orditkplot.Rd
branches/1.11-0/man/ordixyplot.Rd
Log:
General clean-up
Modified: branches/1.11-0/inst/ChangeLog
===================================================================
--- branches/1.11-0/inst/ChangeLog 2008-02-19 17:37:03 UTC (rev 236)
+++ branches/1.11-0/inst/ChangeLog 2008-02-20 07:12:53 UTC (rev 237)
@@ -1,3 +1,4 @@
+
$Date$
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
@@ -2,7 +3,15 @@
-Version 1.12-0:
+Version 1.12-0 (Released Feb 20, 2008)
* Made a realese branch (1.11-0) based on the the rev. 204, and
relabelled this devel branch to 1.12-0.
+ * Removed nestedtemp and associated function: there was an
+ implementation error to be fixed in the trunk.
+
+ * Added a NEWS file for user visible changes, and updated
+ vegandocs() to know abot NEWS.
+
+ * Doc updates (also merged to the trunk).
+
Version 1.10-13 (closed Feb 15, 2008)
Modified: branches/1.11-0/inst/NEWS
===================================================================
--- branches/1.11-0/inst/NEWS 2008-02-19 17:37:03 UTC (rev 236)
+++ branches/1.11-0/inst/NEWS 2008-02-20 07:12:53 UTC (rev 237)
@@ -2,125 +2,138 @@
VEGAN RELEASE VERSIONS
- VEGAN 1.11-0
+ CHANGE IN VEGAN VERSION 1.11-0
-- Based on devel version 1.10-13 (rev. 205 at R-Forge).
+GENERAL
-- Gavin Simpson joined the vegan team.
+ - Based on devel version 1.10-13 (rev. 205 at R-Forge).
-- Suggests now 'tcltk' (for orditkplot).
+ - Gavin Simpson joined the vegan team.
+ - Suggests now 'tcltk' (for orditkplot).
+
NEW FUNCTIONS
-- betadisper: new functions for Marti Anderson's analysis of
- homogeneity of multivariate dispersions.
+ - anova.cca can gained a new support function to analyse marginal
+ effects of individual terms (which are similar to Type III
+ effects). Defined with argument 'by = "margin"'.
-- biplot.rda: biplot function for PCA run with rda. Arrows are used
- instead of points.
+ - betadisper: new functions for Marti Anderson's analysis of
+ homogeneity of multivariate dispersions.
-- CCorA: Canonical correlation analysis with a robust algorithm, with
- permutation test and plot function.
+ - biplot.rda: biplot function for PCA run with rda. Arrows are
+ used instead of points.
-- oecosimu: functions to analyse nestedness of communities (such as on
- islands or patches). Function oecosimu is a general wrapper, and
- commsimulator generates null-communities of various types (r00, r0,
- r1, r2, c0, swap, trial swap, backtracking, quasiswap). The
- nestedness can be analysed with functions like nestedchecker (number
- of checkerboard units), nestedn0 (measure N0), nesteddisc
- (discrepancy), but users can supply their own functions or even use
- some standard R functions such as chisq.test.
+ - CCorA: Canonical correlation analysis with a robust algorithm,
+ with permutation test and plot function.
-- ordiresids: similar diagnostic plots as in plot.lm for constrained
- ordination: Residuals ~ Fitted, sqrt(abs(Residuals)) ~ Fitted, and
- qqmath(~ Residuals) using Lattice graphics.
+ - oecosimu: functions to analyse nestedness of communities (such
+ as on islands or patches). Function oecosimu is a general
+ wrapper, and commsimulator generates null-communities of various
+ types (r00, r0, r1, r2, c0, swap, trial swap, backtracking,
+ quasiswap). The nestedness can be analysed with functions like
+ nestedchecker (number of checkerboard units), nestedn0 (measure
+ N0), nesteddisc (discrepancy), but users can supply their own
+ functions or even use some standard R functions such as
+ chisq.test.
-- orditkplot: interactive and editable plotting function. Function
- displays one set of points (species, sites) using both points and
- labels (text). The points are fixed, but labels can be dragged to
- better positions with mouse. The edited plots can be saved as EPS,
- exported to various graphical formats (EPS, PDF, PNG, JPEG, BMP,
- XFIG depending on the system) or dumped back to the R session for
- plotting and further processing.
+ - ordiresids: similar diagnostic plots as in plot.lm for
+ constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals))
+ ~ Fitted, and qqmath(~ Residuals) using Lattice graphics.
-- ordixyplot: a set of functions for Lattice graphics of ordination
- results. Includes ordixyplot for 2D graphics, ordisplom for pairs
- plots, and ordicloud for 3D graphics. All can be subsetted and
- formatted in the usual Lattice way.
+ - orditkplot: interactive and editable plotting function. Function
+ displays one set of points (species, sites) using both points
+ and labels (text). The points are fixed, but labels can be
+ dragged to better positions with mouse. The edited plots can be
+ saved as EPS, exported to various graphical formats (EPS, PDF,
+ PNG, JPEG, BMP, XFIG depending on the system) or dumped back to
+ the R session for plotting and further processing.
-- permuted.index2: New version of permuted.index() that now allows
- restricted permutations. Can produce permutations for time-series or
- line transects and for spatial grids. These can also be nested
- within 'strata'. permuted.series() and permuted.grid() are the
- relevant workhorse functions. Permutation options are set by new
- function permControl(). Currently used only in betadisper, but we
- plan to migrate vegan functions to permuted.index2() in the devel
- version, and will eventually replace the current permuted.index().
- With support function permCheck for checking permutation schemes.
+ - ordixyplot: a set of functions for Lattice graphics of
+ ordination results. Includes ordixyplot for 2D graphics,
+ ordisplom for pairs plots, and ordicloud for 3D graphics. All
+ can be subsetted and formatted in the usual Lattice way.
+ - permuted.index2: New version of permuted.index() that now allows
+ restricted permutations. Can produce permutations for
+ time-series or line transects and for spatial grids. These can
+ also be nested within 'strata'. permuted.series() and
+ permuted.grid() are the relevant workhorse
+ functions. Permutation options are set by new function
+ permControl(). Currently used only in betadisper, but we plan to
+ migrate vegan functions to permuted.index2() in the devel
+ version, and will eventually replace the current
+ permuted.index(). With support function permCheck for checking
+ permutation schemes.
+
NEW DATA SETS
-- sipoo: birds in the Sipoo archipelago (Finland, too close to Helsinki).
+ - sipoo: birds in the Sipoo archipelago (Finland, too close to
+ Helsinki).
NEW FEATURES AND FIXES
-- adonis: accepts any 'dist' object as input.
+ - adonis: accepts any 'dist' object as input.
-- as.mlm.cca, as.mlm.rda use now correct names for variables in
- aliased models. The data were pivoted correctly in R, but the labels
- were not.
+ - as.mlm.cca, as.mlm.rda use now correct names for variables in
+ aliased models. The data were pivoted correctly in R, but the
+ labels were not.
-- anova.cca can now analyse marginal effects of individual terms
- (which are similar to Type III effects). Defined with argument by =
- "margin".
+ - anova.cca assesses now P value as (hits+1)/(tries+1).
-- anova.cca assesses now P value as (hits+1)/(tries+1).
+ - anova.cca: anova(..., by = "axis") failed when fitted model had
+ terms like poly(x,2) or log(x).
-- anova.cca: anova(..., by = "axis") failed when fitted model had
- terms like poly(x,2) or log(x).
+ - bgdispersal uses now a more powerful statistic for the McNemar
+ test (in terms of Type 1 error rate).
-- bgdispersal uses now a more powerful statistic for the McNemar test
- (in terms of Type 1 error rate).
+ - calibrate.cca does correct pivoting in aliased models.
-- calibrate.cca does correct pivoting in aliased models.
+ - capscale: negative scaling in plot works similarly as in rda.
-- capscale: negative scaling in plot works similarly as in rda.
+ - decorana does not crash R when called with NULL row data, such
+ as decorana(dune[FALSE,]). Method predict(..., type="sites")
+ works correctly with downweighted analysis.
-- decorana does not crash R when called with NULL row data, such as
- decorana(dune[FALSE,]). Method predict(..., type="sites") works
- correctly with downweighted analysis.
+ - fitted.cca, fitted.rda gained argument type = "working" to get
+ the fitted values and residuals used internally in calculation
+ (in cca() these are weigthed and Chi-square standardized
+ values).
-- fitted.cca, fitted.rda gained argument type = "working" to get the
- fitted values and residuals used internally in calculation (in cca()
- these are weigthed and Chi-square standardized values).
+ - isomap checks that input data are dissimilarities or can be
+ changed into dissimilarities without warnings.
-- isomap checks that input data are dissimilarities or can be changed
- into dissimilarities without warnings.
+ - metaMDS gains argument wascores (defaults TRUE) to suppress
+ calculation of species scores.
-- metaMDS gains argument wascores (defaults TRUE) to suppress
- calculation of species scores.
+ - orditorp now handles "..." more cleanly.
-- orditorp now handles "..." more cleanly.
+ - scores.cca, scores.rda accept display = c("species", "sites").
-- scores.cca, scores.rda accept display = c("species", "sites").
+ - summary.prc honours argument 'axis'.
-- summary.prc honours argument 'axis'.
+ - taxa2dist issues now a warning if called with 'check = FALSE'
+ and some distances == 0, typically meaning that basal taxa
+ (species) were not coded.
-- taxa2dist issues now a warning if called with 'check = FALSE' and
- some distances == 0, typically meaning that basal taxa (species)
- were not coded.
+ - varpart failed if there were unused levels in factors.
-- varpart failed if there were unused levels in factors.
+ - wascores returns now NA for missing (all zero) species instead
+ of failing.
-- wascores returns now NA for missing (all zero) species instead of
- failing.
-
DOCUMENTS
-- new documents: FAQ, a simple introduction to ordination in vegan, a
- detailed explanation of diversity methods. New formatting.
+ - new documents: FAQ, a simple introduction to ordination in
+ vegan, a detailed explanation of diversity methods. New
+ formatting.
- OLDER VERSIONS
+ - Added these NEWS.
+
+
+
+ OLDER VEGAN VERSIONS
+
Version 1.8-8 (Oct 2, 2007)
* Minor bugfix release for upcoming R-2.6.0. Based on the
Modified: branches/1.11-0/man/oecosimu.Rd
===================================================================
--- branches/1.11-0/man/oecosimu.Rd 2008-02-19 17:37:03 UTC (rev 236)
+++ branches/1.11-0/man/oecosimu.Rd 2008-02-20 07:12:53 UTC (rev 237)
@@ -11,13 +11,16 @@
\alias{print.nesteddisc}
\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 only
+ should occur on 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)
@@ -43,10 +46,10 @@
\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
@@ -65,9 +68,9 @@
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
@@ -187,7 +190,7 @@
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: branches/1.11-0/man/orditkplot.Rd
===================================================================
--- branches/1.11-0/man/orditkplot.Rd 2008-02-19 17:37:03 UTC (rev 236)
+++ branches/1.11-0/man/orditkplot.Rd 2008-02-20 07:12:53 UTC (rev 237)
@@ -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: branches/1.11-0/man/ordixyplot.Rd
===================================================================
--- branches/1.11-0/man/ordixyplot.Rd 2008-02-19 17:37:03 UTC (rev 236)
+++ branches/1.11-0/man/ordixyplot.Rd 2008-02-20 07:12:53 UTC (rev 237)
@@ -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}},
More information about the Vegan-commits
mailing list