/usr/lib/R/site-library/vegan/OldChangeLog

VEGAN DEVEL VERSIONS at https://github.com/vegandevs/vegan

	ChangeLog provided a detailed development history of vegan, but it
	is not updated after September 11, 2014. Vegan moved to git source
	code management and linear ChangeLog is poorly suited for
	branching git development. Use git log to track the history in
	your current branch. The main upstream repository of vegan is
	currently https://github.com/vegandevs/vegan.

	ChangeLog gave technical details and was mainly provided for vegan
	developers. Most important user-visible changes are listed in the
	NEWS of the current release and its patched version.

Version 2.1-43 (opened September 11, 2014)

	* cca, rda, capscale: remove u.eig, v.eig and wa.eig items or
	scores scaled by eigenvectors. We have had a warning of their
	eventual removal since vegan 1.6-8, and now we finally did
	so. Scaling of scores happens when scores() function access
	normalized score items of the results.

	* commsimulator: commented out deprecation warning at the moment,
	because this triggered warnings in CRAN packages bipartite and
	metacom. Contacted the maintainers of these packages, and will put
	back the warning in 2.2-1.

	* getPermuteMatrix: works also when 'strata' are
	missing. Triggered an error in CRAN package mpmcorrelogram.

	* permustats: new function to extract permutation results from
	vegan objects, with support functions summary, density,
	densityplot, qqnorm and qqmath. Deprecated previous density and
	densityplot methods directly accessing the same results.

	* ordirgl, ordiplot3d: 3D functions using rgl or scatterplot3d
	packages were removed from vegan and moved to a new CRAN package
	vegan3d (released Oct 7, 2014).
	
	* scores.hclust: combined documentation with other hclust methods.
	
	* scoverage: removed from vegan.

	* dispweight: veganified so that uses nullmodels. Added
	gdispweight(): a new generalized method taking any glm() formula
	instead of one grouping.
	
	* betadisper Permutation tests via the `permutest()` method
	are now parallelised. The number of cores to parallelise over
	is specified by argument `parallel` in common with the
	implementation for `cca()`.

	Fix a couple of bugs in the examples; number of permutations
	was specified using `control` which is not an argument to the
	`permutest()` method for `betadisper()`.

	* text.cca: was incorrectly testing if factor constraints were
	in the biplot scores when user-suppiled lables for factors were
	given.

	* ccanova: removed from vegan. These were backup functions of old
	anova.cca, and were completely rewritten for new vegan.

	* metaMDSrotate: made defunct (replaced with MDSrotate).

Version 2.1-42 (closed September 11, 2014)

	* Opened a new version to prepare release 2.2-0.

	* Moved main development from R-Forge to GitHub.com.

	* NAMESPACE, DESCRIPTION: adapted to current R CMD check that has
	more stringent tests on attaching and importing external packages
	and using their functions.

	* getPermuteMatrix: routines have a common API based on the new
	function.

Version 2.1-41 (closed September 4, 2014)
	
	* ordiellipse, ordihull, ordispider: can now handle (omit) NA
	cases in 'groups'. They were able to omit to NA cases in scores,
	but having NA in 'groups' triggered really cryptic error
	messages. 

	* adipart, multipart, hiersimu: it is now an error to provide
	non-nested sampling hierarchy (used to be a warning).

	* new version opened with the CRAN release of vegan_2.0-10 on
	December 12, 2013.

	* anosim, mantel, mantel.partial: R CMD check told that "... may
	be used in an incorrect context". The dots were added in r2765,
	and now removed.

	* ordistep: add1.cca reported P=0 for redundant terms with 0 Df,
	and this caused an error in ordistep.

	* as.hclust.spantree: a new function to cast a "spantree" result
	object to an "hclust" tree.

	* hclust: add reorder() and rev() methods for standard "hclust"
	trees of R.  I have no clue why base R does not have these
	methods, but I provide them now in vegan. An additional reason for
	providing these methods is that reorder(<dendrogram-object>, wts,
	agglo.FUN = mean) will use unweighted mean of merged groups even
	when these are of very unequal sizes. The reorder method provided
	here will use group sizes as weights and the value of the group
	will be the mean of its leaves (terminal nodes).

	Add scores() method to extract coordinates of internal nodes or
	leaves from a plotted hclust() tree. The function is whimsical and
	may be removed before release (it is documented separately to make
	this easier).

	* biplot.rda: failed in axis scaling with negative 'scaling'
	values when some species had zero variance (and hence species
	scores was 0/0 = NaN).
	
	* cascadeKM: Calinski index for one group will now be NA instead
	of randomly chosen Inf, -Inf or NaN which can cause confusion (see
	http://stackoverflow.com/questions/21022848/r-produces-different-result-after-io-on-file
	
	* ordiellipse: failed if all points were on a line. Now handles
	these cases by drawing a line trhough the points, and issuing a
	warning from chol(): "the matrix is either rank-deficient or
	indefinite". Earlier we required at least three points for an
	ellipse, but these could still be on a line and fail. Now we
	accept two points, and draw the line with a warning. The problem
	with three points was reported by Paul Bacquet (Louvain,
	Belgium). 

	* radfit: plotting of radfit frames of several communuties failed
	if there were one-species or no-species (empty) rows. Part of this
	was fitted.radfit that now returns sensible and consistent output
	for these cases as well, and radfit.data.frame() completely
	removes empty rows from the data (with a warning).

	* RsquareAdj: return list(NA, NA) for capscale objects with
	imaginary component, and use rda method if there is no imaginary
	component. 

	* tabasco: "hclust" objects (use, sp.ind) are reordered using
	weighted means. This is a better method than the unweighted means
	used for reordering of dendrograms. Earlier "hclust" objects were
	changed to dendrograms, but now we provide reorder.hclust() and
	rev.hclust() in vegan, and can use improved method of ordering the
	table. Dendrogram and hclust labels must match the community data
	names, and now the community matrix is internally reordered to
	match the dendrograms. This requires that the clusterings do have
	labels attributes.

	* treedive, treedist: default is now match.force = TRUE, and
	treedive() gained new argument 'verbose' to turn of most messages
	-- which is practical in oecosimu().

	* BCI: names checked after http://www.theplantlist.org, but kept
	the old (alphabetic) order of species. The changes are: Abarema
	macradenium -> A. macradenia, Apeiba aspera -> A. glabra,
	Aspidosperma cruenta -> A. desmanthum, Cassipourea ellipitica ->
	C. guianensis, Chlorophora tinctoria -> Maclura t., Coccoloba
	manzanillensis -> C. manzinellensis, Cupania sylvatica ->
	C. seemannii, Dipteryx panamensis -> D. oleifera, Eugenia
	coloradensis -> E. florida, Eugenia oerstedeana -> E. oerstediana,
	Inga marginata -> I. semialata, Lonchocarpus latifolius ->
	L. heptaphyllus (this is ambiguous, since Hebestichma cubense is
	another alternative), Maquira costaricana -> Maquira guianensis
	var. costaricana, Phoebe cinnamomifolia -> Cinnamomum triplinerve,
	Swartzia simplex var. ochnaceae -> var. continentalis, Tabebuia
	guayacan -> Handroanthus g. Guarea is ambiguous: data have three
	taxa (fuzzy, grandifolia and guidonia), but theplantlist.org says
	grandifolia is an ill. synonym of guidonia. This change allows
	matching 206 of 225 BCI species with
	http://datadryad.org/resource/doi:10.5061/dryad.63q27. In
	addition, there are two vars of Swartzia simplex in BCI which
	could be matched at species level.
	
	* dune data sets: use 4+4 letter CEP names for species instead of
	old 3+3 names. Botanical nomenclature was updated: Leontodon
	autumnalis -> Scorzoneroides (Leoaut -> Scorautu), Potentilla
	palustris -> Comarum (Potpal -> Comapalu). Rows are now arranged
	numerically, and species names alphabetically, vascular plants
	first, and then the two bryophytes.

	Added data 'dune.phylodis' which are ages of dune species
	extracted from
	http://datadryad.org/resource/doi:10.5061/dryad.63q27 (Zanne AE et
	al. 2014, Nature doi:10.1038/nature12872, published online Dec 22,
	2013).

	dune.taxon was updated to APG III.

	* varespec: use 4+4 letter CEP names instead of 3+dot+3.
	Nomenclature was cautiously fixed. Most important changes: Ledum
	palustre -> Rhododendron tomentosum (Led.pal -> Rhodtome),
	Cetraria nivalis -> Flavocetraria nivalis (Cet.niv ->
	Flavniva). In addition, Dip.mon was corrected to Diphcomp
	(Diphasiastrum complanatum, should perhaps be Lycopodium c.), and
	Barbilophozia lycopodioides to B. hatcheri.

	* plot.envfit: when `envfit()` is called as
	`envfit(ord, foo[, "bar"])`, there are no useful rownames on the
	objects returned. Hence the logic in `plot.envfit()` when called
	with argument `labels` was failing.

	* rarecurve: line colour and type for each sample can now be
	specified through formal arguments `col` and `lty`. Incidental
	wish of http://stackoverflow.com/q/22714775/429846.

	* simper: now doesn't fail with obscure error when groups have a
        single member.

Version 2.1-40 (closed December 12, 2013)	
	
	* anova.cca: Function is now based on the new code, but the old is
	avaialable in a function called ccanova. The API changes:
	arguments 'step' and 'perm.max' are gone and replaced with
	'permutations' that accepts a how() object defining permutations,
	or a single number like previously or a permutation matrix. The
	new anova.cca adds an option of analysing a sequence of ordination
	models. This also means that '...' is now the second argument and
	the names of all arguments must be written in full. This change
	can be expected to cause trouble outside vegan. Currently the
	tests in examples are passed, but tests fail (looks like being
	caused by the change in API). 

	* add1.cca, drop1.cca, ordistep, ordiR2step: functions were
	adapted to new anova.cca and this brought along similar changes in
	API. 

	* envfit: function assumed that environmental variables are either
	factors or numeric, and choked if they were neither but, say,
	character strings. Now the function tries to coerce all
	non-numeric variables into factors, including character strings
	and logical. This is one possible reason for problems reported in
	https://stat.ethz.ch/pipermail/r-sig-ecology/2013-December/004217.html,
	although the reported case is irreproducible and we cannot be
	sure. Also fixed handling of tied values in assessing the P-values
	in vectorfit.

	* nestednodf: vegan 2.1-36 (release 2.0-10) changed the function
	so that weighted analysis of binary data was equal to unweighted
	binary analysis, but this broke consinstency with the original
	software and publication by Almeida-Neto & Ulrich. The fix was now
	made optional, and the default is to follow published method by
	adding argument 'wbinary' (defaults FALSE). Based on the
	suggestion by Matt Barbour in GitHub.

	* ordispider: can now use spatial medians as centres instead of
	the default centroids. The kind of centre is defined by new
	argument 'spiders'.

	* tests for cca/rda/capscale: commented out test that failed with
	the anova.cca. Known issue was that 'by = "term"' and 'by =
	"axis"' stop with error with missing data. This was designed and
	and can be re-designed to handle missing data by listwise deletion
	so that models will have the same number of observation for every
	variable.  An unknown issue was that 'by = "margin"' failed in
	capscale(). This may be a scoping issue an needs inspection. We
	keep the old vegan-tests.Rout.save file so that we are reminded of
	the problems at every check.
	
Version 2.1-39 (closed December 3, 2013)

	* anova.cca: started to rewrite the anova.cca family of functions
	for permute package. At the first stage, a temporary development
	function anovacca was created. The user interface was changed, and
	the function no more adapts the number of iterations for the
	P-value, and arguments 'step' and 'perm.max' were removed.
	Instead, permute package is used to create a permutation matrix
	used in all cases with fixed number of permutations.

	In addition to the overall test, the function allows now testing
	a sequence of models (anova.ccalist). Specific tests provided are
	by = "term" (anovacca.byterm) which is fitted as a sequence of
	models in anova.ccalist. Case by = "margin" directly calls
	permutest.cca and gets the significances from differences of
	residual variation similarly as anova.ccalist. Case by = "axis" is
	is implemented as a marginal model.

	Simple permutations give identical results for "term" and "axis"
	cases, but by = "margin" is different. Marginal models were
	implemented as partial models with other parameters partialled out
	in vegan 2.0 and earlier, but the current implementation is an
	anova.ccalist model where the parameter in question was removed
	and model compared against the complete model.

	* commsim: documentation (commsim.Rd) was restructured so that
	nullmodels were collected under separate sections with a brief
	introductory text and shorter specific text of the
	algorithm. Hopefully this makes easier for an outsider to grasp
	the width of the choices.

	* oecosimu: change printed quantiles to match the direction of the
	test as changed in r2495.

	* permutest.betadisper: updated to the new permute API and operates
	similarly to permutest.cca in respect of how the permutation test
	can be defined. It currently doesn't support the parallel processing
	of the cca method, however.

	* tests: vegan examples and vegan-tests have been out of sync for
	a long time. These have not been updated because most of the
	changes seem to be triggered by switching to R 3.0-x, and we have
	not had time to analyse the reasons. The differences also seem to
	be platform specific, and Linux and MacOS give slightly different
	results. In particular, there seem to be differences in
	permutations, constrained ordination, in particular in capscale()
	and rounding of output. We have also introduced some changes in
	output that were not yet synced.

	* janitorial: vegan has been dependent on R >= 2.14.0 since
	version 2.1-34 (r2597 Wed 28-Aug-2013). Now superfluous references
	and tests for the older R version were removed in R code and
	documentation. FIXME: cca() returns residuals.zombie item that was
	supposed to be needed in R < 2.13.0. This was not yet removed: we
	must first check that this can be safely done.

	vegan also now depends on permute version 0.7-8 or later.

Version 2.1-38 (closed November 10, 2013)

	* DESCRIPTION: depends on permute >= 0.7-5, where the
	permute::how() result object can be updated.

	* bioenv: returns now the number of the best model ('whichbest'),
	the standardized environmental data ('x') and the distance
	function used for the environmental data ('distfun'). New function
	bioenvdist() uses these to re-calculate the environmental
	distances for the best model, or any other model selected by its
	number.

	* permutest.cca: permutation test uses 'permute' package. The old
	interface was retained, and 'permutations' can be a single number
	or a permutation matrix (as previously), but now it can also be a
	how() object of the 'permute' package. The argument 'strata' was
	also retained, but it is planned to be deprecated in the future,
	and it is recommended that users switch to defining 'blocks' in
	how(). 

	* renyiaccum: plot() works also when only one index ('scales') was
	used. The function gained new argument 'collector = FALSE' to
	accumulate sites in the order they are in the data set in addition
	to the summary statistics of permutations. This can be used to
	analyse the randomness of the particular order of sites (looks
	like my student would need this).
	
Version 2.1-37 (closed November 5, 2013)

	* anova.cca: added new function anova.ccalist() to compare a
	sequence of models. The function is still experimental ("proof of
	the concept") and unexported. If this stays in vegan, it should
	eventually be called from anova.cca(). This would bring along a
	change of API to anova.cca(object, ..., alpha=...): the dots must
	follow the first argument which turns of positional and partial
	matching of arguments so that the function can collect the "cca"
	models. We must decide whether the new function is worth such a
	change that can make life harder for ordinary users.

	One potential advantage is that the code in anova.ccaby* functions
	could be simplifed to a anova.ccabylist() calls.

	The function is based on calling permutest.cca for each model with
	identical permutations. We can then compare the change in model
	for each permutation and collect the test statistics for
	differences. This requires that the models really are nested so
	that residual deviance certainly decreases in bigger model
	(testing theory requires nesting, but this is commonly violated by
	users: here nesting is necessary). 

	* parellel: default cluster defined by setDefaultCluster() is no
	longer used in functions with parallel processing. Using default
	cluster would need querying an unexported environment
	parellel:::.reg, and this gives a NOTE in R CMD check.

	* specaccum, renyiaccum, tsallisaccum: gained argument to select a
	'subset' of sites (looks like my student would need them).
	
Version 2.1-36 (closed October 14, 2013)

	* opened with the release of vegan 2.0-9.

	* decostand(..., "normalize") uses now .Machine$double.eps to
	replace zero sum of squares instead of matrix minimum.

	* envfit: if a variable is constant, no fitted vector can be
	calculated and results will be given as NA (with warnings).
	Plotting of all vectors will fail in such cases because no finite
	scale was found for arrows. Fixed on ordiArrowMul.

	* envfit: try to produce something sensible if fitted variable has
	constant values (invariable vector, one-level factor). Report
	arrow heads as all zero, and R2=0 for vectors, and the centroid to
	the data centroid and R2=0 for factors. Tied values are now
	treated differently in factorfit: now they support null
	hypothesis, previously they decreased the P-values. 

	* fisherfit: completely rewritten and estimates of standard error
	removed: I could not find no justification for these. Actually, it
	seems that the value of Fisher alpha as estimated in the function
	was independent of the abundance distribution of species, but will
	be defined by the number of species (S) and number of individuals
	(N). Now the Fisher alpha is estimated from the relationship S =
	alpha*(1 + log(N/alpha)) using function uniroot(). Because of
	this, standard errors cannot be estimated and they were
	removed. In addition, functions confint.fisherfit,
	profile.fisherfit and plot.profile.fisherfit were removed. The
	estimation of standard errors was also removed in function
	fisher.alpha (that only calls fisherfit).

	* nestednodf: matrix fill was wrongly calculated in weighted
	analysis. The nominator was length of 'comm', and if input was a
	data frame that was the number of columns instead of the number of
	cells. The fill was correct in non-weighted analysis because there
	data were transformed to a matrix, and the length of a matrix is
	the number of cells (unlike in data frames).

	* nestednodf: weighted analysis gave all statistics as zero if
	binary data were supplied. Some ">" comparisons were changed to
	">=" and now weighted analysis of binary data gives same results
	as non-weighted analysis. However, this can change results of
	weighted analysis of quantitative data. The change needs
	endorsement by the function author Gustavo Carvalho.

	* oecosimu: warns user if the specified nullmodel 'method' changes
	quantitative input data to binary data under cover. Some people
	have not noticed this.
	
Version 2.1-35 (closed September 25, 2013)

	* ordilabel: colour arguments ('col', 'fill', 'borderä) can now be
	vectors and will be recycled if needed. May need care if used with
	'select', but should work with 'priority'. This was needed for a
	function under development and testing: when labelling over lines,
	it may be nice if the border has the same colour as the line
	covered.

	* MDSrotate: can now rotate a solution to more than one vector,
	provided that the number of dimensions is higher than the number
	of vectors. Because fitted vectors usually are correlated, only
	the first vector is aligned to dimension 1, but second vector and
	further are oblique to the corresponding axis. In any case they
	will have zero correlation to all subsequent dimensions.

	* simulate.rda, simulate.cca: gained argument 'correlated' for
	using covariances of species in generating correlated multivariate
	normal residuals in parametric simulations. The covariances are
	estimated from the residual ordination of species. The argument
	defaults FALSE which implements the old parametric simulation
	where each species is simulated independently.  The argument has
	no effect in capscale() which stores no information on species.
	
Version 2.1-34 (closed September 5, 2013)

	* DESCRIPTION: dependent on R >= 2.14.0.
	
	* DESCRIPTION, vignettes: R 3.0.2-to-be checks with --as-cran
	requires (with a NOTE) the vignettes source files (Rnw) to be in
	vignettes/ directory.  Because Makefile is not executed in
	inst/doc if vignettes/ directory is present, all other sources had
	to be moved to vignettes/ as well with vignettes/.install_extras
	to move those to inst/doc after building. This also made
	/.Rinstignore unnecessary. The vignettes directory was introduced
	and made recommended in R 2.14.0 so that the this version of vegan
	depends on R >= 2.14.0. 

	* tweaks for R < 2.12.1 removed: code to fix buggy naming of
	columns in qr.X before 2.12.1 (as.mlm.cca/rda, intersetcor), and
	change in the cmdscale() output (eigenvals.default).

	* tweak for R < 2.13.0 removed: change in cmdscale() output
	(capscale).

	* vegandocs: does not use unexported tools:::httpdPort. Now only
	remaining ':::' case is querying default cluster in the
	environment parallel:::.reg.
	
Version 2.1-33 (closed August 28, 2013)

	* DESCRIPTION: new dependence on lattice. Passes new strict R
	checks with NOTE on ':::' calls to tools:::httpdPort (to launch
	reading vegan NEWS.html in existing browser window) and
	parallel:::.reg to acces the defaultCluster in an unexported
	environment within 'parallel' Namespace.
	
Version 2.1-32 (closed August 19, 2013)

	* opened a new version with the CRAN release of vegan 2.0-8.

	* merged Eduard Szöcs's code on dispersion weighting of
	overdispersed species following Clarke, K. R., M. G. Chapman,
	P. J. Somerfield, and H. R. Needham.  2006. Dispersion-based
	Weighting of Species Counts in Assemblage Analyses. _Marine
	Ecology Progress Series_, 320, 11–27. The basic development was
	made in github.com and merged to R-Forge.

	* nullmodel: replaced internal indshuffle() function in
	make.commsim() with much faster stats::rmultinom(). The
	rmultinom() function takes argument 'n' for the number of random
	vectors, and using this could be still faster, but we only
	generate one vector in time. Using 'n' would require better
	analysis of individual nullmodels. The commit changes random
	sequences, but passes tests.

	* oecosimu: Gained argument 'batchsize' to set the maximum size of
	simulated nullmodels (in Mb). If a larger object would be
	produced, the analysis is broken into several batches to avoid
	exceeding the maximum size. This avoids exhausting memory which
	can make whole R unresponsive and analysis very, very slow. In
	general, the argument is needed with large data sets and/or large
	number of simulations.

	* orditkplot: bmp has been available in unix-alike OSes since
	2008, or a moth after writing orditkplot. Thanks to Brian Ripley
	for informing us.

	* vignettes: vignettes use now standard article style instead of
	hacked jss style. Decision and diversity vignettes are in two
	columns, but intro in one (R output did not fit in one
	column). The common packages, macros and definitions were moved to
	new vegan.sty which is written so that it should work both with
	amsart and article, and with one and two columns. Figures are now
	in standard figure environment, but intro redefines this to use
	sidecaption figures.  
	
Version 2.1-31 (closed July 10, 2013)

	* Dependencies: Vegan now depends on a version equal to 0.7-4 or
	later.

	* betadisper, permutest.betadisper: Modified to use the new
	permute package API (from version 0.7-3 onwards). The `permutest`
	method gains a new argument `permutations`, which takes a matrix
	of permutations to be used.

	* protest: modified to use the new permute API. Gains argument
	`control` which describes the design. As a result, `strata`
	argument has been removed and `permutations` argument can only
	be used to supply your own matrix of permutations. The number of
	permutations and other features of the design are set via `control`
	and function `how()` from permute.

	* ordipointlabel: now uses `ordiArgAbsorber()` to stop the warnings
	about non-graphical paramters being passed to plotting functions.

	* ordisurf: can now pass in a line width for the contours via
	argument `lwd.cl`.

	* ordiArrowTextXY: New (internal) support function that finds
	coordinates of text box at the point of the arrow so that the
	arrow point just touches the text.  This should improve
	positioning of the arrow labels and avoid writing labels over the
	arrows.

	* plot.envfit, plot.cca, text.cca: use ordiArrowTextXY() for arrow
	labels instead of expanding arrow heads by 10%.

	* plot.envfit: plot(..., add = FALSE) estimated string (text)
	dimensions after plot.new() but before plot.window(). Since
	plot.new() sets xlim, ylim to c(0,1) and then plot.window resets
	the limits to the data values, string dimensions in user units
	were poorly estimated. This became evident with new positioning of
	arrow text based on string dimensions.

        * plot.ordipointlabel: gains a plot method that is very similar to
        `plot.orditkplot()` but which does not mess with graphical
        parameters. This allows it to fit more naturally into a standard
        R workflow (it plays nicely with `layout()` for example.

	* stressplot: metaMDS and monoMDS stressplot() use now
	expression(R^2) instead of ascii R2.  The stressplot.monoMDS()
	function returns the plotting structures in the original input
	order.

	* vignettes: Brian Ripley urged as to remove
	\usepackage{inconsolota} as this package is on the way to be
	removed from CTAN.

Version 2.1-30 (closed June 12, 2013)

	* bioenv: can now use Mahalanobis, Manhattan and Gower distances
	for environmental variables.  The Mahalanobis distances are based
	on orthogonalized data, Manhattan distances give the direct sum of
	differences of environmental variables, and Gower distances can
	also handle factor variables. This involves adding internal
	function veganMahatrans() for Mahalanobis transformation.  The
	change was triggered by a recent email by Lydia Beaudrot (UC
	Davis) to implement Mahalanobis distances, and in the same I also
	implemented Robby Marotte's suggestion of using Gower distances
	(vegan Forum item in R-Forge in July 2012). The output is changed
	to show the 'metric' and the name of the 'method' is fully
	expanded. No more fails if 'upto' is too large. Passes "..." to
	cor() like documented, but never done.

	* rankindex: can now use Mahalanobis or Manhattan
	distances. Scales automatically gradient variables to unit
	variance (Euclidean) or range (Manhattan), and the scaling is
	already inbuilt in Mahalanobis and Gower.

	* vegdist: added Mahalanobis distance.

Version 2.1-29 (closed April 19, 2013)

	* ordisurf: significant changes were made to this function:

	 - The default for `method` and `select` were changed to `"REML"`
	and `TRUE` respectivelt.

	 - Argument `thinplate` is deprecated in favour of `isotropic`. A
	warning is now issued if `thinplate` is used.

	 - The spline basis for the smoother can now be specified from a
	subset of those implemented in the mgcv package. This is achieved
	via the `bs` argument, which defaults to `"tp"` for thin plate
	regression splines.

	 - Argument `knots` and `bs` can now be a vector of length two, one
	per ordination dimension considered. This is only of use with
	anisotropic surfaces with `isotropic = FALSE`.

	 - New argument `fx`; indicates whether the smoothers are fixed
	degrees of freedom regression splines (`fx = FALSE`) or a
	penalised regression spline (`fx = TRUE`). Can be a vector of
	length 2 for anisotropic surfaces (`isotropic = FALSE`).

	 - The number of locations in each ordination dimension at which the
	fitted surface is evaluated can now be specified via new argument
	`npoints`.

	 - The formula passed to `gam` is now built in greater detail. When
	the model is printed the user can see exactly how the smoother was
	constructed.
 
	* oecosimu: the interpretation argument "alternative" was really
	twisted. We now changed the test direction and have a much clearer
	explanatory text in printed output. The issue was raised by Juan
	Manual Barreneche (jumanbar) in GitHub (issue #14). NB. The
	direction of the test changed from previous versions.

	* raupcrick: adapted to the change in oecosimu() to define the
	direction of the test.

Version 2.1-28 (closed April 19, 2013)

	* betadisper: failed with type = "centroid" when there was only
	one group (i.e., in estimating the overall beta diversity in the
	data). Reported by Pierre Legendre.

	Now correctly reports distance to "medoid" in the print method
	when type = "median". Reported by Pierre Legendre. The print
	method also now shows only the first 8 eigenvalues.

	* eigenvals: new method for class "betadisper".

	* rda: eigenvalues are now regarded as zero if they are very small
	compared to the first eigenvalue. Earlier we used fixed limit of
	1e-4, but now the limit is first eigenvalues * 1e-5. Similar
	change was not made in cca, since there the theoretical maximum of
	the eigenvalue is 1, and comparison to an absolute minimum
	threshold of 1e-4 makes sense.
	
Version 2.1-27 (closed March 17, 2013)

	* cca/rda/capscale: removed references to 'u.eig' and 'v.eig'
	items in support functions. These now use 'u' and 'v' items and
	scale these with 'eig' (or diag(sqrt(eig))) when needed. This
	prepares for removing items 'u.eig', 'v.eig' and 'wa.eig' in vegan
	2.3 and 2.4. Concerns fitted.capscale, goodness.cca and
	goodness.rda. The documentation has warned about removing these
	*.eig items for years, and most vegan functions already avoided
	using them. We have no idea if any external packages depend on
	these and therefore we delay the removal till vegan 2.3 and 2.4
	release. However, we warn about this in NEWS for 2.0-7 and also
	say this clearly in cca.object documentation.

	* nestedtemp: function failed if the matrix fill was < 0.38%,
	because the fill line parameter was outside the original
	estimation bracket. Now bracket is moved up if the estimation
	fails. The problem was reported by Carsten Dormann (Univ Freiburg)
	and Benjamin A. Sikes (Lincoln University, NZ).
	
	* specaccum: gained argument 'w' for weights to give the sampling
	effort. This resurrects a feature that was introduced in r1505 (22
	Feb 2011) and 1507, and removed in r1606 (26 May 2011). It seems
	that BiodiversityR::balanced.specaccum() provides the same feature
	but we still try it here.  The feature was resurrected after a
	user query by Bastien Mérigot (Univ Montpellier II). The working
	of the new argument is still untested with specaccum() support
	functions.

	* fitspecaccum: model = "asymp" was actually fitting logistic
	regression (the same as model = "logis").

	* text.cca, points.cca: gained argument 'axis.bp' (defaults TRUE)
	to suppress drawing axes for scaled biplot arrows. Only effective
	if 'bp' scores were requested.

	* wcmdscale: setting only weights 'w' does not force full
	"wcmdscale" output but returns only the matrix of coordinates of
	real axes. Similarly, setting 'add = TRUE' would not force
	"wcmdscale", but 'add' is not implemented.
	
Version 2.1-26 (opened February 11, 2013)

	* New version opened with the release of vegan_2.0-6 on February
	11, 2013.

	* metaMDS: exposed argument 'maxit' in metaMDSiter() so that users
	can set the number of iterations in monoMDS() or isoMDS().
	metaMDS(..., trace = 2) show the stopping criterion used in with
	engine = "monoMDS". After wishes by Jon Bakker, Univ Washington
	(U.S.A.).

	* tabasco: a sister function of vegemite() to display a compact
	community table using heatmap(). Both vegemite() and tabasco() can
	handle cluster::agnes() trees.

	* wcmdscale: return a full "wcmdscale" object if any argument is
	set to non-default value. This also implies that if weights 'w'
	are set, the result will be full "wcmdscale" object with a
	"weights" item, instead of a simple matrix with no information
	about weights used.
	
Version 2.1-25 (closed February 11, 2013)

	* FAQ: new entry on impossibility of using random effects in cca,
	rda, capscale & adonis, and telling how to do this
	approximately. Please comment and correct.

	* oecosimu: changed the structure of the oecosimu() result
	object. It now returns a list of two items: "statistic" is the
	observed statistic, and "oecosimu" which contains the simulation
	records. In previous version the function returned the statistic
	and added item "oecosimu" there. Previously, the result object was
	of type c("oecosimu", class(statistic)) as the original
	"statistic" object was returned amended with an "oecosimu" item,
	but now it is only of type "oecosimu" with the original
	"statistic" as a separate item. So "statistic" is now one level
	deeper instead of being the main object.

	* predict.cca, predict.rda: In rev2412, 2413 we studied including
	partial (pCCA) component in predict(..., type="response") and
	predict(..., type="working") models, but then adopted a policy of
	never having partial component, but always returning only the
	component requested for. Therefore warning messages of ignoring
	pCCA component were removed. This log entry was made to emphasize
	that there is a policy decision, and an alternative policy can be
	tracked in the repository.

	* fitted.[cca,rda,capscale]: can now return partial component with
	argument 'model = "pCCA"'.

	* simulate: the simulate functions for "rda" and "cca" return
	objects with original row and column names. Function capscale()
	already did so, and simulate.nullmodel() was changed so in vegan
	2.1-24 (r2396).
	
Version 2.1-24 (closed February 2, 2013)

	* simulate.nullmodel: output array inherits dimnames after the
	input data matrix, this is often required by oecosimu.
	Dimension names are now only stored once for all nsim
	simulations, so it is an improvement over the implementation
	in commsimulator.

	* oecosimu: the 'oecosimu' list cannot be added to the result if
	the nestfun() returns a data frame. In that case, the 'oecosimu'
	list is treated like a variable, and this gives either an error of
	wrong length or if the length matches, a mess.  Now data frame is
	silently turned into a list which also means that it will not be
	printed with the output. The name of the 'statistic' is not used
	for unnamed vector output where it would only name the first item
	(like would be the case if the 'statistic' was extracted from a
	data frame). It is now checked that only one 'statistic' is given
	and a comprehensible error message is issued instead of the
	current confusing one. The changes were trickered when testing
	picante::pd().

	* protest: huge speed-up. Instead of calling procrustes() in every
	permutation step, we only calculate the goodness of fit statistic
	in svd(). This avoids a huge overhead of procrustes(). In a test
	with a 160 x 12 matrix (RDA scores from Bryce Canyon data
	'bryceveg') with 9999 permutations, the time went down from 12 sec
	to 0.8 sec in my desktop. The analysis prints now also the 'ss'
	term (residual sum of squares) which for symmetric analysis is
	equal to squared m12.

	* procrustes: marginally faster way of getting sum of squares of a
	matrix. This should not influence the results, but one metaMDS()
	trace result has a small difference in nearly-zero rmse (was
	1.094382e-06, is 1.09439e-06) in my desktop.

	* treedive, treedist: treedive() did not correctly match data and
	tree when the tree contained species that did not occur in the
	data. Function treedist() tries to match tree and data when their
	sizes differ, and argument 'match.force' was added to force
	matching even when sizes do not differ.
	
Version 2.1-23 (closed January 25, 2013)

	* clamtest: Richard Telford reported an extreme case 
	{rbind(a=c(1,0,5,10,4),b=c(0,10,5,2,1))} where
	clamtest failed due to inadequately setting up minimum
	abundance thresholds for rare species. The issue is solved
	by hard coding the minimum values to be 1 when no suitable 
	solution is found. Also, clamtest failed when the community matrix 
	had no column names, this is now fixed.

	* capscale: It was wrongly assumed that eigenvalues could be used
	in normalization of species scores, but this worked only with
	Euclidean distances. Now normalization is done explicitly with
	decostand() function. This change means that scaling of species
	scores will change, and graphs can look different than
	previously. All analyses should be redone. Function now displays
	the value of the additive constant with 'add = TRUE'.

	* stressplot: added stressplot() methods for wcmdscale(),
	capscale(), cca(), rda(), prcomp() and princomp() results.  These
	also work with constrained ordination. These methods display the
	ordination distances in given number of dimensions (defaults 'k =
	2') against original observed distances.  These original distances
	are found from the full space solution, and in capscale() and
	wcmdscale() they are correct for the imaginary axes. The weights
	are used in wcmdscale() and cca() so that their distances differ
	from plotted ordinations, but agree with eigenvalues. Partial
	models (p-dbRDA, pRDA, pCCA) add the partial component both to the
	original dissimilarities and the fit.

	The row scores (u) alone will not correctly estimate original
	dissimilarities in constrained (or partial) ordination. In
	unconstrained ordination we can get the distances as dist(u %*%
	diag(sqrt(eig))), but in constrained ordination this will not give
	the observed dissimilarities with all axes. Currently we get the
	ordination distances from a (low-rank) approximation of the data
	as dist(u %*% diag(sqrt(eig)) %*% t(v)). However, it is not sure
	that this the right thing to do, but perhaps we should acknowledge
	the fact row ordination with constraints does not approximate
	distances. So this may change.

	* wcmdscale: added method functions print(), plot() and
	scores(). Now class "wcmdscale" results also retun the function
	call and dimensions have names.

	* ordilabel: was missing ordiArgAbsorber() on the plotting calls
	to text() and polygon(). Thus lots of warnings were raised in use.

	* orditorp: added argument select, to choose which of the rows of
	scores are plotted, so matches with ordilabel() and
	ordipointlabel().
	
Version 2.1-22 (closed January 8, 2013)

	* multipart: argument global was printed as TRUE regardless of the
	actual argument value. This did not affect calculations. Reported
	by Valerie Coudrain.

	* monoMDS, metaMDS: Default convergence criteria were changed in
	monoMDS. Most importantly, now scale factor of the gradient is
	sfgrmin = 1e-7. The former limit 1e-5 was much too slack with
	large data sets and iterations stopped too early without getting
	close to the solution. In addition, scores() ignore now requests
	to scores beyond those calculated instead of failing, and
	scores.metaMDS() does not drop dimensions.

	* metaMDS: Iteration sometimes finds a false convergence, or an
	identical solution to the previous best although a better solution
	can exist. These are undetected except sometimes in parallel
	processing. Therefore we first label convergence false when we
	find a new best solution, and then study if it really
	converged. This is a rare effect, and can only be seen with
	parallel processing. An example is

	set.seed(7)
	metaMDS(BCI, k=4, parallel=2)

	which will converge in run 7 with the old code although run 8
	would be better, but converges in run 18 with the new code.
	
	* nestednodf: added plot() method modelled after
	plot.nestedtemp().
	
	* ordiR2step: gained argument 'R2scope' (default TRUE) which can
	be used to turn off the criterion of stopping when the adj-R2 of
	the current model exceeds that of scope.  This option allows model
	building when the 'scope' would be overdetermined (number of
	predictors higher than number of observations). Pierre Legendre
	needed this option for some checks with huge AEM/PCNM scopes.

	* envfit, plot.envfit: Plotting an object fitted by envfit() would fail
	if p.max was used and there were un-used levels for one or more factor
	constraints. The un-used levels could result from deletion of
	observations with missing values or simply the result of supplying
	a subset of a larger data set to envfit(). Both cases are now handled
	through the use of droplevels().

Version 2.1-21 (closed November 19, 2012)

	* New version opened with the CRAN release of vegan 2.0-5 on Oct
	8, 2012.

	* dispindmorisita: output gained a new column for Chi-squared
	based probabilities that the null hypothesis (random distribution)
	is true.

	* clamtest: output was wrong when some of the possible
	species groups were missing (bug report submitted by R Telford).

	* procrustes: plot() of two-dimensional solutions often draw
	original axes in a wrong angle. The problem was reported by
	Elizabeth Ottesen (MIT).

	* msoplot: gained legend argument for positioning the legend
	according to user needs.

Version 2.1-20 (closed October 8, 2012)

	* anova.cca: Dr Sven Neulinger (Christian Albrecht University,
	Kiel, Germany) reported several problems with anova.cca cases. All
	these were problems in scoping. Two problems solved with this
	commit were: (1) anova.cca(..., by = "axis") always failed in
	partial analysis (with conditions), (2) anova.cca(..., by =
	"term") failed in partial models when there was no 'data='
	argument, but the variables were in the global workspace. The
	first fix also seems to allow anova(<prc.object>, by = "axis")
	that used to fail. In addition, there is one unsolved problem with
	search order: stats function C() is found instead of variable 'C'
	and this gives an error message "object is not a matrix".

	* radfit: The methods are now more consistent over different
	levels of radfit models (radline, radfit, radfit.frame).  The
	common methods to all include now AIC(), coef, deviance(),
	logLik(), predict() and fitted(). The radfit() objects gained
	points() and lines() methods. The data frame method also works
	with matrices.  The predict() method gained new argument to change
	the expected 'total' size of communities. The fitted() returns now
	named vectors or matrices. It seems that radlattice() never
	displayed BIC contrary to documentation and labelling in graph.
	This has been wrong since the introduction of radlattice in r551
	(2008-11-09).  Now radlattice also check that it gets the "radfit"
	object it can handle.

	* Rd: documentation files upgraded to the third English edition
	(2012) of Legendre & Legendre.
	
Version 2.1-19 (closed September 16, 2012)

	* adonis: Small changes in calculations. Simplified calculations
	of matrix G as centred distance matrix, and does not keep n x n
	matrices that are not needed (A) or used only once (identity
	matrix I). These can make calculations marginally faster and
	reduce the memory usage, but probably there are no observable
	effects in most data sets. The new centring is probably more
	accurate than older, and therefore the last significant digits can
	slightly change (magnitude 1e-12 in tests).

	* betadisper: An effective R stats .C function was used for double
	centring, but it was removed from the API in r60360 | ripley |
	2012-08-22 07:59:00 UTC (Wed, 22 Aug 2012). This removal stopped
	betadisper() with error. Now we have a less efficient R code for
	the same purpose. However, the effects in timing should be
	negligible.
 
	* density methods: all vegan functions that return simulated or
	permuted statistics have now density() methods that directly
	access the returned statistic. The functions return an object of
	class "vegandensity" that inherits from class "density". The
	object is identical to class "density", but it is amended with
	item "observed" that contains the observed statistic. The observed
	statistic is also put among permuted values when estimating the
	density. This can cause a pimple in density lines when the
	observed statistic is very different from simulated values, but it
	is consistent with the permutation tests.

	The function has a plot.vegandensity() function that is similar to
	plot.density(), but it also draws a vertical line for the observed
	statistic.

	The density methods were made available for adonis, anosim,
	mantel & partial.mantel, mrpp, permutest.cca and procrustes. The
	anova.cca function does not return permutated statistics.

	All density methods handle only one statistic. Function adonis()
	can return a matrix of permuted F-values for each term, and it
	gained a densityplot method (lattice package) that can handle all
	these simultaneously.
	
	Functions adipart, hiersimu and multipart were made
	oecosimu-compliant earlier and simultaneously they also gained the
	density and densityplot methods.

	* mantel, mantel.partial: Gained argument na.rm (defaults FALSE)
	to remove missing values from dissimilarities. To implement this,
	there were some internal changes in functions (that should not
	influence the results): The functions mixed cor.test() and cor(),
	but now only use cor(). Function cor.test() was only used to get the
	textual presentation of the correlation 'method', but this is now
	found internally.

	* protest: do not return the observed statistic as one of the
	permuted values but separately.

	* radfit: gained a predict method which works for single models
	('radline'), radfit, and radfit.frame. All predict functions
	accept 'newdata' which need not be integer, but extrapolation may
	fail for some models.  Needs still documentation. The function was
	provided due to a user request.
	
Version 2.1-18 (closed August 20, 2012)

	* cIndexKM: internal function count() triggered a warning in R CMD
	check with R-devel because the funtion used .C() call to an
	unloaded packages "cclust". count() was never called in the
	current cIndexKM() and was removed together with the following
	currently unused functions: withinss(), varwithinss(),
	maxmindist(), vargss(). These deletions should have absolutely no
	visible effects.

	* envfit: the plot() method gained argument 'labels' to change the
	default labels. The default labels are displayed with the new
	labels() function.

	* vignettes: building vignettes failed in CRAN and R-Forge. These
	sites use TeXLive 2012 distribution which was not yet used by any
	vegan developer when vegan 2.0-4 was released. Ubuntu Linux still
	stocks TeXLive 2009, and new version is promised first for the
	12.10 release, and many other Linuxes are just as old. TeXLive
	2012 for MacOS was released in July 2012 and with that we could
	pin down the problem. There is hardly any user visible changes
	except that building vegan succeeds with vignettes.
	
Version 2.1-17 (closed July 30, 2012)

	* New version opened with the CRAN release of vegan 2.0-4 on June
	18, 2012.

	* biplot.rda: bug in specification of `type` argument if not supplied
	by the user; should have been a vector of length == 2.

	* adipart, hiersimu, multipart: default and formula methods of
	these functions were identical (also for the calculations) except
	in interpreting the input. Now the formula method only interprets
	the formula and calls the default method for the actual
	calculations without replicating its code. The "call" attribute of
	these functions now returns the generic function name without
	".default", ".formula" suffix. 

	Functions use now print.oecosimu() for displaying results and
	their specific print.*() functions were deleted. This involved
	changes in attributes: the printed attributes are now in
	object$oecosimu$simulated instead of object.

	* oecosimu: returns "call" attribute similarly as adipart(),
	hiersimu() and multipart(). The print.oecosimu() output changed,
	and shows the call. print.oecosimu() is able to display adipart(),
	hiersimu() and multipart() results, but does not show all
	informations that those dedicated functions showed about options. 

	* Formula methods for adipart/multipart/hiersimu functions
	use a new internal (hierParseFormula) to interpret the formula.

Version 2.1-16 (closed June 18, 2012)

	* envfit: plot() gained new argument 'bg' that triggers labelling
	with ordilabel() using the colour given in 'bg' as the background.

	* simper: added parallel processing for permutation tests in
	accordance with other vegan functions and with similar user
	interface. The code was developed by Eduard Szöcs in
	http://github.com.

	* predict.cca: number of rows must match in the original data and
	'newdata' of cca() result, because original row weights are used
	in scaling the results.  Now the match is checked, and
	non-matching 'newdata' is ignored with warning.  Earlier this gave
	an error.  Reported by Glenn De'ath.

	* betadisper: the method is biased with small, unequal group
	sizes. Bias corrected version can now be used with new argument
	'bias.adjust' (defaults 'FALSE'). The problem was analysed and
	bias correction developed by Adrian Stier and Ben Bolker.

	* .checkSelect: standardise those plotting functions that have a
	'select' argument that controls which rows of the scores are
	plotted. All these functions now use .checkSelect() to check and
	apply 'select' as appropriate.

	* ordipointlabel: gains argument 'select' which allows some rows
	of the plotted scores to be skipped in the same manner as for
	text.cca(). This only applies when a single set of scores is
	plotted. Otherwise it is ignored and a warning issued.

	* ordihull, ordiellipse: defaults to use semitransparent fill
	colour with 'draw = "polygon"', and gain argument 'alpha' to set
	the transparency.

	* ordihull: gained explicit 'col' argument and adds labels after
	drawing convex hulls so that filled hulls (with 'draw = "polygon")
	do not cover labels. With these changes, the behaviour of
	ordihull() is similar to ordiellipse(). The labels are centred
	more correctly.

	* metaMDS: A warning is issued on too good stress (zero or nearly
	zero).  This is often a symptom of insufficient data.  In general,
	you need n > 2*k + 1 points for k dimensions, and Kruskal's advice
	is to have n > 4*k + 1.  With low number of points there can be
	several complete (zero stress) but different results, and no two
	convergent solution can be found.  The warning is issued also when
	convergence was obtained, and information on dimensions is
	printed.  FAQ gained an entry on the issue.

	* bioenv: accepts now dissimilarities or a square matrix that can
	interpred as dissimilarities instead of a community data frame.
	This allows using other dissimilarities than those in vegdist(). 

	* update.nullmodel: explicit assignment is required to update
	the input object (nm <- update(nm, ...)).

	* ordiplot3d: the returned envfit.convert() function did not
	recognize 'choices'.

Version 2.1-15 (closed May 11, 2012)

	* rrarefy, drarefy: check the data are integers -- the functions
	do not give sensible results with real values.

	* monoMDS: checks now that there is a sufficient number of non-NA
	dissimilarities for the analysis. People really try to use NMDS
	with too small data sets. The change was triggered by a user who
	had tried to find a six-dimensional solution for seven points
	(21 dissimilarities, 42 scores) using 100,000 random starts in
	metaMDS. With over-defined models there is an infinite number of
	different solutions with nearly zero stress, and no convergence is
	found. 

	* ordiplot3d: function returns the projected coordinates of the
	origin, and function envfit.convert() that can project a
	three-dimensional envfit() result to the current plot. Unlike
	originally assumed, the function will not set equal aspect ratio
	for all axes.  We try to compensate this by setting equal scaling
	to all axes.
	
Version 2.1-14 (opened March 9, 2012)

	* Opened a new version with the CRAN release of vegan 2.0-3 on
	March 3, 2012.

	* Warton, Wright & Wang (Methods Ecol Evol 3, 89-101; 2012) had a
	paper where the analysed the confusion of location (differences
	between groups) and dispersion (variability within groups) in
	dissimilarity-based analyses.  We have warned on this for long in
	vegan, but now we can get support from this paper. Explicit
	arnings added to anosim, mrpp, simper (where this is worst) and
	adonis (where this was already analysed by Marti Anderson when
	introducing the method).

	* adipart, multipart, hiersimu: permutation tests assumed constant
	full gamma diversity in all simulations even when the null model
	could produce variable gamma diversities. The default method
	("r2dtable") had constant gamma diversity.

	* adipart, multipart, hiersimu: these are now generic functions
	with default and formula methods. The formula method is identical
	to the previous function, the default method can take two matrices
	as input, but the second argument describing the hierarchy can be
	missing. In this case a trivial two-level hierarchy will be
	assumed (each row is a seperate group, all rows are in same
	group).

	* anova of prc() objects by "axis", "terms" or "margin" failed due
	to NAMESPACE issues. Reported as issue #7 by Eduard Szöcs in
	github.com.

	* clamtest: wrongly used frequencies instead of the counts
	when calculating sample coverage to test x < coverage.limit. 
	No detectable differences were produced when rerunning 
	examples from Chazdon et al. 2011 (Ecology, 92, 1332--1343)
	and vegan help page.

	* envfit: failed if some of the environmental variables were
	factors with unused factor levels. Fixed in centroids.cca.
	Reported as issue #8 in github.com by Eduard Szöcs.

	* msoplot: expose 'ylim' as an argument. Previously, 'ylim' was
	set internally and user could not change it setting, although
	y-axis maximum was sometimes so low that standard errors were
	outside the plot, and legend covered lines. The default setting of
	'ylim' was improved, and the function follows R idiom more
	closely. Reported in a private email to J.O. by Ricardo Pita.

	* scoverage: new function for sample coverage based correction for
	calculation of relative frequencies in count community matrices
	(Good 1953, Biometrika 40, 237--264).
	
Version 2.1-13 (closed March 9, 2012)

	* cca/rda/capscale: names of levels could be dropped if a
	two-class factor was used as the only constraint. Noticed in an
	email of Sascha Kirchner (Univ Helsinki, Finland).
	
	* scores: expand description of the default method to avoid
	confusion with specific vegan methods.
	
	* scores.monoMDS: did not know 'choices' and hence plot() was also
	unable to choose dimensions. 
	
	* vegdist: Added Cao dissimilarity (CYd). Thanks to Yong Cao for
	consultation. 
	
Version 2.1-12 (closed February 23, 2012)

	* scores.default: failed if users asked scores of non-existing
	axes. This was reported as an error in ordiplot() when the user
	tried to plot 2-dim graph of 1-dim solution in
	https://stat.ethz.ch/pipermail/r-sig-ecology/2012-February/002764.html

	* simper: new function to implement "similarity percentages" of
	Clarke (Austral. J. Ecol. 18, 117-143; 1993) contributed by Eduard
	Szöcs (Uni Landau, Germany).

Version 2.1-11 (closed February 9, 2012)

	* indpower: now can handle input objects without dimnames.  This
	caused problems with oecosimu, because nullmodel objects have no
	dimnames to save memory.  Extended example on indpower help page
	shows the p-value and heterogeneity calculations suggested in
	Halme et al. 2009.

	* adonis, anosim, mantel, mantel.partial, mrpp, permutest.cca: do
	not need clusterEvalQ(parallel, library(vegan)) for socket
	clusters. 

	* adonis: added missing 'mc.cores=' for multicore parallel
	processing. 

	* bioenv: implemented parallel processing.

	* metaMDS: implemented parallel processing which runs iterations
	(tries) in batches of 'parallel' iterations. However, it seems
	that this does not work completely with monoMDS: basic results are
	OK, but 'diss' and 'dist' vectors are scrambled (tested in Linux &
	R 2.15.0) which is evident if you try to run stressplot() on the
	result.  The problematic behaviour can also be generated directly
	with monoMDS():

	mods <- mclapply(1:8, function(i) monoMDS(d), mc.cores=2)
	stressplot(mods[[1]])

	The 'diss' and 'dist' seem to contain random rubbish as soon as
	mc.cores > 1.  On the other hand, there are no similar problems
	with isoMDS() -- but it does not directly return 'diss' and
	'dist'.  If this cannot be solved, the parallel processing (r2069)
	will be reverted.

	* nesteddisc: new argument 'niter' to give the number of
	iterations to reorder tied columns.

	* renyi.Rd: fixed a broken link reported by Arne Erpenbach (Uni
	Frankfurt, Germany). 

Version 2.1-10 (closed February 5, 2012)

	* adonis: print info that terms are added sequentially -- this
	seems to confuse users. Make this change in adonis() instead of
	print.adonis to be prepared to add other policies.

	* adonis, anosim, mantel, mantel.partial, mrpp: implemented
	parallel processing.

	* RsquareAdj: implemented adjusted R2 for partial RDA results.
	The adjusted R2 of model rda(Y ~ X1 + Condition(X2)) is defined so
	that it is the same as component '[a] = X1|X2' in
	varpart(). Removed some dead code from RsquareAdj.cca().

	* varpart: do not scale constraints to unit sd -- this makes
	constant columns (like all zero) into NaN and causes an error in
	simpleRDA2.  Not scaling may help in problems like that reported
	in "[vegan-help][5477] Nested factors in function "varpart"?" by
	Katie Shelef on 26 Jan 2012.

	* use inconsolata fonts in vignettes.

	* added .Rinstignore file to list inst/doc files that should not
	be installed (Makefile, tex, bib, sty). Background: R 2.13.0
	mandated to put vignettes to their specific vignettes/ directory,
	but this is incompatible with R 2.12.* where vegan also should
	work.  The inst/doc directory can still be used (it isnow
	'deprecated'), but system files (such as Makefile) and
	intermediate files (such as tex) are silently copied to the
	installation.  R 2.15.0 (under development) added R CMD check test
	for these extra files.  File .Rinstignore allows maintaining R
	2.12.* compatibility and silences R 2.15.0 tests.
	
Version 2.1-9 (closed January 22, 2012)

	* public launch of parallel processing in vegan. First step was to
	explain the implementation in decision-vegan.Rnw. 

	* DESCRIPTION: vegan suggests 'parallel'. The 'parallel' package
	was released with R 2.14.0. If you need to check or use vegan with
	older R, you should set environmental variable
	_R_CHECK_FORCE_SUGGESTS_=FALSE (see, e.g., discussion
	https://stat.ethz.ch/pipermail/r-devel/2011-December/062827.html).

	* oecosimu, permutest.cca: new parallel block which honours
	setDefaultCluster() in R-devel (becoming R 2.15.0) and
	automatically uses parallel processing with socket clusters if
	setDefaultCluster was defined. Tested in R (unstable) (2012-01-16
	r58122) with full features, in R 2.14.1 without setDefaultCluster,
	and in R 2.13.1 (2011-07-08) without parallel processing

	* anova.ccabymargin failed if none of the terms was analysed (all
	were aliased) and no permutations were performed.  This would
	happen with, e.g.,
	
	A <- dune.env$Management
	anova(rda(dune ~  Management + A, dune.env), by = "margin")

	or in general if all marginal effects were aliased. 

	* capscale: plotting failed for mod <- capscale(dune ~
	Condition(Management) + A1, dune.env). The centroids for
	Management were completely removed leaving a zero-row matrix of
	centroids, and this caused an error in plot() and would probably
	fail elsewhere.  The same problem can appear with completely
	aliased classes, or when class centroids are nearly zero.

	* ordistep: handle cases where the marginal effects for
	adding/dropping are completely aliased. This should avoid problems
	like that reported in
	https://stat.ethz.ch/pipermail/r-help/2012-January/300167.html

Version 2.1-8 (closed January 8, 2012)

	* betadisper: failed with an error in internal function
	betadisper() if there were empty levels. This could happen when
	'groups' was a factor with empty levels, and was reported in 
	https://stat.ethz.ch/pipermail/r-sig-ecology/2011-November/002525.html
	The behaviour is now corrected in ordimedian() which will return NA
	for empty factor levels. 

	* nestedbetasor, nestedbetajac: New functions that implement
	decomposition of Sorensen and Jaccard beta diversities into
	components of turnover and nestedness following Baselga (Global
	Ecology and Biogeography 19, 134-143; 2010). These are documented
	with nestedness indices and are ready to be used with oecosimu().

	* oecosimu: more informative text on 'alternative' hypotheses in
	the printed output. Return also the mean of simulations and show
	that in the printed output.

	* plot.cca: works with degenerate solutions where constraints are
	aliased and 'biplot' scores have zero rows. Stops with a
	comprehensible error message if a user requests non-existing
	scores (such as "bp" scores for unconstrained ordination).
	
	* rarecurve: new function to draw rarefaction curves for each
	plot, optionally with sample size vertical and corresponding
	horizontal richness lines. Soil microbiologists with sequencing
	data seem to want these, and I have seen them used elsewhere as
	well. 
	
Version 2.1-7 (closed November 19, 2011)

	* adonis: speed up implemented in r1636 was not passing the
	transposed matrices to internal f.test function. Reported by
	Nicholas Lewin-Koh.

	* metaMDS: arguments 'noshare = 0' and 'noshare = FALSE' are now
	different: zero is taken as the numeric threshold and always
	triggers stepacross(), whereas FALSE is logical and never triggers
	stepacross.

	* vegan 2.0-2 was released on November 15, based on this version.

Version 2.1-6 (closed November 12, 2011)

	* FAQ: correct mark-up of hyper links (@uref{} instead of @url{}),
	add new entries on RDA scaling, scaling of NMDS stress and scaling
	of environmental arrows in cca/rda/capscale/envfit, plus some
	minor updates of old entries.

	* ordiarrows, ordisegments: gained argument 'order.by' that can be
	used to order the points within groups before drawing the arrows
	or segments. This message in R-sig-ecology seems to need this: 
	https://stat.ethz.ch/pipermail/r-sig-ecology/2011-November/002464.html

	* ordispider: returns invisibly the coordinates to which each
	point is connected. Triggered by an email query of this
	functionality. 

	* ordiplot3d: expanded example to show how to use xyz.convert() to
	add points as per
	https://stat.ethz.ch/pipermail/r-help/2011-October/293955.html

	* oecosimu: new proposition for implementing parallel processing
	following suggestions of Peter Solymos.  The only relevant
	argument is now 'parallel' which can be either the number of
	parallel processes (defaults getOption("mc.cores", 1)) or a
	pre-defined socket cluster or NULL in which case it is taken as
	the default cluster defined by setDefaultCluster (this last option
	only works in R-to-be-2.15.0 unstable, and using NULL is a user
	error in R 2.14.0 and hence undocumented). The 'parallel' defaults
	to 1 (no parallel processing), but if the user sets the "mc.cores"
	option, all parallel processing functions will automatically use
	that number of parallel processes.  (The "mc.cores" argument is
	used by the 'parallel' package, but it is normally unset.) If
	'parallel' is a socket cluster or there is a default cluster
	('parallel = NULL'), this will be used without setting up and
	closing the cluster. This (1) saves time, (2) allows using of
	other packages than 'vegan' if user has given command
	'clusterEvalQ(library(foo))', and (3) makes unix-like OS
	(incl. MacOS X and Linux) to use the socket processing instead of
	forking.

	* permutest.cca: parallel processing modelled after oecosimu().

Version 2.1-5 (closed October 30, 2011)

	* opened a new version with the release of vegan 2.0-1 on Oct 20,
	2011.

	* metaMDSdist: the default value of "noshare" was inconsistent
	with metaMDS(), and therefore stressplot() could fail for
	engine="isoMDS". Usually metaMDS() sets the 'noshare' depending on
	the engine, but metaMDSdist() is called directly from
	capscale(..., metaMDSdist = TRUE) and metaMDSredist (for
	stressplot), and now these default to extended dissimilarities.
	The problem was reported by Falk Hildebrand

	* capscale: could fail if constrained component had zero rank,
	typically in partial models where constrained component was
	completely aliased. This was observed when checking an R-News
	query of October 19, 2011
	(https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html)
	
Version 2.1-4 (opened October 20, 2011)

	* adonis, anosim, CCorA, envfit (factorfit, vectorfit), mantel,
	mantel.partial, mrpp, protest: user interface changed and
	'permutations' can now be a matrix where each row gives permuted
	indices. Internally first find a permutation matrix or use the
	given permutation matrix, and then find the statistics with single
	{ls}apply. Functions adonis and mrpp already worked like this, but
	they gained the option of matrix input. This makes the functions
	ready both for the 'permute' package and for parallelization
	(replace {ls}apply with mclapply, par{SL}apply).  Function
	envfit() was much simplified by generating a common permutation
	matrix in envfit.default() and using that as the input to
	vectorfit() and factorfit(). The anova.cca* cases should also be
	made to use a single generated permutation matrix, as
	permutest.cca() allows this.

Version 2.1-3 (closed October 16, 2011)

	* added plot.preston, lines.preston and plot.fisher (that also can
	add points and lines). These are similar as plot.prestonfit and
	plot.fisherfit, but without the fitted model. Among other things,
	they can be used to add alternative models to fisherfit and
	prestonfit models.

	* sd() function for matrix or data.frame columns was deprecated in
	R r57185 (R-to-be-2.15.0). The reason seems to be that users were
	confused when median() did not work on data.frames, and as a
	solution the R developers decided to take care that mean() or sd()
	will not work either (it would be nice to understand how these
	people think). Fixed in rda.default, capscale and
	simulate.rda/cca/capscale. It seems that this was also implemented
	in soon released R 2.14.0 as r57209 | maechler | 2011-10-10
	19:28:33 +0300 (Mon, 10 Oct 2011), but as message() instead of a
	warning(). 
	
	* nesteddisc: use only max 200 tries to reorder columns: tracing
	showed that in most cases an improved ordering is found rather
	quickly, and trying up to 1000 times takes awfully long. Now
	faster, and usually as good as earlier, but slacker.

	* simulate.rda/cca: implemented 'nsim' or an option to generate an
	array of simulated matrices inheriting from "simmat" object and
	using print.simmat() for a compact display. If 'nsim = 1', similar
	2-dim matrix is returned as before so that cca(simulate(mod))
	still works. For 'nsim > 1', the 'indx' argument should have
	'nsim' rows, but if 'nsim' is missing, number of rows in 'indx'
	will give the number of simulations, and 'indx' can be made with
	permute::shuffleSet().  Implemented for rda() and cca() results,
	but not for capscale() where simulate returns a "dist" object
	which is nasty to pack into an array.

	* oecosimu: An attempt to set 'parallel' processing in evaluating
	the statistic, and only evaluating the statistic -- the simulation
	of null models is not influenced. Both "multicore" (fork) and
	"snow" (socket) style parallelization are implemented. 

	* permutest.cca: implemented 'parallel' processing in
	permutest.cca.  The parallelization only works in R 2.14.0 (alpha)
	and later with the 'parallel' package. Function permutest.cca gets
	a new arguments 'parallel' (defaults 1) that gives the number of
	parallel process, and 'kind' that selects the parallelization
	style which is either "snow" (large overhead, but works in al
	OS's) and "multicore" (faster, but only works in unix-like systems
	like Linux and MacOS X). The arguments are silently ignored if the
	system is not capable of parallel processing. The functionality
	cannot be included cleanly: it depends on the package 'parallel',
	but suggesting 'parallel' fails R CMD check in the current R
	release (2.13.2) which does not yet have 'parallel'. So we get
	warnings: 'library' or 'require' "call not declared from:
	parallel", and "permutest.cca: no visible global function
	definition for ‘mclapply". However, with these warnings,
	the function passes tests in R 2.13.2.

	* permutest.cca: the user interface changed so that argument
	'permutations' can be either the number permutations (like
	previosly), or a matrix of permutations like produced by
	permute::shuffleSet(). This was done to move RNG outside
	parallelized code. This will also allow much simpler and
	anova.cca* code. Currently, the 'strata' argument will not work,
	but this will be fixed "real soon now".

Version 2.1-2 (opened October 4, 2011)

	* permutest.cca could not be update()d, because "permutest.cca"
	was not exported from NAMESPACE -- only "permutest" was
	exported. Another buglet (and this calls for checking other 'call'
	items that return non-exported calls).

	* metaMDS did not reset 'tries' when the analysis was started from
	'previous.best' of a different model (except when no. of dims 'k'
	changed). I think this was a bug(let). Fixed in metaMDSiter.R.
	
	* commsimulator is going to be deprecated: it is no longer used in
	oecosimu() ore elsewhere in other functions. Currently, functions
	make.commsim(), nullmodel() and simulate.nullmodel() do the same,
	and more. As the first step, its documentation in oecosimu.Rd is
	moved to vegan-deprecated.Rd.
	
	* examples: cut donw some excessively time consuming examples.
	Profiling of all vegan examples showed that 25% of total time was
	spent in anova.cca, and 12.6% in ordistep, but they probably are
	sufficiently documented more quickly. 

Version 2.1-1 (opened September 20, 2011)

	* oecosimu: the 'comm' argument can be either 1) community data,
	2) a nullmodel object or 3) a simmat object. If 'comm' is a
	nullmodel, simulation method is found from the nullmodel object,
	and if 'comm' is a simmat object, its matrices are analysed
	without simulations within oecosimu(), and different statistics
	can be swept out based on the same set of simulated matrices.

	* permatfull/swap is using the new simulate.nullmodel(...)
	infrastructure. permatfull1 and permatswap1 removed from vegan 
	devel.

	* Value of 'mode' is set to "double" for the following
	null model algorithms in make.commsim: abuswap_r, abuswap_c,
	r00_samp, r0_samp, c0_samp. These can take any nonnegative real 
	valued matrix as input. nullmodel function now handles storage
	mode reliably.

	* meandist bug fix: tapply() function used to find mean group x
	group dissimilarities could reorder the class levels and return a
	confused matrix. This could happen in particular when the
	'grouping' was a vector of integers which then were ordered
	alphabetically so that "1" < "10" < "2". Now uses internally more
	stable way of applying tapply() which should have the danger of
	reordering the levels.  Incidentally, this also seems to be
	faster. The problem was found by Dr Miguel Alvarez (Univ Bonn).

	* nestedness.c: changed interface in "swapcount" and "rswapcount"
	which now require integer data matrix. The first argument in .C
	call should now be defined as as.integer() instead of old
	as.double().

	* str.nullmodel: new function to display the *str*ucture of the
	"nullmodel". The "nullmodel" is an environment and therefore does
	not show in usual str() although its items can be accessed with
	$-notation. No documentation, but alias in nullmodel.Rd.

	* New functions: commsim is used to define Null Model Algorithms
	via a function that returns n x m x nsim array of simulated
	matrices based on structural constraints. make.commsim contains
	Null Model Algorithms already defined in vegan from commsimulator
	and permat* functions (and some more).  The nullmodel function
	creates an environment, where statistics of the input matrix are
	stored. The environment also stores updated status of sequential
	algorithms and current number of iterations. The update and
	simulate methods are used to update the nullmodel (for sequential
	algorithms) or simulate random matrices, respectively. The
	simulate method returns the n x m x nsim array (simmat class).
	Efficiency gains are sometimes high (because marginal statistics
	are calculate only once by nullmodel), but not significant in most
	cases.  Most advantageously, this implementation can unite the
	commsimulator and permat* branches and can serve as basis for
	further extensions.  Current intent is to investigate how this low
	level infrastructure can be used within oecosimu and permat*
	functions without breaking current vegan functionality.

Version 2.1-0 (closed September 20, 2011)

	* New major version opened with the release of vegan_2.0-0 on
	September 8, 2011.

	* nestedness.c: isDiag* uses now switch(sX) where sX is the number
	of non-empty cells. The "swapcount" method uses new isDiagFill
	which finds the largest swappable element that does not change the
	fill, and "rswapcount" uses isDiag which finds both the largest
	swappable element the change in fill. The swap and trialswap also
	find first the fill of the 2x2 submatrix, and continue only if
	fill == 2. The measurable effects are small again (perhaps 1%).

	* tests: added tests for commsimulator, permatswap1 and
	permatfull1 before starting the adventures with nestedness.c.

	* commsimulator: a bit less overhead -- all attributes set
	simultaneously instead of setting separately dim, rownames and
	colnames. The results should be identical(), running should be
	marginally faster or neutral.

	* permatswap: there was a bug in internal C routine, and therefore
	not all permissible swaps were performed. Based on limited
	analysis, the effects of this bug seem to be negligible.  It is,
	however, recommended to re-run all analyses. The C code was made
	faster by getting quickly out from isDiag* if there are only 0 or
	1 filled items, because there is nothing to swap. Tests show that
	the C code indeed is ca 10% faster in permatswap(BCI,
	method="swa", thin=1000, times=999), but only a 20-25% of time was
	spent in C, and the new permatswap/permatswap1 spends 2.2x longer
	in other parts. With faster C code the net slowdown is 1.7x.

	* various attemps of speed-up (often in vain): The speed-up
	started with permatfull/permatswap which appeared to be by far the
	slowest functions in R CMD check --timings. Later this proved to
	be a feature of checking these functions in MacBook Air/MacOS X:
	the functions were not slow in Linux, nor in MacBook when the very
	same tests were run outside R CMD check. However, several changes
	were made: 

	- permatfull/permatswap avoid data.frame/matrix casting, and save
	results in matrices. This was based on misleading test statistics
	in MacOS, and it is not sure what are the real effects.
	- commsimulator: smaller overhead.
	- sample.int was used in place of sample in commsimulator,
	nesteddisc, permuted.index and poolaccum (the effects may be
	measurable for permuted.index, but not large).
	- centroids.cca: much faster. This was perhaps real -- profiling
	(not timing) showed that cca.formula/rda.formula have a large
	overhead over cca.default/rda.default, and centroids.cca was
	responsible for a lot of that -- most is due to ordiParseFormula.
	- permutest.cca uses La.svd, but the effects are non-measurable
	and only concern case first = TRUE.
	- MDSrotate example: envfit does not do permutations.

	* New functions: permatfull1 and permatswap1. Both functions
	return a single permuted matrix. These functions are now called
	repeatedly by the corresponding permatfull and permatswap
	functions.

	* New function: clamtest (with summary and plot methods).  The
	method uses a multinomial model based on estimated species
	relative abundance in two habitats, it minimizes bias due to
	differences in sampling intensities between two habitat types as
	well as bias due to insufficient sampling within each habitat. The
	method permits a robust statistical classification of habitat
	specialists and generalists, without excluding rare species a
	priori. Based on Chazdon et al. 2011 (Ecology, 92, 1332--1343).

	* raupcrick: new function to implement Raup-Crick (dissimilarity/
	probability) index with unequal sampling probabilities of species.
	Brian Inouye informed about their paper (Chase et al., Exosphere
	2:art24 [doi:10.1890/ES10-00117.1]; 2011) where they showed that
	Raup & Crick said that we should use sampling probabilities
	proportional to species frequencies in assessing their index, but
	vegdist(x, "raup") uses equal probabilities. Unequal sampling
	probabilities cannot be directly implemented in vegan, but the
	Chase et al. method can be implemented as oecosimu(x, function(x)
	designdist(x, "J"), method="r1"). Basically, the current function
	uses this, but with boosted code that is much faster than
	designdist(). 

Version 2.0-0 (released September 8, 2011)

	* opened the release candidate of vegan_2.0-0 on September 3,
	2011. 

	* some old functions used attributes(x)$which instead of more
	correct attr(x, "which"), and in addition postMDS() used
	attributes(x)$names instead of names(). Concerns anosim(),
	initMDS(), postMDS(), mantel(), mantel.partial() and
	mso(). initMDS() was one of the two functions that was unchanged
	since the first vegan release on 6/9/01, and it was changed day
	before it turned ten-years-old. After this, wisconsin() is the
	only unchanged function from the first release.

	* vegan-defunct: put definitions of removed "new" permutation
	functions to vegan-defunct and have a vegan-defunct.Rd for them. 

Version 1.92-2 (closed September 3, 2011)

	* monoMDS: saves and displays info on the dissimilarities used,
	and displays the number of points. Checks that input is
	dissimilarities, and warns on negative ones.

	* MDSrotate: metaMDSrotate() was renamed to MDSrotate(), and
	metaMDSrotate() was .Deprecated. 

	* meandist: warns if some dissimilarities are negative (small
	negative values are tolerated).

	* vegandocs: copied branches/1.17/inst/NEWS as ONEWS (old news),
	and adapted vegandocs. Expanded documentation of vegandocs().
	
Version 1.92-1 (closed August 28, 2011)

	* adonis, betadisper, mrpp: check that dissimilarities are
	non-negative (small negative values are tolerated). The test was
	not added to meandist: there may be legitimate usages for
	correlation-like objects although summary.meandist() is
	invalid. The addition was triggered by a user who tried to analyse
	Chase et al. Raup-Crick values in the range -1 .. +1 in
	betadisper().

	* anosim: warn if some dissimilarities are negative. Function can
	handle negative dissimilarities because it is based on ranks, but
	probably this is a user error (but can be intentional and
	correct).

	* metaMDSrotate: can rotate monoMDS() results.

	* monoMDS: gained argument 'pc' (defaults TRUE) to rotate the
	final scores to principal components.

	* specaccum, fitspecaccum: gained predict() methods. With
	specaccum() predict(..., newdata) can estimate values for
	'newdata' with linear or spline interpolation if necessary.
	Without 'newdata' the function returns the the fitted expected
	richness.  With fitspecaccum(), the predict.nls() is performed to
	each fitted model. Function fitspecaccum() is written so that
	default fitted(), residuals() and coef() work.

	* specpool: failed if 'pool' had NA values or empty factor
	levels. Checks that 'pool' length matches nrow of data.

	* NAMESPACE: imports nobs from permute_0.5-3 in R 2.12.2 and older
	which do not yet have nobs() generic. Do not export orderingKM &
	ordimedian. Remove aliases to non-exported and non-documented
	print and print.summary methods in Rd files (but leave documented
	ones).

	* vegandocs: shows the permutation vignette of the 'permute'
	package. 
	
Version 1.92-0 (closed August 23, 2011)

	* open new version with the release of vegan_1.17-12 on August 17,
	2011. 

	* fitspecaccum: a typo and a condition was never true.

	* monoMDS & metaMDS: always print types of stress and ties.

	* NAMESPACE: export pasteCall for analogue.

	* NEWS: added file NEWS.Rd for vegan release 2.0 news in Rd format.
	Keeping neat formatting of this file may be challenging to many
	text editors, but it is worth trying. This file should list the
	important items for regular vegan users, whereas this ChangeLog
	should explain the changes to other vegan developers. If
	getOption("help_type") == "html", should start a browser to show
	the NEWS, and use text console otherwise ("html" tested on MacOS
	R.App GUI, text mode in Linux and MacOS bash shells, no testing on
	Windows yet). Although the browser knows how to display NEWS.Rd,
	it does not format the page properly (\code{foo} shows as ordinary
	text etc). As a kluge we now make a NEWS.html file in the inst/doc
	directory. NEWS.html cannot be made in the inst/ directory since
	browser only agrees to show NEWS (plain) in the main directory or
	files in doc directory.
	
Version 1.91-0 (closed August 18, 2011)

	* NAMESPACE: added namespace to vegan. Currently hides all that
	can be hidden, and exports only main functions: Some method
	functions will be probably exported later. Superfluous aliases
	were removed with the registration of S3 methods, and scoping was
	changed a bit in anova.ccabyterm, model.matrix.cca and
	model.frame.cca. as.mcmc is not yet registred: it need changes in
	Imports field of DESCRIPTION (same with vif.cca: vif is defined in
	car, but we could have our private vif generic here?).

	* Vignettes: use now jss.cls shipped with R instead of amsart.cls
	for better consistency with R and permute style.

	* plot.envfit: When `add == FALSE`, make sure we leave enough room
	around the plotting locations to contain the arrow and centroid
	labels.

	* plot.isomap: will always plot points or text above net so that
	they are visible. Gained argument 'type'.

	* ordiplot: expose arg 'cex' so that user can change its value.
	Age shows in this function, and it is badly in need of complete
	re-writing to improve its flexibility.

Version 1.90-2 (closed August 6, 2011)

	* ordilabel: gained argument 'select'.

	* orditorp: works with NA scores.

	* make.cepnames: ignores duplicated and trailing dots. It is
	assumed that the names to be changed came via R make.names()
	mechanism which changes all blanks and non-accepted characters to
	dots, and this may give extra dots in names. Gained argument to
	take the second item of the name instead of the last which may
	help in names like "Vaccinium vitis-idaea" (which becomes
	"Vaccinium.vitis.idaea" -> "Vaccidae") or names which have authors
	or other rubbish at the end.
	
Version 1.90-1 (closed July 23, 2011)

	* cca/rda/capscale support functions: cca/rda/capscale were
	changed to return zero components instead of NULL for completely
	aliased constraints (CCA) or saturated models (CA), but several
	support functions still checked for is.null() only, although they
	also should check if rank == 0. Some functions failed, and these
	are fixed here: anova.cca, bstick.cca, goodness.cca/rda,
	predict.cca/rda, screeplot.cca. The following functions did not
	fail, but were fixed: anova.ccanull, calibrate.cca, ordirgl,
	ordiresids, ordiplot3d, deviance.cca/rda (simplified),
	ordixyplot.

	* swan: gained argument 'maxit' that can be used to restrict the
	number of beals() passes on zeros. The default is 'maxit = Inf'
	which is the old behaviour: beals() passes on zero entries
	continue until there are no zeros or the number of zeros does not
	change. Probably only 'maxit = 1' makes any sense (in addition to
	the default 'maxit = Inf'), but all values are allowed.

	* metaMDSrotate: results could be a bit off with NA in
	environmental vector and >2D solution. The starting scores must be
	orthogonal, but the initial orthogonalizing PCA was run without
	removing NA cases.

	* ordiellipse, ordihull, ordispider: will remove NA scores that
	can appear with na.action in cca/rda/capscale (and perhaps in
	other cases).

	* betadiver: argument 'index' was renamed to 'method' for
	compatibility with dist() objects. Argument 'index' is
	still recognized with a warning.

	* metaMDS: Documentation and interface adapted to monoMDS().
	Argument 'noshare' defaults to FALSE with monoMDS(), since tie
	breaking seem to handle tied maximum dissimilarities even better
	than stepacross(). For 'engine = "monoMDS"' 'noshare' defaults to
	TRUE. The 'noshare' argument now accepts logical arguments in
	addition to old numeric (FALSE worked previously because it was
	interpreted as numeric 0, but TRUE has now meaningful
	interpretation). Remove argument 'old.wa' introduced in rev280 on
	24/3/08 for backward compatibility when calculating WA scores
	started to use the same transformed data as analysed.

	* ordiplot: Now handles non-par arguments to plot.default without
	warnings. Things like `axes = FALSE` in the call now just work!

Version 1.90-0 (closed July 3, 2011)

	* vegan now depends on the permute package for new permutation
	designs. This initially version strips out all the old "new"
	permutation code from the R and Rd files, and patches up
	permutest.betadisper to use shuffle() to generate permutations.

	The 1.90-0 devel series will lead the way to vegan 2.0-0. There
	may well be build problems as we iron out permute / vegan
	meshing.

	* capscale: could not be embedded in another function after fixing
	the update() in 1.18-31 -- problems were anticipated in ChangeLog,
	and they were realized.

	* monoMDS: text for a proper help (Rd file). Other help files
	updated for monoMDS. Stress type 2 is printed both in monoMDS and
	metaMDS. stressplot() prints now R2 for monoMDS() results, and
	docs tell that "linear fit" of stressplot() is related to "stress
	2".

Version 1.18-33 (closed June 21, 2011)

	* adonis: made faster (much faster in tests) by polishing the
	f.test() in the innermost loop.

Version 1.18-32 (closed June 14, 2011)

	* closed with the release of vegan_1.17-11.

	* anova.prc: new function that casts prc() result to a
	corresponding rda() and submits this to anova.cca(). With this is
	it is possible to analyse anova(..., by = "axis"). Other cases are
	possible as well, but not very useful as "margin" and "term" only
	analyse all constraints as a single matrix. Now some functions
	that were made refuse prc() results in 1.18-30 work again, and
	anova.ccabyaxis() even makes sense. This fixes a problem Jae
	Pasari raised in his email.

	* vegdist docs: Brian Inouye informed us that we are not
	calculating the Raup-Crick index like originally suggested: we use
	equal probabilities for all species, but the species probabilities
	should vary with their frequencies. Doing this would break
	vegdist.c design, and require Fisher's non-central hypergeometric
	distribution, and that is not available in base R. However, it
	seems that a simulation version could be implemented in
	oecosimu(). Now we document the problems in vegdist.Rd, but do not
	correct the behaviour. The key paper is available over
	http://www.esajournals.org/doi/full/10.1890/ES10-00117.1

	* rda & capscale: similar changes as in cca in r1517 (version
	1.18-24). CA component is always returned, even with zero rank,
	and CCA and pCCA components are NULL only if they were not
	specified originally, and if they become zero rank because of
	aliasing etc, they are returned as zero components (instead of
	NULL). 

	* print of cca/rda/capscale: do not "Proportion" column in
	unconstrained ordination which only has one component. However,
	this will be printed also with zero pCCA or CCA (but not with
	NULL). 
	
Version 1.18-31 (closed May 30, 2011)

	* ordiR2step: more informative about rejecting 'scope': partial
	models are not (currently) accepted due to the design of
	RsquareAdj.rda().

	* specnumber: gained argument 'groups' to find total richness
	within each group. An example shows how to use this to find one
	index that Whittaker suggested to estimate beta diversity.

	* capscale: species scores will be NA if input data were
	dissimilarities and no 'comm' was given. update(capscale_result)
	failed because LHS data were evaluated in the
	environment(formula).  Now removed the explicit environment: I ran
	some tests and found no problems, but let's see what the real life
	brings along. The changed point is commented so that this change
	can be reconsidered if necessary.
	
	* oecosimu: reverted r1557 of version 1.18-26, or splitting tied
	values. This was introduced because Chase et al. (Ecosphere 2011,
	http://www.esajournals.org/doi/pdf/10.1890/ES10-00117.1) used this
	in their Raup-Crick index. This is against established practice in
	order statistics and therefore we cancelled this.

	* specaccum: reverted r1505 & 1507, or introduction of weighted
	species accumulation model in version 1.18-23. The method was
	introduced because of user request, but these persons lost their
	interest and therefore there is no reason to see the trouble that
	finalizing these functions would require (see comments on version
	1.18-23 about some of the work needed, and there is more).

Version 1.18-30 (closed May 26, 2011)

	* opened with the release of vegan 1.17-10 on April 27, 2011.

	* nobs: documented nobs() methods for vegan. These seem to be
	needed in R 2.13.0 and should be released soon (there is no need
	to add R >= 2.13.0 dependence as long as we do not use these
 	functions ourselves within released vegan code).

	* treeheight: dramatic simplification and speed-up of the code.

	* scores.cca/rda: failed if user requested only non-existing
	scores. Now return an empty list of scores instead (with possible
	attributes). 

	* prc: several support methods did not work with 'prc' results,
	and these now stop with an informative error instead of an
	uniformative error. Concerns anova.ccabymargin, anova.ccabyaxis,
	drop1.cca, add1.cca, model.frame.cca, model.matrix.cca. This was
	found out after a private user query about having signficance test
	for the sencond PRC axis.
	
Version 1.18-29 (closed April 27, 2011)

	* capscale: could fail with add = TRUE in R 2.13.0. A kluge was
	necessary in cmdscale() pre 2.13.0, but the feature was fixed in R
	2.13.0 and unnecessary fix failed. Now the kluge is used only in
	older versions of R and capscale should be working both in 2.13.0
	and older R.

	* adipart.Rd, multipart.Rd: cancelled some excessive speed-ups in
	example code made in r1204. Some of these speed-ups never made to
	the release version, but were only made in the devel branch. The
	sped-up examples were also merged to the release (adipart.Rd,
	kendall.global.Rd, multipart.Rd, mantel.correlog.Rd,
	pertmatfull.Rd, radfit.Rd). Also reverted r1224 so that
	Guillaume's original r1206 (49 permutations instead of 99) is used
	again. Probably we should speed up some other examples. The five
	worst cases (timing in MacBook Air) are: ordistep (19.0 sec),
	add1.cca (7.2 sec), tsallis (7.0 sec), prc (5.6 sec),
	vegan-package (5.2 sec).

	* vegan-package.Rd, ordistep.Rd: speed up examples.
	
Version 1.18-28 (closed April 11, 2011)

	* Peter Minchin joined the vegan team.

	* monoMDS: a new function with Peter Minchin's Fortran90 code for
	NMDS. The full Fortran90 code has global, local, linear and hybrid
	MDS, configurable and valid tie treatment, handles missing values,
	and allows adding new points to existing ordinations. The Fortran
	code is highly tuned, and much faster than other alternatives in
	R. The R interfaces allows access to most features of the Fortan90
	code, except adding new points to the ordination (which will need
	a separate function). The missing values in dissimilarities are
	also handled in the R interface. The function will eventually
	replace isoMDS() of the MASS package as the main NMDS engine in
	metaMDS().

	* metaMDS: uses monoMDS() as its default engine (and gained
	argument 'engine' to select either monoMDS() or isoMDS()).

	* stressplot: is generic with a specific method for "monoMDS"
	objects, and the old function as the default method.

	* goodness: got a new method for "monoMDS" objects. The function
	handles all monoMDS() models, but does not take into account
	possible missing values in input dissimilarities.

	* metaMDSrotate: gained argument 'na.rm' (defaults FALSE) to
	remove missing data from the continuous vector.
	
Version 1.18-27 (closed April 1, 2011)

	* orderingKM: Kurt Hornik found a problem when inspecting the
	Fortran subroutines with gcc 4.6 tools when checking vegan release
	1.17-9. 
	
Version 1.18-26 (closed March 31, 2011)

	* version closed with the release of vegan 1.17-9.

	* oecosimu: added argument 'tiesplit' (defaults FALSE). If TRUE,
	simulated values tied with the observed statistic are split so
	that half of them are regarded as satisfying the condition, and
	removed from those cases which are greater or less (as given by
	'alternative'). This is usually *not* done, but implementing
	Raup-Crick dissimilarity in oecosimu() following
	http://www.esajournals.org/doi/pdf/10.1890/ES10-00117.1 (Chase et
	al., Ecosphere 2011) uses this option. However, cross-checking
	the "r0" null model against the vegdist(..., "raup") indicates
	that the options should be set FALSE (and this would mean that the
	change is reverted).

	* anova.ccabyaxis: I (JO) noticed in an ORDNEWS message that
	anova(..., by = "axis") ignores the original Conditions in partial
	models and so gives wrong results in partial models. The fix finds
	the conditioning matrix as qr.X(object$pCCA$QR), and uses this as
	a Condition in updated models. Added a regression test that checks
	that statistics and residual df match.

	* tolerance: new function to compute species tolerances and sample
	heterogeneities as Canoco does. Includes a method for objects of
	class "cca".

	* plot.contribdiv: plot now draws axes and box *after* doing the
	drawing - stops polygons overplotting the axis and box.

Version 1.18-25 (closed March 23, 2011)

	* ordilabel: gained argument 'xpd' to draw labels outside the plot
	region.

	* ordisurf: got a formula interface as an alternative to define
	the model. Also now accepts `gam()` argument `select` to add an
	extra penalty to smooths so they can be penalized to zero (i.e.
	removed from the model). This is a form of model selection.
	Estimation of smoothing parameters can now be determined via
	argument `method`. Both `select` and `method` have been set to
	defaults that were implied in previous versions of the function.
	If smooth is penalized to (effectively) 0, countour plotting is
	suppressed. New argument `gamma` can be used to increase the cost
	of each degree of freedom used by a model in the GCV or UBRE/AIC
	scores used in smoothness selection. New argument `plot` can be
	used to stop ordisurf producing any graphical output.
	A plot method is now provided that can draw contour or perspective
	plots of ordisurf results, or plot the fitted GAM surface.

	* metaMDSrotate: can now rotate > 2-dim solutions so that the
	first axis is parallel to a given vector and all others are
	orthogonal to the vector (and rotated to PC if they were
	originally). Earlier had argument 'choices' which was supposed to
	select only two axes to be rotated (but failed before rev 1533),
	but now lost 'choices' and always uses all dimensions, and
	orthogonalies dim 2 and beyond against the given vector. There was
	a query in R-sig-ecology on having two vectors in 3-dim ordination
	which triggered the current changes, but this does not still
	answer to the question of
	https://stat.ethz.ch/pipermail/r-sig-ecology/2011-March/001947.html.
	It would be possible to have this with recursive metaMDSrotate for
	1..N for first 'vec', then 2..N for the second 'vec', but the
	later 'vec's could be correlated with previous axes.

	* metaMDS: 'previous.best' can now be a user-supplied
	configuration, or a result of isoMDS(). If 'previous.best' is an
	isoMDS() or a metaMDS() result, it can have different number of
	dimensions than the current 'k': extra dimensions are dropped off,
	or noisy extra dimensions are added as needed. This may help in
	running metaMDS() with a range of 'k'. Not yet documented.

Version 1.18-24 (closed March 10, 2011)

	* cca: will return NULL item for CCA only if constraints were not
	given. If the CCA component has zero rank (= constraints were
	aliased or were orthogonal to the data), will still return a CCA
	item with zero eigenvalue, rank, scores etc plus info on
	"alias". The residual component will never be NULL, but similar
	zero-containing component is returned even when there is no
	residual variation.  Usually these changes only manifest in
	arbitrary data sets, but we have had email queries in R-sig-eco on
	completely aliased constrainsts when users assumed that model
	cca(y ~ A + Condition(A)) would be similar to a random effects
	model and A could be analysed both as a Condition and as a
	Constraint instead of being aliased. Naturally, overfitted models
	with empty residual components do appear often. Currently the
	printed output includes these zero items with Inertia and Rank 0,
	whereas NULL components are not displayed. The changes so far only
	concern cca(); rda() and capscale() are only changed after (and
	if) this change appears sensible and correct in cca().

	* drarefy: a new function to return the probabilities that a
	species occurs in a rarefied sample (= sampled without
	replacement) of a given size, (or given sizes specified
	separately for each row if 'sample' is a vector)..

	* diversity, rarefy, rrarefy, specnumber: accept vector input. All
	functions documented in ?diversity now accept vector input.
	Function fisher.alpha and drararefy already accepted vectors.

Version 1.18-23 (closed February 28, 2011)

	* opened with the release of 1.17-7 based on version 1.18-22 on
	February 16, 2011.

	* does not use unnecessary return() plus other stylistic
	twitches. This touches 24 functions, but users should see no
	difference. 

	* procrustes: checks and reports different number of rows instead
	of failing in crossprod() with incompatible arguments.

	* prestonfit, as.preston: default now 'tiesplit = TRUE'.

	* as.preston (prestonfit, prestondistr): uppermost octave could be
	NA with 'tiesplit = TRUE' (a bug).

	* decorana: Cajo ter Braak notified about false expansion of
	computed zero eigenvalues in rescaling which then are used in
	estimating eigenvalues. They are now zeroed. Cajo's example was a
	6x5 petrie matrix:

	petrie <- matrix(0, 6, 5)
	diag(petrie) <- 1
	petrie[row(petrie) - 1 == col(petrie)] <- 1
	decorana(petrie)

	Gavin Simpson had another failing case:

	dummy <- matrix(c(1,3,1,0,0,0,0,0,0,
                   0,0,0,1,3,1,0,0,0,
                   0,0,0,0,0,0,1,3,1), nrow = 3, byrow = TRUE)

	which also failed in orthogonal CA ('ira = 1'). Now the zeroing is
	done after estimating each axis, and the results are similar as in
	Canoco. However, the results of orthogonal CA with 'dummy' are
	wrong in both: there should be two eigenvalues of 1, but only one
	is reported. This is a fundamental problem in the
	orthogonalization algorithm in the Fortran code presumably shared
	between vegan:decorana and Canoco.

	* specaccum: first step in implementing weights on
	method="random".  Not yet documented nor supported.  Issues that
	must be solved are plotting (all lines? summaries?), summarizing
	(use approx to get average predictions?) and the very natural link
	to fitspecaccum models.

	* nobs: R 2.13.0 will introduce new generic nobs() that will
	return the number of observations. This is at least needed in
	functions to evaluate BIC and in step() and functions it
	calls. Implemented nobs() for several vegan classes -- some of
	these may be unnecessary. Not yet documented but aliases in
	vegan-internal.Rd. 

	* FAQ updates: using 'select' in ordination text() and points(),
	using 'xlim' to flip axes or zoom into ordination plot(), the
	non-effects of 'strata' in adonis(). All these indeed are
	frequently asked.

	* scores.default: clarified documentation (PR#1300).

	* vegdist: rephrased Chao index following PL.
	
Version 1.18-22 (closed February 16, 2011)

	* nestednodf: did not go to 'weighted = FALSE' with quantitative
	data if 'order = FALSE'. Reported by Daniel Spitale.  

	* eigenvals: learnt to know 'dudi' objects of the ade4 package,
	and 'pco' an 'pca' obejct of the labdsv package.

	* betadisper: streamlined code somewhat.

	* prestonfit: implemented splitting "tied" counts (1, 2, 4, 8 etc)
	between octaves following Williamson & Gaston (J Anim Ecol 43,
	381-399; 2005) with argument 'tiesplit = TRUE'
	
	* specaccum: fixed typo -- 'individuals' instead of
	'invidividuals'. plot() gained argument to use "individuals" as
	x-axis instead of "sites" with method = "rarefaction".
	
Version 1.18-21 (closed January 19, 2011)

	* Fixes bug report #945 at R-Forge: anova.cca should now work with
	subset, missing data, functions of constraints (like log(x)),
	constraints or subset variables in data=, attached data frames or
	in working environments. 

	* capscale: return additive constant ('ac') when 'add = TRUE'. 

	* fitted.capscale, predict.rda: additive constant ('ac')
	subtracted from the estimated distances when 'add = TRUE' was used
	in capscale().

	* predict.rda: type = "working" for capscale returns now scaled
	scores that produce the dissimilarities as Euclidean distances --
	like was claimed in the help page.

	* simulate.capscale: implemented simulate() for capscale. This
	uses internal metric scaling mapping to simulate data and add
	error, but returns Euclidean distances adjusted to the original
	scale of input dissimilarities. The function uses only the real
	axes, and imaginary dimensions are ignored.

	* anova.cca: by = "term" and by = "axis" work now both with the
	data= statement and with variables in the GlobalEnv and subset=
	both in cca/rda. It seems that 'subset' is not implemented for
	capscale(), but otherwise models work.

	* cca/rda: added item 'subset' that is the subset argument
	evaluated to a logical vector.

	* capscale: implemented 'subset' (and this also works with
	anova.cca). It looks like all anova.cca tests pass also with
	capscale (but more thorough test will be run before closeing the
	anova.cca bug in vegan-forge). It seems that subset and na.action
	also work. 

	* anova.cca: most cases work now when terms are given in
	attach()ed data frame after changes to anova.ccabyterm() and
	ordiParseFormula(). 

	* anova.cca: works (mostly) when there are missing values. The
	exception found was 'by = "term"' when the data frame is not given
	as a 'data=' argument, but as an attached data.frame. In this case
	'by = "term"' detects a change in the number of rows and stops
	with a message.

Version 1.18-20 (closed January 9, 2011)

	* base of vegan release 1.17-6 (released on Jan 10, 2011).

	* capscale: the total inertia was defined as the sum of absolute
	values of inertia so that negative eigenvalues of imaginary
	dimensions increase inertia (changes in 1.18-17 and release
	1.17-5). Torsten Hauffe reported this as a bug in vegan
	open-discussion forum in R-Forge on Dec 22, 2010. I (JO) answered
	on Jan 1, 2011 and justified the change, and said this is a design
	decision, and not a bug. Now I have reconsidered this design
	decision, and it really seems to me that it was wrong. Now the
	negative eigenvalues again reduce the total inertia, and are
	similar as in vegan 1.17-4 and earlier. The capscale() output got
	a new item of "Real Total" that gives the sum of eigenvalues
	without the imaginary component, and the proportions are given
	only within this real component (if there are negative
	eigenvalues).  The eigenvalues of negative eigenvalues are not
	added to the result, because they are not strictly for the
	unconstrained component only like previously indicated. However,
	summary.eigenvals() estimates the proportions explained using
	absolute values of eigenvalues since this seems to make sense
	there (the proportion explained is now based on absolute
	eigenvalues to give more sensible output).

Version 1.18-19 (closed January 3, 2011)

	* new version opened with the release of vegan 1.17-5 (submitted
	Dec 17, 2010, released at CRAN on on Dec 18, 2010).

	* CCorA: Pierre Legendre's minor fixes, including scaling of
	scores Cy an Cx, and removing requirement of MASS.

	* wascores: checks input -- weights (species abundances) must be
	non-negative and not all zero.
 
	* metaMDS: function was written for community data with all
	entries non-negative, but it is used increasingly often with other
	data types with a risk of failure (especially in wascores()). Now
	data are checked for negative entries, and arguments wascores,
	autotransform and noshare are set to FALSE with negative data
	entries. Triggered by email queries and problem reports.

Version 1.18-18 (closed December 17, 2010)

	* mantel.correlog: proper treatment of ties in permutation
	statistics. Function uses mantel() to evaluate p-values, and this
	uses one-sided test. If the statistic is negative, the test
	direction is reversed, but then p-value cannot be directly
	complemented if there are ties: the observed statistic must be
	switchec to another side of the tied block. Therefore
	mantel.correlog() now evaluates the p-value directly in reversed
	test.

	* nestedtemp: updated the literature reference to Almeida-Neto &
	Ulrich (2011).

	* vegdist.Rd: fixed legends to Gower indices and checked binary
	formualations (ok).

	* vegan-package.Rd: added a package intro file (to be merged to
	the release version 1.17-5).

	* sipoo.rda: got island names, and decision-vegan.Rnw vignette was
	changed accordingly.

	* ordistep: Pierre Legendre's edits of the help page.

	* prc: got back the formula interface and with that the na.action
	lost in r1356 (9 Nov, 2010).

	* plot.procrustes: user can select the direction of the arrow with
	argument 'to.target', and the 'type' of the plot. With 'type =
	"text"', ordilabel() is used to mark the tails of the arrows.

	* plot.betadisper: would fail when plotting anything other than
	axes 1 and 2. Now fixed and an example included in the Rd file to
	make sure this doesn't happen again. Reported by Sarah Goslee.

Version 1.18-17 (closed December 1, 2010)
	
	* predict.procrustes: gained 'truemean' so that new points can be
	added to the plot.procrustes() graph.

	* alpha release version: preparing release (1.17-5) of
	vegan. Mainly clean up and checking of functions intended for the
	release. 

	* mantel.correlog: vegan mantel() was used standard order
	statistics or (hits+1)/(nperm+1) since May 2009, but
	mantel.correlog() did not notice the change and still tried to
	correct the mantel() result.

	* as.mlm.cca/rda and intersector: should get the pivoting of names
	in qr.X() correct both in the current buggy R and hopefully fixed
	next version 2.12.1.

	* vif.cca: aliased terms must be removed when calculating
	VIFs. Test case vif.cca(cca(dune ~ Manure + Management, dune.env))
	should give decent values all below <100 (used to give magnitude
	10^31). VIF of aliased terms is NA. Pierre Legendre noticed this.

	* print.eigenvals uses zapsmall.
	
Version 1.18-16 (closed November 17, 2010)

	* procrustes: fixed centring of fitted(). Added predict() method
	that can be used to add new rotated coordinates to the target. The
	function cannot be used for symmetric analysis with 'newdata'.

	* vignette on design decision: updated to changes in 'const' in
	scores.rda()  in 1.18-15 and to Canoco 4. Explains now 'const'
	more thoroughly.

	* pcnm: gained argument 'dist.ret' to return the distance matrix
	on which PCNMs were based.

	* cca/rda/capscale: JO yielded to the pressure, and added
	proportions of inertia components in the printed output.

	* capscale: failed with na.action -- fix in ordiParseFormula().
	na.action was introduced in rev1002 (Sept 11, 2009), and then
	ruined with a change in ordiParseFormula() in rev1007 (Sept 15,
	2009) so it lived four days and was broken when released. The
	problem was reported by Nevil Amos.

	* SSgleason: a new SS-species-area-model.

	* SSlomolino: improved starting values for 'xmid' (and
	'Asym'). Now fitspecaccum(..., "lomolino") works in several cases,
	including BCI and bryceveg (but fails in <1% of cases). Now 'Asym'
	and 'xmid' are estimated from Arrhenius at log-log scale: 'Asym'
	is the predicted value at max(x), and 'xmid' is the value of x
	giving 'Asym/2'.

	* capscale: defines total inertia as the sum of absolute values of
	eigenvalues to be consistent with cmdscale(), wcmdscale(),
	eigenvals(), Gower and Mardia, Kent & Bibby.

	* eigenvals: added a method for "pcnm" and docs discuss handling
	negative eigenvalues in summary.eigenvals(). Function is ready for
	the new version of cmdscale() in R 2.12.1.

	* prc: Cajo ter Braak wrote new code for more direct
	implementation of PRC. This drops formula interface and directly
	finds model matrices avoiding aliased terms.
	
Version 1.18-15 (closed November 9, 2010)

	* procrustes: 'translation' needs to take into account 'scale',
	although Mardia et al. omit it. Reported, analysed and fix
	suggested by Christian Dudel (Bochum). 

	* fitspecaccum: uses now new SS-models for species-area
	relationship and several of standard SS-models for
	nls(). Placeholders for documentation added. Has a plot()
	function. 

	* Self-starting nls() models for species-area relationship: added
	Gitay and Lomolino models from Dengler 2009 (J Biogeog 36,
	728-744). Some more should be added, but these were among the best
	in Dengler's simulation. The starting values of the Lomolino model
	(SSlomolino) need work, as do several other candidate models. The
	purpose is to use these also in fitspecaccum(). 

	* rda: the scaling 'const' can now be a vector of two items: the
	first is used for species and the second for sites. This allows
	compatibility with Canoco 3.x (but Canoco 4 changed scaling): if
	'mod' is an rda() result, and 'nr' is the number of rows in data,
	then "scaling = -2, const = c(sqrt(nr-1), sqrt(nr))" in scores(),
	summary() or plot() will use default scaling of Canoco 3.x. Help
	page now points to decision vignette explaining scaling and
	'const' (and the vignette needs updating).

	* prc: coefficients folded in a wrong way. Diagnosed, reported and
	fixed by Cajo ter Braak. CtB also fixed the scaling of species
	scores and coefficients to be more consistent with Canoco and
	common standards. The function now ignores user settings of
	contrasts and will always use treatment contrasts. Cajo ter Braak
	is now recognized as a co-author of the function.

	* nestednodf: breaks ties in column and row totals by row sums and
	column sums in quantitative data ('weighted = TRUE'). Version
	submitted by Gustavo Carvalho in a follow-up to Feature Request
	#1097. 

Version 1.18-14 (closed November 1, 2010)

	* treedist: works now with zero-height trees (for instance, only
	one item in a tree).  Function gained a new argument 'relative'
	(defaults TRUE): if FALSE, finds raw dissimilarities of tree
	heights.  Help page now tells that relative tree distances are in
	range 0..2 instead of 0..1, since combining two trees may add a
	new common root.

	* isomap: returns only axes associated with positive eigenvalues.

	* wcmdscale: give two goodness of fit statistics for 'k' axes: one
	is for the real part and based on the sum of positive eigenvalues,
	and second is for all axes and based for the sum of absolute
	values of all eigenvalues.

	* summary.eigenvals: handle now possible negative eigenvalues from
	capscale() or wcmdscale(): cumulative sum and proportions are now
	based on the sum of absolute values of eigenvalues, and all real
	eigenvalues explain less than 100% if there are negative
	eigenvalues.

Version 1.18-13 (closed October 15, 2010)

	* anova.cca(..., by = "axis"): now really uses marginal tests for
	every axis. Significance of axis k with LC scores lc is from model
	update(object, . ~ lc[,k] + Condition(lc[,-k])). That is, axis k
	is used as constraint and all other axes as conditions, when axis
	k is analysed. This also solves the failure of anova(..., by =
	"ax") of rda(dune ~ poly(pH, 2) + Baresoil, varechem) of PR#945,
	but no other problems of the same report.

	* treedive: handles trivial cases of zero (diversity NA) or one
	species (diversity 0). 

	* oecosimu: handles NA values as na.rm = TRUE in simulations for
	cases where these are produced by the function to evaluate
	statistics.

	* oecosimu: takes care that the statistic is evaluated with binary
	data when null models are binary. This was a one-year old bug
	introduced in rev 967 on Aug 31, 2009. Previous time this bug was
	corrected in rev 438 on June 28, 2008.

	* nestednodf: Gustavo Carvalho sent a new upgraded version which
	also implements a new quantitative method of Almeida-Neto & Ulrich
	(Env Mod Software, in press; 2010). Based on feature request #1097
	in R-Forge. 

	* ordistep: name clash if the fitted model contained item or term
	called 'mod'. Reported by Richard Telford (Bergen, Norway).

	* fitspecaccum: Stephen Sefick suggested adding Michaelis-Menten
	fit to random species accumulation and sent his model function.
	These ideas were used to add a new more general function. In
	addition, there is an option of fitting Arrhenius model S = c*A^z
	with a new self starting function SSarrhenius() for nls(). No
	documentation yet: needs work.

	* decorana: gives a warning if residual is bigger than tolerance.
	
Version 1.18-12 (closed September 26, 2010)

	* swan: no eternal loop with disconnected data where zeros will
	remain in the matrix.

	* ordilabel: gained argument 'col' to set the text colour of the
	labels separately from 'border' (default action is to use 'border'
	colour). 

	* ordiellipse: gained argument 'col'. For draw = "lines" this
	works similarly as previously when 'col' was passed on. For draw =
	"polygon" 'col' sets only the polygon fill, and the text of the
	labels will use the colour of the border or of the foreground.

	* ordiR2step: gained argument 'direction = c("both", "response")',
	and with "both" gives also adjusted R2 when dropping terms. I have
	not yet seen a case where a term is dropped. Abandoned dangerous
	practice of getting the R2.all directly from a fitted model of the
	'scope' since this may have different lhs.

	* anova.ccalist: removed. Revisions were 1273, 1274, 1276. Could
	not make this work consistently with other anova models, except
	with 'model = "direct"'. The function would also change the API so
	that "..." come as the second argument breaking partial matching
	of other arguments.
	
Version 1.18-11 (closed September 17, 2010)

	* diversity: example says that rarefy(x, 2) - 1 is the same as
	unbiased Simpson of a true random sample of Hurlbert (1971,
	eq. 5). Added after several wishes to have this function.

	* metaMDS: more verbose about connectivity. Use na.rm = TRUE in
	metaMDSdist(). 

	* FAQ: entry on ade4:cca name clash triggered by an invalid bug
	report #1066 and queries in r-sig-ecology.
	
Version 1.18-10 (closed August 31, 2010)

	* New version opened with the release of vegan_1.17-4 on August
	20, 2010.

	* rankindex: can take a list of dissimilarity functions as an
	argument.

	* deviance.cca/rda: return 0 (instead of NULL) if there is no
	residual variation.

	* vegdist: help page gives equations for binary variants of the
	indices. 

	* biplot.CCorA: resets par that it sets.

	* ordiR2step: can go to the end and include all variables of the
	scope (and checks there is a scope).  Additional stopping
	criterion of exceeding P-value. Looks like being up to specs and
	left for approval.

	* permutest.cca: defaults to 99 permutations instead of 100 (to
	be consistent). Item 'call' now stores the call to permutest()
	instead of the call of the ordination which is now saved in
	'testcall'.  This means that update() works now.

	* anova.cca: use correct degrees of freedom when there is no
	constrained or no residual component.

	* anova.ccalist: Started to work on the concept of permutation
	test comparison of several cca/ rda/ capscale models. The basic
	function was added to the R-Forge (undocumented!).  First idea is
	to run permutest.cca with the same RNG seed and collect the
	permutations from the differences of these models.  This won't be
	consistent with other anova.cca* because permuted residuals differ
	from the corresponding partial model (except with model =
	"direct").  Another option that I have on my mind is that I use
	model.matrix.cca to reconstruct a matrix of RHS of each model, and
	then run a series of partial model ANOVAs. Here the problem is
	that the statistics will be sequential, i.e., the residual of each
	model is from the next model and not from the final model, and the
	models must be in increasing order or ordered programmatically;
	the current test will study differences of any sequence.
	Naturally, we have to figure out how the permutation should be
	done. Probably a note to R-Devel to open up discussion on the
	issue. NOTE: there is no automatic delegation to this function. If
	you try this, you must explicitly write "anova.ccalist(model1,
	model2, model3). NOTE2: There are no tests of the sanity of the
	input: be careful. NOTE3: Does not work with saturated model with
	null residual variance.
	
Version 1.18-9 (closed August 20, 2010)

	* mrpp & meandist: John Van Sickle notified us that his
	Classification Strength (CS) uses 'weight.type = 1' (or n)
	insteaad of 'weight.type = 3' (or n(n-1)/2).  Calculation of CS
	was dropped from mrpp(), because with this weighting it no longer
	has an exact relation to the corresponding MRPP statistic and the
	function mrpp() cannot provide a significance test for both
	statistics together. CS is kept in meandist(), where its
	calculation is corrected for the correct weight type.

	* vegdist: Anderson et al. (Ecol Lett 9, 683-693; 2006) defined
	their "alternative Gower" without range standardization of
	columns.  Reported as bug #1002 in http://r-forge.r-project.org/
	by Sergio Garcia. Also some small edits of vegdist man page.

	* msoplot: legend mixed symbols and labels. 

	* Rd (help) files: removed some superfluous \-characters that were
	visible in rendering text (accented letters, Latex notation in
	wrong places).

	* predict.rda/cca: document 'newdata' with 'type = "response"' or
	'type = "working"'. The feature was added in vegan
	1.18-4 (rev1180, April 15, 2010).

Version 1.18-8 (closed August 12, 2010)

	* DESCRIPTION: does not suggest package 'ellipse'.

	* FAQ: new entry on negative or non-numeric data, and updates of
	variance explained by ordination.

	* intro: ordispider uses label.

	* adonis: uses print.anova for cleaner output.

	* plot.MOStest: uses veganCovEllipse instead of
	ellipse:::ellipse.glm.

	* ordiellipse: failed to plot labels with filled polygons, since
	the same colour was used for polygon filling and labels. Now uses
	ordilabel() with draw == "polygon" (but still text() with draw ==
	"lines").

	* decorana: change order of data checks so that non-numeric data
	is detected (by rowSums()) before checking negative data entries.

	* ordigrid: arguments lty, col and lwd to use different lines for
	levels and replicate of the grid.

Version 1.18-7 (closed July 19, 2010)

	* new version opened with the release of vegan_1.17-3.

	* veganCovEllipse: new internal function for drawing covariance
	ellipses (to be used both with ordiellipse() and plot.MOStest()).

	* ordiellipse: uses veganCovEllipse.
	
Version 1.18-6 (closed June 16, 2010)

	* Version 1.18-6 closed simultaneously with the release of
	vegan_1.17-3 on June 16, 2010).

	* mantel, mantel.partial: considerable speed up by cleaning
	innermost loop and replacing as.dist() with direct extraction of
	lower diagonal.

	* treedist: documenting tree dissimilarity function that has been
	in vegan devel since Aug 17, 2009 (rev928).

	* betadisper: 'type = "median"', the default, was not computing
	the spatial median on the real and imaginary axes separately.
	Reported by Marek Omelka.

	* permutations: First attempt to document within Vegan the general
	workings of permutation tests. See ?permutations for details.

Version 1.18-5 (closed May 31, 2010)

	* cca, rda: plot() failed if Condition() had factors, but
	constraints had no factors. An example of failure:

	m <- cca(dune ~ A1 + Condition(Management), dune.env)
	plot(m) ## failed

	* ordiarrows: gained 'label' argument which uses ordilabel() on
	arrow starts.

	* ordisegments: gained 'label' argument which uses ordilabel() on
	both ends of the segment.

	* ordispider: gained 'label' argument (uses ordilabel()). Can now
	handle ordihull() result objects: connects points in the line to
	the hull centroid. Extended examples.
	
	* ordiR2step: new function to perform forward model selection
	following Blanchet, Legendre & Borcard (Ecology 89, 2623-2632;
	2008) or by adjusted R2 until the adjusted R2 of the full model
	(scope) is exceeded or adjusted R2 starts to decrease.

	* RsquareAdj.default: handles vector arguments.

	* ordiellipse: works only with 2D data, and now uses only first
	two dimensions of input if more given. For instance, the following
	works now, but gave very cryptic error message previously:

	m <- decorana(dune)
	plot(m)
	with(dune.env, ordiellipse(m, Management))

	* ordiresids: removes now the row weights from Residuals and
	Fitted in CA. Now shows the same values that are shuffled or
	resampled in simulate.cca() where they are again weighted after
	being added to the new fitted value.

	* mantel.correlog: changes the Sturges rule to conform with the
	standard R nclass.Sturges ('ceiling' instead of 'round'). Extends
	and corrects documentation and messages.

Version 1.18-4 (closed May 21, 2010)

	* envfit: defaults now to 999 permutations. Used to be 0 or no
	permutations. 

	* metaMDS: can handle NA values in dissimilarities (but I do not
	know if isoMDS can handle them correctly).

	* mantel.correlog: accepts now user supplied breakpoints or number
	of classes like intended.

	* RsquareAdj.rda: uses now correct model df in rank deficit RDA
	models. 

	* adonis: implemented tie handling in permutations. 

	* predict.cca/rda: implemented 'newdata' for type =
	"response". For CCA, 'newdata' must be constraints (environmental
	data), and for CA they must be community data. Test version, not
	yet documented (except here).

Version 1.18-3 (closed April 15, 2010)

	* new version opened with the release of vegan 1.17-2 (March 8,
	2010). 

	* DESCRIPTION: Corrected the name of Bob O'Hara (also in release
	1.17-2). 

	* scores.cca/scores.rda: scores will always have names even if the
	input data have no names. This fixes some display issues that
	Pierre Legendre had with biplot.rda(), and makes redundant the
	name checking code in summary.cca (the redundant code was not yet
	removed, but I see that this fix here was sound).

	* permutest.cca: re-weighting of permuted CCA data matrix is now
	done with compiled code using existing C function 'wcentre' (in
	goffactor.c). This may give huge speed-up (>50% time save in first
	tests) both in CCA and pCCA.  The print function of permutest puts
	now the observed statistic among permutations (the P-value is only
	evaluated at printing so that this does not influence any
	anova.cca function using permutest.cca).
	
Version 1.18-2 (closed March 8, 2010)

	* ordistep: documented the 'anova' component added to the result
	object. 

	* densityplot.oecosimu: gives no warning if there is only one
	statistic and hence only one panel.

	* nesteddisc: failed if highest species frequencies were tied. The
	error message was "Error: dims [prodcut 15] do not match the
	length of object [0]". Found by Eric Fuchs in the help forum of
	vegan.r-forge.r-project.org. The function does not try as hard to
	optimize the index, and hence it is much faster (but slacker).

	* screeplot: New argument 'legend' for all methods (except
	'decorana') to draw a legend if the observed and broken stick
	distribution are both plotted. Now also respects 'pch' for the
	broken stick line.

	* permutest.betadisper: print method got ordering of permutation
	p-values wrong in displaying the matrix of pairwise tests. The
	computed values were correct. The formatting for printing contained
	the bug. Reported by Dan O'Shea.

Version 1.18-1 (closed February 18, 2010)

	* closed with the release of vegan 1.17-1. The release contains
	bug fixes and multipart of 1.18-1, but excludes MOStest and 1.18-1
	upgrades to ordistep.

	* ordistep: saves model changes in the 'anova' item similarly as
	standard step(). Experimental feature: not yet documented.

	* envfit: did not pass weights to factorfit or to vectorfit when
	the environmental variable was a single vector. Reported for
	vectors by Richard Telford. Broken in rev1004 (Sep 12, 2009).

	* CCorA: Fixed bug in presentation of variables in plots. Adds new
	biplot types. General improvement in checking exceptional cases
	improve stability.

	* predict.cca, predict.rda: match 'newdata' by row names or column
	names in type = "wa" and type = "sp". This is similar as
	predict.prcomp/princomp. Gained choice type = "working" for
	working residuals (as fitted.cca/rda).

	* simulate.rda, simulate.cca: gained argument rank passed to
	predict.rda() or predict.rda(). This also allows simulation under
	null model by setting rank = 0.

	* permatfull.Rd: fixed braces in the help file + mark-up.

Version 1.18-0 (closed January 11, 2010 with release 1.17-0)

	* Documented na.action in cca.object.

	* Opened concurrently with copying 1.16-34 (at rev 1087) to
	branches/1.17 for a new release.

	* betadisper: 'type = "median"' is now the default type of
	analysis.

	* fieller.MOStest: removed erroneous multiplication of variances
	by overdispersion, because this was already done in cov.scaled,
	and therefore was doubled and gave much too wide (up to Infinite)
	limits.

	* MOStest uses now ANODEV of free model and model where the
	hump/pit is forced to a given location instead of the test based
	on the Wald statistic (coefficient/sd) of the coefficient of the
	linear term. The ANODEV and Wald statistic are equivalent in
	Gaussian models, but in with other error families the ANODEV is
	more correct. This fix removes the conflict between the basic
	MOStest() and its profile() and confint() methods in non-Gaussian
	families.

Version 1.16-34 (closed January 2, 2009) -- (codename: Lucia)

	* twostagechao: deleted, because question regarding the
	notation in the original article remained unanswered.

	* permat* cleanup: permat.control deleted, not needed any longer
	due to changes in oecosimu, documentation for plot.permat merged
	with permat* help page.

	* goodness.cca: was not using correct weights. Broken in r992 (Sep
	6, 2009).

	* vegdist: added UI for the alternative Gower index ("altGower")
	that skips double zeros. The C code has been in vegan since Oct 24
	(r1051), but no R interface. Together with decostand(..., "log")
	of r1052 this closes Feature Request #473 submitted by Etienne
	Laliberte in R-Forge.

	* anova.cca: tied values could be randomly broken due to
	numerical precision, and this gave false P-values, for instance in
	anova(cca(dune ~ Management, dune.env),
	strata=dune.env$Management).  Now rounds statistics to 12 decimal
	places in permutest.cca and in anova.ccabyterm.

	* permutest.cca: uses pasteCall() in print.

	* betadisper: added spatial median code written by Jari to betadisper.
	All associated methods work OK, and this should be the default method
	but needs a little checking first. This requires the new function
	'ordimedian', which is currently undocumented in ?betadisper.

Version 1.16-33 (closed December 13, 2009)

	* DESCRIPTION: Guillaume Blanchet added to the Authors.

	* spandepth: New function to find the depths of nodes in a
	spanning tree from spantree() function. Per request of
	W. E. Sharp.

	* bstick: refuses to analyse capscale() models with imaginary
	components because I have no idea how to do it. Reported by
	Richard Telford, Bergen (who probably wanted another
	solution...). 

	* predict.rda: works now with rank = 0 -- returns matrix of column
	means.  (Not yet done for predict.cca.)

	* simulate.rda: can now add permuted residuals to the fitted
	values. Experimental, low level interface that requires giving the
	index of right length. The permutation index can contain
	duplicates such as from sample(nrow(data), replace = TRUE) so that
	bootstrapping is possible unlike in anova.cca/permutest.cca. Works
	now with partial model: adds partial fit to the constrained fit.

	* simulate.cca: implemented by cloning simulate.rda. Function
	works with internal Chi-square standardized form and
	back-transforms the result by marginal totals and matrix grand
	total at the end. The marginal totals may still be negative. Not
	explicitly documented, and needs a connoisseur user. 
	
Version 1.16-32 (closed November 13, 2009)

	* alias.cca: gained argument 'names.only' (defaults FALSE) to only
	return the names of the aliased variables insted of their defining
	equations. 

	* rarefy: failed with one site and many sample sizes like
	rarefy(rpois(10, 2), sample=2:3).

	* msoplot: uses standard legend() to display info instead of hand
	crafted positioning of the legend information.

	* ordisurf: plotting main title was broken with NA handling in
	1.16-31 (r1049). Also increased grid density and adjusted pushing
	out limits of convex hull.

	* pcnm: new function for PCNM (Principal Coordinates of
	Neighbourhood Matrix) with option for row weighs allowing PCNM for
	cca. Based on Stéphane Dray's PCNM function in his (unreleased)
	SpacemakeR package. Imported with history from sedarVegan in
	http://sedar.r-forge.r-project.org/. Has scores.pcnm to select all
	(default) or some vectors of 'choice'.

	* decostand: implemented Marti Anderson's log scaling of type
	log(x, base = logbase) + 1 as a part of Feature Request #473. The
	coding follows closely Etienne Laliberte's suggestion, and also
	handles non-negative non-integer data. 

	* vegdist: C code for an alternative version of Gower Index that
	skips double zeros. No R level interface yet. If this function is
	to be used from vegdist.R, it should be added as item 14 in
	'method' list, and the R level preprocessing should be done
	similarly as for "gower" (method choice 6). This was implemented
	for inspecting the implementation of second part of Feature
	Request #473, but may be removed if that part of the request is
	not implemented.
	
Version 1.16-31 (closed October 24, 2009)

	* ordisurf: removes observation with NA in scores (as result of
	na.action) or in predicted variable.

	* specaccum: "accumulations" in one-site collections are handled
	with a message() instead of stop()ping with error. Per request of
	Roeland Kindt.

	* constrained ordination (cca, rda, capscale) could not handle all
	anova(.., by= "something") cases when the data were not defined by
	data=, but were in the working environment or given using
	with(). The attach'ed data frames that were later detach'ed won't
	work. This means some potentially unstabilizing changes in scope:
	please report all problems.

	* envfit: could drop data frame to a vector with na.action (broken
	in 1.16-28).

	* model.frame.cca, model.matrix.cca: new support functions to
	reconstitute the model frame and model matrix (or  a list of
	condition and constrain model matrices) from a cca/rda/capscale
	result object. Documented separately.

	* constrained ordination (cca, rda, capscale) did not analyse
	constrained component in model like cca(varespec ~ Al:P +
	Condition(Al + P)) or in constrained interaction terms if the
	corresponding main effects were partialled out.

	* constrained ordination (cca, rda, capscale) failed if they only
	had partial term Condition() without constraints.

	* ordistep: new function for automatic model choice in the cca
	family of methods. This is similar to step(), but uses permutation
	P-values instead of AIC (that does not exist for these methods,
	and sometimes fails). This is similar to forward.sel() in Stephane
	Dray's 'packfor' package at R-Forge. Better things here are that
	the function has both drop and add instead of only forward
	selection, handles correctly factors, and works with cca(), rda()
	and capscale(). On the other hand, it is much slower than
	forward.sel(). The function has similar user interface as step():
	it knows 'scope' and 'direction'.

	* ordisurf: pushes out limits of convex hull so that contours
	better cover corners and margins of points.

	* plot.decorana & plot.cca: use linestack() if only one dimension
	was chosen.

	* scores.lda: new function to extract row scores and predictor
	coefficients from "lda" objects (MASS package). Magically,
	ordiplot() started to work with "lda" results. Not yet documented,
	but alias in scores.default.Rd.

	* ordiplot: uses linestack() to plot 1-col results, and now really
	is able to identify if there were no species scores (tried
	earlier, but failed because species had different names than
	sites). 
	
	* scores.default: returns vector scores as 1-col matrix.

	* linestack: passes "..." to plot(), handles missing names.
	
Version 1.16-30 (closed October 3, 2009) 

	* manual pages (Rd files) were run through aspell. With this, an
	error in an argument choice was corrected also in
	plot.nestedtemp function.

	* meandist: plot method has a new alternative of drawing
	histograms (van Sickle 1997) as an alternative to dendrograms. A
	histogram connects groups at theri within-cluster dissimilarity
	level to the average between-cluster dissimilarity.

	* oecosimu: gained new keyword 'alternative' for "two.sided",
	"less" and "greater" one-sided tests.
	
	* oecosimu: tied values in simulations and observed statistics
	treated more correctly. 
	
	* oecosimu: if all simulations were constant, their sd became
	zero, and z became NaN. Now z = 0 for these cases. A response to
	the query of Martin Kopecky at the vegan-help forum in R-Forge.

	* densitplot.oecosimu: panels keep the order of statistics. The
	panels were ordered alphabetically, but the vertical line for the
	observed statistic was in the original order (and thus often in
	the wrong panel).

	* calibrate: is now a a generic function and has a new method for
	the 'ordisurf' object in addition to the old 'cca' method.

	* FIXED BUG in cca, rda & capscale interpretation of
	formulae. This was introduced in rev 972 (Sep 1, 2009), and fixed
	in rev 1011 (Sep 18, 2009). Basically, all evaluation of 'subset'
	and 'na.action' is done after extracting the model frames with
	proven methods so that the first half of 'ordiParseFormula' is
	more similar to pre-972 versions. Function 'ordiParseFormula'
	could be re-written more elegantly, but deliberately breaking it
	twice instead of breaking it once is just too much.

	* cca/rda/capscale: cca(dune ~ poly(A1, 2), dune.env)
	failed. Internal changes in 'ordiTerminfo' which now always looks
	at the model frame returned by 'ordiParseFormula' instead of
	looking at the 'data' (and the 'data' arg is now unused in
	'ordiTerminfo'). 

	* FIXED (minor): cca(dune ~ Management, dune.env, subset =
	Management == "SF") failed in 'contrasts()' called from
	'model.matrix()' because there is only one level in Management.
	Now 'ordiParseFormula' adds a level with an unlikely name of
	.ThisVarHasOnly1Level, so that model.matrix works, but
	predict.cca(..., newdata=, type = "lc") rejects unknown factor
	levels.
	
Version 1.16-29 (closed September 18, 2009)

	* meandist: plot got an 'ylim' argument. This is practical when
	users want to display several plots side by side, and requested by
	Heli Suurkuukka.

	* WARNING OF A BUG in cca, rda & capscale: all versions have
	failed since rev 972 (Sep 1, 2009) if an argument in a model was a
	matrix. Now these things work so that tests pass, but results are
	wrong , because get_all_vars() does not get names right for matrix
	columns in the model frame. This is manifest in the example of
	varpart() that uses matrix items (such as mite.pcnm). It can be
	also seen with this:
	p <- poly(dune.env$A1, 3)
	cca(dune ~  p + Management, dune.env)
	The following seems to work:
	cca(dune ~  poly(A1, 3) + Management, dune.env)
	
	* cca, rda etc. drop unused levels of factors. This became actual
	with 'subset' and 'na.action'.
	
	* cca & rda (but not (yet?) capscale) gained argument 'subset' to
	select rows for analysis. A 'subset' can be a logical vector (TRUE
	for kept rows), or a logical expression which can contain
	variables in 'data' or species (variable) names of the dependent
	data. Some valid examples are:
	cca(dune ~ A1 + Moisture, dune.env, 
	    subset = Management %in% c("HF","BF"))
	cca(dune ~ Moisture, dune.env,
	    subset = Lolper > 0 & Management != "SF")
	S <- specnumber(dune)
	cca(dune ~ 1, subset = S > 9)

Version 1.16-28 (closed September 15, 2009)

	* drop1.cca: 'scope' given as a formula was not recognized and
	permutation tests were not run. Only character vectors of names
	worked.  

	* envfit: handles missing values in ordination scores or in
	environmental variables using na.rm argument.  This also changes
	the user interface so that 'vectorfit' and 'factorfit' clearly
	become low level functions which only accept scores (no ordination
	objects), and all processing is done in envfit.default. 

	* wcmdscale: scores (points) with zero weights (w = 0) and other
	non-finite entries will be NA.

	* capscale: implemented na.action. The WA scores are always NA for
	missing observations in capscale.
	
Version 1.16-27 (closed September 10, 2009)

	* cca & print.cca: no warning on removed species in cca.default,
	but print information on their number.
	
	* predict.rda: failed when rda was based on correlations (scale =
	TRUE), and there were missing data (0/0 division in scaling).

	* cca & rda: New way of handling na.action. Function ordiNAexclude
	adds items CCA$wa.excluded or CA$u.excluded for NA rows into
	ordination result, and function ordiNApredict called in scores.cca
	and scores.rda pads the results with these excluded data. In this
	way the internal structure of the cca object remains unchanged,
	but functions accessing the result with scores will get the NA
	data. 

	* anova.cca(..., by = "term") and step() did not work correctly
	with na.exclude or na.omit. These fitted sequential models, and
	due to missing value removal the data set could change in the
	sequence. The problem case was step() which relies on standard
	stats functions add1.default and drop1.default. They detect the
	change in data by length(object$residuals). Therefore
	ordiNAexclude adds item 'residuals.zombie' to the ordination
	result so that step() works. The same mechanism is also used in
	anova.ccabyterm (not all NA deletions change the numbers of
	observations).

	* weights.cca and weights.rda know na.action.

	* Fixing cca/rda functions for changes in weights(). The rule is
	that you can mix scores() and weights(), but if you have internal
	cca object stuctures (like x$CCA$u), you should have internal
	weights x$rowsum. Concerns as.mlm.cca, goodness.cca,
	permutest.cca, spenvcor, inertcomp and intersetcor. (The inertcomp
	solution is a kluge.)
	
	* plot.cca: works when there are NA values in scores.

	* anova.cca(.., by = "axis") works when there are omitted or
	excluded observations due to missing values. 
	
Version 1.16-26 (closed September 1, 2009)

	* cca and rda: can now handle missing values in constraints or
	conditions. With 'na.action = na.omit', the rows with missing
	values are removed, and with 'na.action = na.exclude' all rows are
	retained but results that cannot be computed are NA. The LC scores
	cannot be computed with missing values, but WA scores (usually)
	can be computed. The results with 'na.exclude' probably fail with
	most support functions because these do not expect missing values
	in the results. These functions are fixed with time. capscale does
	not (yet) handle missing data.

	* oecosimu: does not depend on permatfull/permatswap, but method
	can be a function. The r2dtable method implemented also
	to be used with adipart and related functions.

	* bioenv: uses standard R function combn() and removes
	ripley.subs() and ripley.subsets() from vegan. The result should
	be unchanged.

	* ordiNAexclude: internal infrastructure to implement na.action =
	na.exclude for cca and rda (and capscale?). The option returns
	scores where the excluded sites get NA results and are not
	omitted. In constrained ordination, LC scores will be NA, but WA
	scores are found from the community data, and the current function
	uses predict.cca/predict.rda with 'newdata' of removed
	observations to estimate WA scores of excluded observation.
	
	* ordiParseFormula: handles missing values with na.action. 

Version 1.16-25 (closed August 31, 2009)

	* mantel.correlog: updated to the version 1.4 of Pierre Legendre's
	package. 

	*  RsquareAdj: documented.

	* ordiellipse & ordihull: argument 'draw' got a new alternative
	"none". With this, nothing is drawn but the invisible plotting
	structure is returned. This was added so that it is easier to
	develop permutation tests for hulls and ellipses.

Version 1.16-24 (opened August 17, 2009)

	* ordiellipse & ordihull: gained new argument 'label' to put the
	name of the group in the centre of the ellipse or the hull. The
	functions now return invisibly data on their plots for each
	plotted item: ordiellipse() the covariance matrix (cov.wt()
	result), and ordihull() the coordinates of the hull vertices.
	These inivisible results have a summary() method that displays the
	centres of the hulls or ellipses and their surface areas.

	* ordiellipse: does not depend on the 'ellipse' package, but finds
	the coordinates of ellipse using the equation taken from the 'car'
	package. However, this devel version of 'vegan' still must SUGGEST
	'ellipse', because 'plot.MOStest' requires 'ellipse'. The current
	release version does not include 'plot.MOStest' and could be
	liberated from the 'ellipse' dependence.

	* spantree: first argument 'd' like in hclust()instead of 'dis'.
	Got a 'call' item so that update() works.

	* treedive & treeheight: accept 'spantree' objects. EXPERIMENTAL
	CHANGE THAT MAY BE CANCELLED.

	* treedist: average distance of species trees for two
	sites. Generalization of treedive(): builds a species tree of two
	sites and sees how much of the tree is shared between two sites,
	and how much is unique to the combination. The measure is similar
	to Jaccard index: the proportion of unique (unshared) tree of the
	combined tree. In principle, this is similar to UniFrac metric
	(C. Lozupone & R. Knight, Appl. Environ. Microbiol. 71:8225-8235;
	2005), but numerically and computationally different (and the
	current implementation may specify a new unpublished method). AN
	EXPERIMENTAL CHANGE THAT MAY BE CANCELLED.
	
Version 1.16-23 (closed August 17, 2009)

	* poolaccum: new function to find the extrapolated richness
	values (or specpool() estimates) for random accumulation of
	sites (with summary and plot methods). 

	* specaccum, specpool, specpool2vect and friends: index names are
	now all lower-case.

	* estaccumR: new function similar to 'poolaccum', but uses
	'estimateR' for individual (count) based estimates of extrapolated
	richness. Inherits from 'poolaccum' and shares its print, summary
	and plot methods. 
	
Version 1.16-22 (closed August 11, 2009)

	* metaMDS: accepts now user supplied dissimilarities either as a
	"dist" structure or as symmetric square matrix (Susan Letcher's
	wish). As a side effect, dissimilarity matrices are now correctly
	detected and will not be wrongly treated as raw data.

	* summary.cca: fix in 1.16-20 failed if all variables were
	continuous and there were no centroids of factor levels.
	
	* indpower: new function to calculate indicator power for a
	species (Halme et al. 2009, Cons. Biol. 23: 1008-1016)

	* mantel.correlog, print.mantel.correlog & plot.mantel.correlog: 
	new functions to construct multivariate mantel correlograms --- 
	use in ecology: to describe the spatial structure of species
	assemblages. See Legendre and Legendre, Numerical ecology; 1998,
	section 13.1.5. Written by Pierre Legendre.

Version 1.16-21 (opened July 4, 2009)

	* capscale: has now 'fitted' method (and hence, 'residuals'), and
	'predict' works with 'type = "response"'. These give
	dissimilarities that produce same ordination as original data, or
	their low-rank approximations. Function 'fitted' has 'model =
	"Imaginary"' that returns correction distances of complex
	eigenvectors with negative eigenvalues.  The dissimilarities are
	not additive, and the "Imaginary" component is not used in
	estimating the unconstrained component.

	* capscale: really works now either with argument 'dfun' or
	'metaMDSdist' (but not with both!).

	* wcmdscale: returns negative eigevalues scaled by
	sqrt(abs(eigenvalues)) if 'k' is not given or 'k' would include
	any negative eigenvalue.

Version 1.16-20 (closed July 4, 2009)

	* new version opened concurrently with the release of vegan 1.15-3
	on June 17, 2009.

	* orditorp: works now when axes are reversed like xlim = c(1,-1).

	* rrarefy: a new function to generate randomly rarefied
	communities.

	* betadisper: fix bug in removal of (effectively) zero Eigenvalues.

	* summary.cca: takes care that all scores have rownames --
	head/tail fail without names. No  ugly printing for constrained
	eigenvalues when these do not exist in unconstrained models.

	* biplot.rda: honour args to scores ('scaling', 'const').

	* points/text for cca: accept 'const' argument for rda scores.

	* ordilabel: no superfluous warnigns when args ('scaling',
	'const') are given to scores.

	* ordiplot3d: honour args to scores ('scaling', 'const') and
	without warnings.

	* ordixyplot: honour ags to scores ('scaling', 'const'). 

	* spantree: plot honours args to scores ('scaling', 'const'). 
	
Version 1.16-19 (closed June 17, 2009)

	* capscale: handles now negative eigenvalues with semimetric
	indices. These cause no more warnings. The MDS engine is now
	'wcmdscale' instead of 'cmdscale' unless 'add = TRUE' was
	specified (and then negative eigenvalues are not produced). The
	negative eigenvalues are listed after positive unconstrained
	eigenvalues, but no scores are given for them. The total inertia
	is now the sum of all eigenvalues, including the negative ones,
	and inertia components adds item 'Imaginary' for negative
	eigenvalues after 'Uncostrained'. New argument 'sqrt.dist' makes
	square root transformation of dissimilarities, producing metric
	indices in many cases (e.g., Bray-Curtis, Jaccard). Help page and
	examples now show all these, and therefore the entry on negative
	eigenvalues was dropped from FAQ-vegan.texi. The closed (max 1)
	indices are now correctly adjusted for 'rda' and hence the
	eigenvalues and inertia components are now sqrt(n-1) smaller and
	similar as in 'cmdscale' and 'wcmdscale'.

	* wcmdscale: remove zero eigenvalues, keep negative, and do not
	assume that the last eigenvalue is zero. 

	* RsquareAdj: 'cca' returns R2, but no adjusted R2 (which is
	NA). The adjusted R2 is always NA for partial models. 

	* kendall.global: fixed a bug that caused incorrect counts of ties
	in large data sets.

	* tsallis: division by zero occurred with hill=TRUE, scale=1,
	this bug has been fixes to give exp(x) as scales goes to 1.

	* multipart: a sequel to adipart, but implements multiplicative
	diversity partitioning based on Hill numbers (Jost 2007,
	Ecology, 88, 2427-2439.)

	* eigenvals: new function to extract eigenvalues of cca, rda,
	capscale (constrained & unconstrained), wcmdscale, prcomp,
	princomp, eigen and svd. For svd returns squares of singular
	values, and for prcomp and princomp squares of 'sdev'. The
	'summary' of eigenvals() retrurn eigenvalues with the proportion
	explained and cumulatitive proportion explained.

	* summary.cca: uses summary.eigenvals to display eigenvalues.

	* protest: observed value of test statistic is now considered as
	one of the permutations. Default N.perm decreased to 999 to account
	for this.

	* envfit (vectorfit, factorfit): observed value of test statistic
	is now considered as one of the permutations.

	* mantel, mantel.partial: observed value of test statistic is now
	considered as one of the permutations.

	* anosim: observed value of test statistic is now considered as
	one of the permutatons.

	* mrpp: argument defaults and printing adated for having test
	statistic among permutations (like the function always had).

Version 1.16-18 (closed May 14, 2009)

	* tsallis: got new argument 'hill' similar to that of renyi.

	* twostagechao: function that calculates multiple-community
	similarity based on Chao et al. 2008 (Biometrics 64, 1178-86).
	Some debugging is needed since it cannot reproduce the numbers
	in Table 3 exactly (lower estimates and SEs). The Rd file
	also needs more details.

	* anova.cca: there was a name clash and failure in
	anova.ccabymargin, anova.ccabyaxis and anova.ccabyterm if data
	were indexed with 'i' in the fitted model. Now the internal
	indexing uses less likely name (.ITRM) to avoid name clashes.

	* orditkplot: copes with missing or NaN scores (omits them).

	* ordixyplot: failed in constrained ordination (cca, rda,
	capscale). Was broken in rev108 on Nov 7, 2007(!). The biplot was
	rotated 90 degrees: it seems that lattice calls x y and y x. 

	* ordixyplot & ordisplom: Gained a new type = "arrows" that is a
	Lattice version of ordiarrows.

	* RsquareAdj: defined as generic function. The old RsquareAdj is
	now the "default" method, and there are specific methods for
	"rda", "cca" (= NA), "lm" and "glm" objects. Not yet documented,
	but functions are listed as aliases in varpart.Rd. On Pierre
	Legendre's request.
	
Version 1.16-17 (closed April 15, 2009)

	* closed concurrently with the release of vegan 1.15-2.

	* spantree.Rd: example plots use type = "t" to demonstrate the use
	of ordilabel(). 

	* nestedtemp: docs tell that Carsten Dormann's bipartite package
	has a direct port of BINMATNEST programme of Rodriquez-Girones &
	Santamaria. 

	* anosim: uses much less memory allowing analysis of larger
	problems (number of rows, number of iterations). The change
	concerns only internal data structures, and the permutation
	results should be identical with old and new code when the same
	random number seed is used. The Rd file got an example of using
	'strata' in permutations.

	* meandist: a new sister function for mrpp. Function meandist
	calculates a matrix of mean within and between group
	dissimilarities. Its summary function returns the overall averages
	of those distances, and all three variants of MRPP A statistic,
	and classification strength. The plot method draws a dendrogram
	based on the mean dissimilarity matrix, with leaves hanging to
	within-group dissimilarity.

	* betadisper: Fix bug corrects the way distance to centroid is
	computed when only one group is present in the data. betadisper 
	can now also detect if 'd' is Euclidean, zapping zero Eigenvalues. 
	Bug report and suggested improvements provided by Etienne
	Laliberté.

	betadisper now also handles missing observations in either the
	dissimilarity matrix or the grouping variable.

	* decostand: added dots to the argument list to pass (ignored)
	arguments to decostand(). This was done to to fix
	stressplot(metaMDS(x, dist="gower", trymax=40)), which failed
	because metaMDSdist/vegdist were passing 'trymax' to decostand()
	while evaluating "gower" dissimilarity.

	* ordisurf: will fit a linear trend surface if knots = 0 or knots
	= 1, and a quadratic trend surface if knots = 2. All these are
	below the lowest permissible values of 'gam' smoothers and free
	for creative reuse.
	
Version 1.16-16 (closed April 2, 2009)

	* metaMDS: scales ordination scores to the same range as input
	dissimilarities if halfchange = FALSE. Better heuristics to decide
	whether to use halfchange scaling: the old heuristics failed if
	Euclidean or other open-ended dissimilarities were small (max <
	1), like after wisconsin() in metaMDSdist.  The heuristics are now
	in postMDS instead of metaMDS wrapper, and this changed the
	default of internal argument 'halfchage' in postMDS, and now the
	user can set the 'halfchange' argument in metaMDS. The
	undocumented internal 'maxdis' argument is changed to logical in
	metaMDSdist (TRUE if maximum dissimilarity = 1 for a pair of sites
	with nothin shared).

	* mrpp: reports now "classification strength" when weight.type = 3
	or weights n*(n-1) are used. Returns mean dissimilarities and
	counts for classes. Expected delta is now the mean of original
	dissimilarities instead of mean of permutation deltas.

Version 1.16-15 (closed Mar 25, 2009)

	* envfit help page: explains the automatic scaling and 'arrow.mul'
	argument. 

	* add1/drop1 help: better example after a query of usage in R
	mailing list. 

	* oecosimu & permatswap: much faster 'burnin' implemented through
	'thin', and hence using a single C loop instead of multiple calls
	and assignments to an R object.

	* as.mcmc.permat: provides same functionality for permat objects
	as as.mcmc.oecosimu for oecosimu objects.

	* permatswap: same default values of 'burnin' and 'thin'  (0 and 1,
	respectively) are set for permatswap and oecosimu functions.
	Previous defaults for permatswap were in conflict with oecosimu
	when called by permat.control.

	* hiersimu: new function to evaluate a statistic value at
	different levels of a nested hierarchical sampling design. Based
	on oecosimu and null model testing, but with evaluation process
	similar to adipart.

	* metaMDS: automatic stepacross works with Euclidean, Manhattan
	and other distances with no fixed upper limit.  However, this may
	be meaningless, and a warning is issued. Fixed after a query to
	R-sig-ecology by Manuel Spinola.
	
Version 1.16-14 (closed Mar 10, 2009)

	* as.mcmc.oecosimu: a new function to translate sequential null
	models to "mcmc" object of the coda package. The coda package
	provides a wealthy source of the analysis of things like
	stationarity, adequate sample size, autocorrelation, length of
	needed burnin-in etc.

	* density and densityplot: new methods for "oecosimu" objects.

	* as.ts.oecosimu: new function for applying time series methods
	for sequential null models ("swap", "tswap", "abuswap").

	* metaMDSrotate: a new function to rotate metaMDS configuration so
	that the first axis is parallel with a continuous site variable.
	
	* as.ts.permat: extracts summary statistics from 'permat' objects
	as time series, to use for time series diagnostics.

	* permatswap: two new methods (under "abuswap") added based on the
	paper of Hardy 2008 (J Ecol 96, 914-926). These preserve row *and*
	colunm occurrences, and row *or* column sums at the same
	time. Thus these complement the methods available in vegan. Uses C
	code (not thoroughly tested yet). Needs some more work, and
	documentation (examples and reference in Rd file).

Version 1.16-13 (closed Feb 24, 2009)

	* anova.cca: documented the 'cutoff' argument for by = "axis".

	* text.procrustes: added text() function for procrustes() result plots.

	* rad.null: failed with family = gaussian and Gamma.

	* simulate.rda: new method to simulate responses with random error
	for an rda() result object. The function uses Normal error, and
	estimates the sd separately for each species from their rda
	residuals. Normal error is justified by least squares fitting in
	rda. This could be made to use permutations of residuals. Not yet
	implemented for cca or capscale results. For cca we -- at least --
	need to handle weights, and the capscale result would be rda
	result, since the method cannot be directly implemented for
	dissimilarities. The function was triggered by Ben Bolker's email
	to R-devel mainling list
	https://stat.ethz.ch/pipermail/r-devel/2009-February/052116.html
	
Version 1.16-12 (closed Feb 15, 2009)

	* anova.ccabyaxis: gained keyword 'cutoff' (defaults 1) to break
	from permutation tests after exceeding the P-value given in the
	argument. The keyword was introduced because rda and cca are
	occasionally used with a huge number of constraints (like PCNM
	vectors) where tests take a very long time, although only a couple
	of first axes are significant. The keyword is still undocumented,
	and will remain so because this change is still experimental. 
	
	* contribdiv: new functions for contribution diversity as an
	alternative to simple additive diversity following Lu, Wagner &
	Chen, Basic and Applied Ecology 8, 1-12 (2007).
	
Version 1.16-11 (closed Feb 9, 2009)

	* anova.cca: used different random number sequence for the second
	term with by = "margin". 

	* ordirgl & orgltext: removed work arounds for very old versions
	(pre-0.65) of the rgl package.

Version 1.16-10 (closed Jan 28, 2009)

	* commsimulator: failed if input data (x) were a data.frame.

	* metaMDS: really do not evaluate no.shared() if set
	noshare=0. Triggered by a problem report with missing data. 

	* vegdist doc: Morisita and Horn-Morisita were given as
	similarities in the help.

	* ordirgl: fixed wrong warnings in ordirgl(..., type="t"). 

	* kendall.post, kendall.global: knows now all P value adjustment
	methods of 'p.adjust()' plus "sidak".
	
Version 1.16-9 (closed Jan 20, 2009)
	
	* kendall.post: added one line that was accidentally lost in
	editing. 

	* Checked with R version 2.9.0 Under development (unstable) 
	(2009-01-13 r47593) having experimental strict Rd parser, and
	corrected the reported problems in Rd files so that vegan is R
	2.9.0-ready. 

	* adonis: uses now canonical (hits+1)/(tries+1) for P-values
	instead of hits/tries. Default number of permutations increased
	from 5 to 999. Added terms component so that things like update()
	and drop.scope() magically started to work. Renamed design.matrix
	into model.matrix (and documented the item). 

	* permatswap: new algorithm "swsh" is added to keep row/column
	incidences (but not sums) constant. The name refers to the two
	steps: (1) binary *sw*aps are made then (2) individuals in
	non-zero cells are *sh*uffled.

	* permat methods: calculations of the Chi-squared statistic is
	added to summary, and the type argument can be used in the plot
	"bray" or "chisq" values.

	* nestednodf: gained argument 'order = TRUE' allowing tests for
	other orderings than using marginal frequencies (default)
	following suggestion by Almeida-Neto et al. (2008).

	* summary.cca:  cumulative "accounted for" statistics failed in
	unconstrained models.
	
Version 1.16-8 (closed Jan 7, 2009)

	* Fixed unescaped $-signs in documentation files after Ripley told
	to do so ("[Rd] Misuse of $<matn expressions>$ in Rd files",
	https://stat.ethz.ch/pipermail/r-devel/2008-December/051634.html) 

	* kendall.global & kendall.post: new functions to analyse the
	Kendall's coefficient of concordance  --- use in ecology: to
	identify significant species associations. See P. Legendre,
	J. Agric. Biol. Envir. Statistics 10, 226-245; 2005. Written by
	Guillaume Blanchet and Pierre Legendre.

	* nestedness: added nestedness index based on overlap and
	decreasing fill (Almeida-Neto et al., Oikos 117, 1227-1239; 2008).
	Not yet all properties of the Oikos paper are implemented, and the
	UI needs work (print, plot methods).  Coding by Gustavo Carvalho
	as a part of R-Forge Feature Request #265.  Documented with
	nestedtemp.
	
Version 1.16-7 (closed Dec 17, 2008)

	* permat*: functions were rationalised, strata argument is used
	instead of reg and hab, and returned object got several new
	arguments. The tide of changes affected methods as well, and some
	other function (adipart, oecosimu). Stratification was tested and
	corrected.
	
Version 1.16-6 (closed Dec 7, 2008)

	* adipart: got a formula interface, and aggregate() was replaced
	by matrix multiplication. Now it is 10 times faster.  The formula
	interface has some consequences on the specification of the
	sampling design.

	* permatfull: Jari Oksanen made the C port for the quantitative
	quasiswap algorithm. So the permat* null model family now can be
	used for a wide array of null model analyses and is quick enough
	to make reliable testing. The permatswap function and help page
	were modified accordingly.

	* plot.rad: gained argument log = "y", allowing log = "xy" so that
	Zipf model is a straight line, or log = "" with arithmetic
	scales.  Not (yet) implemented for Lattice alternatives.
	
Version 1.16-5 (closeed Dec 4, 2008)

	* adipart: new implementation of adipart is now ready to be
	released (needs some testing). Summary and plot methods have been
	removed. The new implementation is based on oecosimu and
	quantitative null model settings via permat.control.  It contains
	only traditional diversity indices. More features will be added
	later, gradually.

	* plot.nestedtemp: label argument accepts a vector of length 2
	with elements for row and column labels, respectively.

	* mite.rda: Oribatid mites got species names (from Pierre
	Legendre's web pages).

	* text.decorana: failed (bug introduced in rev344, on May 9,
	2008). 

	* commsimulator: simulated null models have same column and row
	names as the original input (as.)matrix. There was a problem
	report by a user who tried to use column names during evaluation
	of the statistic. Done by setting attributes (and it would be
	possible to replace dim() setting by attributes() setting in the
	code).    

	* 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)

	* 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.

	* plot.cca: takes care that plotted items have non-NULL names that
	plot neatly.  This was already take care of with formula
	interface, but now it should work also in other cases in
	plots. Reported by Daniel Borcard.
	
	* 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 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.

	* nesteddisc: replaced with a new function that orders tied
	columns to minimize the discrepancy statistic. If there are <=7
	tied columns, all upto 5040 permutations are inspected, and if
	there are >7 tied columns, 5000 random permutations are
	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 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.

	* betadisper: now works for cases where there is only a single 
	group. 'scores', 'plot' and 'boxplot' methods updated to work in
	such cases. 'anova' and 'permutest' methods stop with an error if
	used for such cases as they implement tests that do not make sense
	for a single group.

Version 1.16-3 (closed November 1, 2008)

	* spantree: saves labels of points, and 'cophenetic' and 'plot'
	use these labels. Function 'plot' uses 'ordilabel' for text
	labels.

	* orditkplot: added option to copy the current graph to a TIFF
	file. The capabilities("tiff") check was added in R-2.8.0, but the
	test works in R < 2.8.0 as well.

	* nesteddisc: Carsten Dormann (UFZ, Leipzig, Germany) turned my
	attention to the sensitivity of discrepancy to ties in column
	frequencies. These are not handled by any way (yet), but the users
	are warned now about ties. For instance, the example matrix 'A' on
	page 259 of Brualdi & Sanderson (Oecologia 119, 256-264; 1999) can
	be ordered to give discrepancy value = 2 instead of value = 3
	reported in the paper with a different ordering of columns.
	Different random reorderings of species in the 'sipoo' data in
	vegan can give discrepancy values 51 to 58 (and the original
	arbitrary ordering gives 55). This means that discrepancy values
	are not very reliable, but ties should be handled better or the
	function withdrawn from vegan. 

	* ordisurf: returns x, y and z used by contour() following a query
	"[R-sig-eco] output from ordisurf" on Oct 23, 2008.
	
Version 1.16-2 (closed October 27, 2008) --- for Annukka

	* beals: replaced old beals.R with the new code by Miquel de
	Caceres with new methods described in De Caceres & Legendre
	(Oecologia 156, 657-669; 2008). This also implements the
	cross-validatory Beals of Munzbergova & Herben (Oikos 104,
	408-414; 2004) plus many new options of unbiasing estimates. 

	* permatfull: bug of row/col margins is fixed, shuffle argument is
	added to enable individual and sample based randomisation of count
	data (or both) when not all the margins are fixed.

	* anosim: API and documentation made similar to mrpp to combine
	their documentation. Now anosim can take data frame input and find
	the dissimilarities internally.
	
Version 1.16-1 (closed October 10, 2008)

	* dispindmorisita: function to calculate Morisita's index of
	dispersion, and its standardized version. Uses the correct way of
	standardizing, see Note section in help.

	* radfit: Should work with empty sites (no species) or when the
	number of species is less or equal the number of parameters
	estimated (like may happen in sweeping analysis of data frames or
	simulations). Takes care that input data frames have row names
	which are necessary for displaying results.
	
	* head.summary.cca & tail.summary.cca: shortcuts to
	print(summary(x, ...), head, tail) for nicer Sweave tutorials.
	
Version 1.16-0 (closed on September 30, 2008)

	* New devel version after branching the release version
	1.15-0. Identical to the release version, but includes MOStest and
	adipart functions that were removed from 1.15-0.
	
Version 1.14-12 (closed September 26, 2008)

	* add1.cca, drop1.cca: new functions that also implement
	permutation tests with argument test = "permutation", but only use
	default methods with test = "none". Function drop1.cca uses
	anova.cca(..., by = "margin"), and add1.cca implements a new type of
	analysis for single term additions. The immediate reason for
	implementing these tests was that I found out that step(..., test
	= "Chisq") worked(!) producing parametric likelihood ratio tests,
	and this hole had to be closed before users notice this.

	* anova.cca: improved treatment of models where constrained or
	unconstrained models are NULL so that permutation tests are
	impossible. These used to stop with error, but now they return a
	zeroed result so that things like anova(..., by = "term") and
	drop1() work. Added function anova.ccanull to handle these cases.

	* anova.cca(..., by = "margin") was handling wrongly 'x' in ~
	Condition(x) + x + z, or model formulae where same variables were
	used both as Conditions and (aliased) constraints. 

	* anova.cca(..., by = "margin") or function anova.ccabymargin
	gained a 'scope' argument which is used in drop.scope(). 

	* orditkplot & ordipointlabel: improved interface allows passing
	font type from ordipointlabel to orditkplot. 

	* copied to version 1.15-0 at rev506.
	
Version 1.14-11 (closed September 10, 2008)

	* anova.cca/permutest.cca: default permutation model changed from
	"direct" to "reduced" after Pierre Legendre's simulation test
	demonstrated slightly better Type I error for "reduced" models in
	by = "axis" and other partial models. This is also consistent with
	CANOCO (but permutation of CCA residuals differs from CANOCO). For
	compatibility with old versions of vegan, you must set model =
	"direct" explicitly.

	* ordiplot: did not use partial match for "sites" and "species".
	
Version 1.14-10 (closed September 5, 2008)

	* treedive: tries to match 'comm' and 'tree' names if forced (by
	an arg), or when sizes do not match. Output vector has names. Docs
	discuss estimating signifcance using oecosimu().

	* oecosimu: accepts now a vector of statistics and plain
	statistics instead of the list item statistics, and the user can
	define the name of the statistic in the function call. This means
	that things like functional diversity (treedive) for sites can be
	analysed with approprite simulation model.

	* nestedtemp & oecosimu documentations split. 
	
	* ordiParseFormula: formula of the partial terms has the same
	environment as the general formula. Cures some tricky issues when
	the partial term of cca/rda/capscale model is updated within a
	function. (The environment() drives me crazy, says J.O.)

	* ordiParseFormula gains new argument 'envdepth' to define the
	depth where the community data (dependent data) is evaluated. Most
	functions evaluate community data in the parent environment of the
	calling function, but capscale() creates new dependent data and
	needs evaluate the community within calling function. (The
	environment() drives me absolutely crazy, says J.O.)

	* specaccum: empty (all zeros) species removed from input
	data. These confused method = "exact" which gave sd = NA.

	* permutest.cca: tells whether the test was for all eigenvalues or
	for the first (this is implicit in anova.cca).

	* vegan-internal.Rd: brief documentation of internal functions for
	developers with some guidelines of good practices.
	
Version 1.14-9 (closed August 20, 2008)

	* closed concurrently with the release of vegan 1.13-2: changes up
	to this version may have been there.

	* adipart: new function to perform additive diversity partitioning
	with corresponding S3 methods.

	* tsallis: new function to calculate Tsallis-entropy, a scalable
	diversity index family

	* treedive: new functions for estimating functional diversity
	defined as the height of a dendrogram of species properties for a
	site (Petchey & Gaston). Still very preliminary.

	* plot.procrustes: could fail if two solutions were *exactly*
	*exactly* identical (noticed by Peter Solymos with wcmdscale
	example). 
	
Version 1.14-8 (closed August 10, 2008)

	* wcmdscale: new function to perform metric scaling
	(a.k.a. principal coordinates analysis) with weights for points.

	* ordiArgAbsorber: now knows about 'choices' and 'display' args
	of scores(). Reported by Michael Denslow.

	* orditkplot: plotting text labels was broken in the default case.
	Zooming works again. Plotting character (pch) is now better
	centred on the canvas, and the code was simplified.
	
Version 1.14-7 (closed July 30, 2008)

	* orditkplot: imitates now plotting character (argument
	pch). Zooming maintains graphical parameters (such as mar). Label
	selection shown by a rectangle, since label may already be
	red. Label family, size and font can be vectors.
	
	* permat.R, swapcount.R: summary method was modified according to
	standard R ways, ylab argument was deleted from plot method.  The
	R version of swapcount was deleted and replaced by the C
	version. Help file was modified accordingly.

	* ordilabel: new function for cluttered ordination plots -- text
	is written on a non-transparent label. Similar to s.label()
	function in ade4.

	* ordipointlabel: new function for cluttered ordination plots --
	points are in fixed positions, but their text label is located to
	avoid overlap. The optimization is based on optim(..., method =
	"SANN"). Similar to pointLabel function in maptools. Returns an
	"orditkplot" object, but orditkplot cannot yet completely handle
	this (and this feature is undocumented).

	* permutations: permuted.index2 and associated functions now allow
	for restricted permutations of strata (i.e. restricted shuffling
	of the blocks). This changes the acceptable 'type' options and adds
	a new argument 'permute.strata' to permControl(), to control how
	and what is permuted.

Version 1.14-6 (closed July 5, 2008)

	* permatswap (nestedness.c): translated Peter Solymos's
	swapcount.R to C. This is still experimental code, and the user
	interface is undocumented, except here: use method = "Cswap" in
	permatswap.

	* permatswap: was not updating swap matrix but using the same
	starting matrix after burnin for every swap.
	
	* swapcount.R:  was advancing 'thin' counter even when a swap was
	rejected so that fewer than requesed 'thins' were done.

	* permat.R, swapcount.R: genereal cleanup, most importantly
	replacing vector operators & and | with logical operators && and
	||. 

	* commsimulator: "quasiswap" written in C and *much* faster
	now. Times are for MacBook Intel 1.86 GHz and 100 matrices:
	"sipoo" from 7 min to 4 sec, "BCI" from 2+ hrs to 45
	sec. Actually, quasiswap is now much faster than ordinary swap
	which also should be written in C. "Backtracking" is so much more
	complicated code that it could probably never reach "quasiswap"
	even if written in C, and it may be dropped in the future. 

	* commsimulator: "swap" and "tswap" written in C, and clearly
	faster now. In MacBook, 100 swaps with "sipoo" went from 8 sec to
	0.5 sec, and thinning hardly influenced timing (it used to
	thin-fold times).

	* oecosimu: takes care that original statistic is found from
	binary data.
	
Version 1.14-5 (closed June 19, 2008)

	* scores.rda: scaling = 0 returns now unmodified scores from the
	object (like documented) without multiplying by the scaling
	constant. Gains argument 'const' for user-settable general scaling
	constant of the scores. The default 'const' is found internally to
	giv a biplot scaling so that species and site scores together
	approximate the original data. The value of 'const' is returned as
	an attribute of 'scores'.

	* summary.cca: prints the value of general scaling constant used
	in 'rda' or 'capscale'.

	* summary.cca: prints 'capscale' like 'rda' (used to have some
	'cca' style output, like calling site scores "weighted averages"
	instead of "weigthed sums").

	* permutest.cca: estimates now residual df as number-of-rows -
	rank-of-constraints-and-conditions - 1 so that df and pseudo-F are
	equal to those reported by lm() for single response variables in
	rda. anova(..., by = "ax") needs rethinking though: it only had
	one df.  Because the test was based on permutation and order
	statistics the change of df does not change the significances:
	the observed pseudo-F and permuted pseudo-F's are influenced
	similarly by the change of df, and order statistic does not
	change. 

	* varpart: long formulae were cut off in printoutwith a cryptic
	warning. 
	
Version 1.14-4 (closed June 12, 2008)

        * permatfull, permatswap and swapcount: functions to generate 
        unrestricted and restricted null model community data matrices
        under diferent constraints (preserving row/columnsums, 
        or incidence pattern), with print, plot and summary methods.
        (submitted by PS)

	* adonis: speed-up and doc updates.
        
Version 1.14-3 (closed June 9, 2008)

        * rda.default, cca.default: vegan naively used only the rank of
        the ordination, but indeed, there are three cases of ranks: rank
        of the ordination or number of axes (returned as rank like
        before), rank of the constraints after conditions (now returned as
        qrank), rank of conditions + constraints (returned in QR$rank).
        When only 'rank' was used, vegan for instance aliased terms beyond
        rank of ordination axes, extractAIC did not get df right when
        going beyond rank of ordination, anova(..., by="t") gave zero df
        for constraints beyond rank of ordination, and calibrate.cca
        ignored those extra variables (now stops). In addition predict.cca
        and predict.rda(..., type="lc", newdata=somedata) gave wrong
        results in partial model.  The following changes were made if
        necessary to cca/rda support functions:

	* alias.cca: QR$rank
	* anova.ccabyaxis: OK 
	* bstick.cca: OK 
	* calibrate.cca: stop with error if qrank > rank
	* extractAIC: qrank
	* mso: OK (HW confirms)
	* msoplot: OK (HW cofirms)
	* permutest.cca: qrank, also fixes anova.ccabyterm
	* predict.cca/rda: QR$rank with type = "lc" & newdata
	* summary.cca/rda: OK
	* scores.cca/rda: OK
	
Version 1.14-2 (closed June 5, 2008)

	* Helene Wagner joined the vegan team.

	* mso: automatically collapses distance classes larger than half
	the maximum distance into a single distance class.

	* mso: plot.mso renamed to msoplot so that plot.cca also works,
	and the example uses now Oribatid mite data set. 

	* mso: gained a print method that also shows the variogram
	(Helene, please check this!), and mso knows about its own call. 

	* lines.spantree: did not pass graphical arguments to lines
	(broken in 1.12-15).

	* ade2vegancca: a new function which tries to change an ade4:::cca
	object to vegan:::cca object (and manages partially). This is used
	internally in print.cca, scores.cca and summary.cca so that vegan
	can display some information from ade4:::cca (with a warning).
	Since scores.cca works for ade4, so do plot, orditkplot etc which
	rely on scores.
	
Version 1.14-1 (closed May 29, 2008)

	* plot.mso: passes extra arguments (...) to graphical functions.

	* mite.xy: new data set with spatial coordinates for the Oribatid
	mite data. From Pierre Legendre's web page.

	* weights failed in several ordination utilities, because
	weights.default in R 2.7.0 (stats) could not cope with objects
	that do not have weights. R 2.6.2 still returned NULL for those
	objects, but now weights.default gives an error. As a workaround
	several vegan functions define internally 
	       weights.default <- function(object, ...) NULL 
	to get back the old behaviour. Concerns orglspider, ordicluster,
	ordispider, ordiellipse, ordisurf, factorfit, vectorfit.

	* inertcomp and intersetcor only work with objects inheriting from
	"cca", but they did not check that the object was of the correct
	type and so could end up with calling weights.default or give
	obscure error messages.

	* permutest.betadisper: Could give the wrong pair-wise permutation
	p-values. Reported by Daniel O'Shea.
	
Version 1.14-0 (closed May 21, 2008)

	* The base of the release version 1.13-0.

Version 1.12-15 (closed May 14, 2008)

	* closed the revision and made it as the base of release branch
	1.13-0 at rev353.

	* capscale: prints info on possible metaMDS transformations, and
	uses metaMDSdist transformed data for getting species scores
	(similarly as metaMDS recently does).

	* ordiTerminfo: does not give superfluous warnings if constrained
	ordination called without constraints and without data=, like
	capscale(x ~ 1).

	* graphical functions: Graphical functions that also pass '...' to
	non-graphical functions (such as scores) now accept non-graphical
	arguments without issuing an warning. These warnings were harmless
	but it is neater to stop them happening in the first place. This
	is facilitated by the new internal function ordiArgAbsorber().

	* MOStest: added fieller.MOStest for approximate confidence
	intervals of the location of the hump or pit. The method is based
	on Fieller's theorem following ter Braak & Looman (Vegatatio 65,
	3-11; 1986) and profile based condifence limits following Oksanen
	et al. (Ecology 82, 1191-1197; 2001).  Both are based on the code
	from the ESA Ecological Archives accompanying Oksanen et
	al. (Ecology 82, 1191-1197; 2001) and published in package optgrad
	(http://www.esapubs.org/archive/ecol/E082/015/default.htm), but
	profile methods heavily borrow from the MASS package.

Version 1.12-14 (closed May 9, 2008)

	* mso: added Helene Wagner's mso function for direct multi-scale
	ordination or spatial partioning of 'cca' and 'rda'
	results (Ecology 85, 342-351; 2004). Thanks to Helene Wagner for
	allowing the inclusion of the code.

	* MOStest: new function to implement Mitchell-Olds & Shaw test for
	the location of quadratic extreme in a defined interval.

	* capscale: accepts now other dissimilarity function than vegdist,
	and optionally uses metaMDSdist to manipulate dissimilarities
	similarly as metaMDS. This provides now a one-shot unconstrained
	principal coordinates analysis ("metaPCoA"), optionally with
	extended (flexible shortest path) dissimilarities. Incidentally
	this also implements a "new" possibly unpublished ordination
	method: extended distance based redundancy analysis.

	* metaMDSdist: argument 'add' gained new alternative "ignore" to
	do nothing with zero distances. This can only and should be used
	with metric scaling (cmdscale(), capscale()). 

	* ordispantree: removed after being deprecated and defunct for a
	long time. Use lines.spantree instead.
	
Version 1.12-13 (closed May 7, 2008)

	* orditkplot: labels can be edited with double clicking, and
	shift-mouse allows zooming into smaller are in the plot.
	
Version 1.12-12 (closed May 1, 2008)

	* adonis: added calculation of coefficients both for the species
	(when data matrix was given) and for sites (both with the data
	matrices and dissimilarities).

	* betadisper: was not calculating distance to centroid correctly
	for observations where the imaginary distance to centroid was
	greater than the real distance (resulting in negative distance) 
	which resulted in NaN when we took the square root. betadisper() 
	now takes the absolute value of the combined distance before taking
	the square root. This is in-line with Marti Anderson's PERMDISP2.

Version 1.12-11 (closed April 23, 2008)

	* adonis: permutation tests fixed. The permutation statistics were
	wrongly calculated. The results will now be different than in
	older version, including the example(adonis). Basically, the
	reported statitistic used SS improvement compared to the residual
	of the complete model, but permutations used SS accumulation
	compared to the residual after the current model.

	* specaccum: returns item "individuals" or the average number of
	accumulated individuals with method = "rarefaction". A user
	request. 

	* rarefy: accepts now a vector of sample sizes, and then returns a
	matrix with a column for each sample size. If also 'se = TRUE',
	returns two rows for each case, one for rarefied richness, and
	after than one for its standard error. This was a recurrent user
	request. 

	* zzz: vegan got package startup message.
	
Version 1.12-10 (closed April 19, 2008)

	* adonis: the fix for the unused factor levels (r312) revealed
	that adonis did not handle properly aliased variables and
	pivoting. Results need checking.

	* designdist: gained argument 'abcd = FALSE' to use the 2x2
	contingency table notation instead of the more tangible default
	notation. 
	
Version 1.12-9 (closed April 13, 2008)

	* ordiArrowMul: added function 'ordiArrowMul' to improve automatic
	scaling of biplot arrows (in plot.cca, text.cca, points.cca) and
	fitted vectors (in plot.envfit). Reversed axes 'xlim=c(1,-1)' work
	now, and shifted origin 'at = c(1,1)' taken into account in
	plot.envfit. 

	* plot.cca: scaling used for biplot arrows is returned as an
	attribute to the 'biplot' item in the 'ordiplot' object (but this
	attribute is not used for anything useful yet).

	* summary.cca: contributions of eigenvalues accumulated for
	constrained and unconstrained axes, and separately (new) for
	constrained axes. 

	* allPerms: Now accepts a vector from which number of observations 
	can be deduced. This was the intended behaviour but allPerms failed
	in such cases.

	* adonis: Was not dropping empty levels of factors, which was
	leading to incorrect results (d.f. was inflated).  Reported by
	Tyler Smith.
	
Version 1.12-8 (closed April 6, 2008)

	* permute: New high-level untility function for facilitating
	the production of permutation tests using the new permutation
	designs allowed by permuted.index2(). An example of the new
	API is shown in ?permute.

	* permutest.betadisper: Pairwise t test function made more
	computationally stable.
	
Version 1.12-7 (closed Mar 30, 2008)

	* permuplot: New function, produces a graphical representation
	of a permutation design given a number of observations and a
	object returned by permControl(). The function handles all the
	permutation designs currently handled by permuted.index2().

	* permuted.index2: was not returning correct sample indices
	for grid designs within strata. Also, was not consitently 
	mirroring series and grid designs when 'constant = TRUE' (i.e. 
	mirroring was not applied the same way within each level of 
	strata).

	* permCheck: Now includes several sanity checks for balance
	in permutation designs ('grid' & 'strata') and when using
	same permutation in each level of 'strata' (constant = TRUE).
	Also works if object is a (numeric or integer) vector of length 
	1, by expanding it to seq(from = 1, to = object). This is now
	in-line with the way numPerms works.

	New argument 'make.all' in permCheck() allows greater control
	over the checking process. Allows user to check a permutation
	design without generating the matrix of all possible permutations.
	Used in allPerms() to allow that function to check permutation 
	designs without getting stuck in infinite recursion, as permCheck()
	calls allPerms() if complete = TRUE. This change allows allPerms()
	to be called by a user without having to make sure the supplied
	design makes sense - the design is checked using 
	'make.all = FALSE'.

	* screeplot: functions return now invisibly the xy.coords of
	bars or points for eigenvalues. They used to return
	invisibly the input data ('x'). Concerns screeplot methods for
	'decorana', 'cca', 'princomp' and 'prcomp' objects in vegan.
	
	* varpart4: result could be wrong if 'varpart' was bypassed and
	'varpart4' was called directly, because 'Y' was not centred before
	calculating sum of squares in 'varpart4' ('varpart2' and
	'varpart3' were OK). Reported by Guillaume Blanchet, Uni Alberta.
	
	* permutest: Now a generic function. permutest.cca is now the
	'cca' method.

	* permDisper: This function has been renamed to permutest.betadisper
	and documentation updated.

	* TukeyHSD.betadisper: Function is now documented with betadisper.
	
Version 1.12-6 (closed Mar 25, 2008)

	* metaMDS: WA scores for species are now based on the same
	transformations and standardization (like wisconsin(sqrt())) as
	the dissimilarities. They used to be based on the original data
	even when the data were transformed for the ordination. The change
	is minimal: data are evaluated similarly as in metaMDSdist if
	wascores are requested. An alternative would have been to split
	data manipulation function into an independent function from
	metaMDSdist, but I try this first. For compatibility reasons, the
	previous behaviour can be re-established using argument old.wa =
	TRUE.

	* allPerms: Now allows unbalanced designs for "series" or "free"
	permutations within levels of strata only (i.e. allows different
	number of observations per level of strata). Unbalanced "grid" 
	designs are not supported (and are unlikely to be so in the near
	future). permuted.index2 has allowed these cases from the
	beginning.

	* allPerms, numPerms: Corrected for situations where type = "series",
	mirror = TRUE with only 2 observations. In this case, mirroring
	does not double the number of permutations.
	
Version 1.12-5 (closed Mar 24, 2008)

	* plot.procrustes: could fail if compared configurations were
	numerically identical.

	* allPerms: New function to enumerate all possible permutations
	for a given permutation scheme and number of samples. Has 'print'
	and 'summary' methods.

	* numPerms: Now accepts a numeric or integer vector of length 1
	as the first argument 'object'. If supplied it is expanded to
	seq(from = 1, to = object). This change allows you to state the
	number of observations rather than pass an object from which the 
	number of observations is deduced. Updated and clarified 
	documentation in this regard.
	
Version 1.12-4 (closed Mar 20, 2008)
	
	* permDisper: Added pairwise comparisons of group dispersions 
	via a classical t test and via permutation test, accessed via
	new argument 'pairwise = TRUE'. 'permDisper' is now documented
	seperately from 'betadisper'.

	* TukeyHSD.betadisper: A method for 'TukeyHSD' to calculate
	Tukey's Honest Significant Differences for the grouping factor
	in 'betadisper'.

	* numPerms: Was incorrectly calculating the number of permutations
	when permuting levels of strata was performed. numPerms was also
	incorrectly reporting too many permutations in the particular
	case of type="grid" and mirror=TRUE with ncol=2.

	* permuted.index2: When permuting levels of 'strata'
	(type = "strata"), permuted.index2 was shuffling both the levels 
	of strata *and* shuffling the samples within levels. The latter 
	was incorrect and is now fixed.
	
Version 1.12-3 (closed Mar 9, 2008)

	* betadiver: a new function that implements all indices of beta
	diversity reviewed by Koleff et al. (J. Anim. Ecol., 72, 367-382;
	2003), with a plot function to produce triangular plots.
	
	* isomap: added dynamic, spinnable 3D graphics using rgl
	(rgl.isomap). 
	
Version 1.12-2 (closed Mar 7, 2008)

	* nestedtemp: Rodriguez-Girones & Santamaria (J. Biogeogr. 33,
	924-935; 2006) have had a look inside the original temperature
	calculator code and give a more explicit description of the
	method. Following their paper, I implemented an iterative
	procedure to alternately pack columns and rows for ones and
	zeros. The fill line is still a parabola, but this seems to be
	very similar to the R-G & S fill line with fills 0.2...0.8 and I
	don't hurry with this. There still are differences in many aspects
	of implementation. The iterative procedure gives slightly
	different results between runs, but here tests: Rocky mountain
	mammals 3.87 (A&P 3.81, was 3.59 in 1.12-1), Baja
	birds (Bajabs.txt) 10.17 (A&P 7.25, was 7.75), Queen Charlotte
	birds 14.78 (A&P 15.87, was 14.51). Some results are indeed more
	different than they used to be...

	* nestedtemp (2): After previous entry implemented the fill line
	of Rodriguez-Girones & Santamaria. This means almost complete
	rewrite of the function from 1.12-1. New test results: mammals
	4.48, Baja birds 10.16, Queen Charlotte birds 15.85. Baja is the
	most different. Atmar & Patterson have five Baja bird data sets
	with these test results: Bajaball 6.33, Bajabl 14.43, Bajabn
	5.98, Bajabo 11.18, Bajabs 10.13. Smaller change is that packing
	is based on indices s and t directly instead of their ranks.

	* vignettes: added discussion on nestedtemp and backtracking in
	"Design decisions and implementation".
	
Version 1.12-1 (closed Mar 2, 2008)

	* biplot.rda: gained argument col to select colours for sites and
	species. 

	* bstick.princomp: used a wrong number of sticks (PCs). Reported
	by Guy Yollin. 
	
	* nestedtemp:  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)

	* Made a release branch (1.11-0) based on the the rev. 204, and
	relabelled this devel branch to 1.12-0.

Version 1.10-13 (closed Feb 15, 2008)

	* preparing for a release and trying to close open threads.

	* nestedtemp: implemented smooth fill line. The kind of the fill
	line was not specified in the original paper, but I used parabola
	which is "as smooth as possible" in the sense that its second
	derivative is constant. Needs checking, though.

Version 1.10-12 (closed Feb 12, 2008)

	* nestedtemp: new try with smooth fill line.

	* anova.cca: by = "margin" stops with informative error message if
	some terms are completely aliased (used to stop with an
	uninformative error message). Type III effects really do not make
	sense with aliased variables.
	
	* calibrate.cca: does correct pivoting of aliased models.

	* orditkplot: Set up all basic features, and added points, text,
	and scores methods. Features that should be added include zooming
	to a rectangle drawn with a mouse, and adding env variables. The
	latter would be trivial in a simple way, but the user should be
	able to move the bunch of arrows to another place, and scale the
	length of arrows with a mouse.
	
Version 1.10-11 (closed Feb 3, 2008)

	* bgdispersal: New, more powerful test statistic (in terms of Type
	1 error rate) for the McNemar test (Pierre Legendre).

	* CCorA: internal functions embedded in CCorA().

	* orditkplot: More resilient against user errors. New output file
	types (bmp, xfig), jpeg uses 100% quality. more aware of operating
	system and capabilities. Accepts graphical par in the function
	call. Gains arguments xlim, ylim. Arguments col, bg, cex renamed
	to pcol, pb, pcex so that the do not shadow par().
	
	* permuted.index2: fixed a bug in permutations with strata.

	* summary.prc: honours now argument 'axis'. Reported by Francois
	Gillet, Lausanne.

	* Documentation: added documentation for permuted.index2,
	permControl, permCheck and helper functions. FAQ and intro know
	now about orditkplot, anova.cca(..., by="margin") and
	permuted.index2. FAQ gained new sections on using different
	plotting symbols and handling congested plots in ordination
	graphics.

Version 1.10-10 (closed Jan 27, 2008)

	* DESCRIPTION: suggests tcltk.

	* orditkplot: new function for ordination plots based on Tcl/Tk:
	you can edit graph by moving labels using a mouse and save the
	edited graph as an eps file, or export via R plot function to
	eps, pdf, png or jpeg, or to dump to R session for further
	processing. 

	* CCorA: removed partial analysis (which needs more work and may
	reappear later).
	
Version 1.10-9 (closed Jan 16, 2008)

	* anova.cca: new option by = "margin" to perform separate tests
	for each marginal effect in a model with all other terms. This is
	similar to Type III tests, but will only work with marginal terms,
	and will exclude main effects when corresponding interactions are
	in the model.  P-value is now assessed in the true blue way as
	(hits+1)/(permutations+1) in all anova.cca methods. Permutations
	should be able to handle now rank deficit cases with pivoting in
	the QR decomposition (permutest.cca).
	
	* 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(). Plan to migrate vegan functions to 
	permuted.index2() in the devel version, and will eventually replace
	the current permuted.index().

	* permCheck: New function for checking permutation schemes under
	permuted.index2. Uses new function numPerms() to generate the 
	number of possible permutations. permCheck() has print, summary
	and print.summary methods.
	
Version 1.10-8 (closed Dec 14 2007, at Rev. 133)

	* metaMDS: gains argument wascores (defaults TRUE) to suppress
	calculation of species scores.

	* wascores: return now NA for missing (all zero) species instead
	of failing.

	* ordiplot: ignore missing scores in plotting and printing.

	* betadisper: new functions for Marti Anderson's analysis of
	homogeneity of multivariate dispersions.

	* nestedtemp: handles now tied frequencies using ties.method =
	"average" in rank(). Function is still preliminary, and may be
	dropped from the release.
	
	* taxa2dist: issues now a warning if called with 'check = FALSE'
	and there are zero distances, typically meaning that basal taxa
	(species) were not coded. Also explained in the help.

	* varpart: failed if there were unused levels in factors (reported
	by Clément Tisseuil, Toulouse). 

	* adonis: loses argument 'distfun'. Instead accepts now any 'dist'
	object as input instead of a data frame or a matrix.
	
Version 1.10-7 (closed Nov 18, 2007 at Rev. 119)

	* adonis: gains argument 'distfun' (default 'vegdist') so that
	other standard conforming dissimilarity functions than vegdist can
	be used (a user request).
	
	* decorana: does not crash R when called with NULL row data such
	as decorana(dune[FALSE,]) (reported by Richard Tellford, Bergen,
	Norway), and predict(..., type="sites") works correctly with
	downweighted analysis (reported by Colin Beale, Aberdeen,
	Scotland).

	* isomap: checks now that input data are dissimilarities or can be
	changed into dissimilarities without warnings.

	* ordixyplot: can now display biplot arrows and factor centroids
	in constrained ordination or from envfit (ordisplom and ordicloud
	cannot display these).
	
	* ordixyplot, ordicloud and ordisplom: no longer have explicit scaling
	argument, but can now pass arguments to scores() as well as to the
	plotting functions.

	* oecosimu: evaluates now two-sided P-value of the statistic from
	simulations. Doc updates.

	* vignettes: use all similar style (amsart, a4paper, sidecap,
	date style).

	* FAQ: tell about docs added to R-Forge versions of vegan. Tell
	about predict() for having "passive" points.
	
Version 1.10-6 (closed Oct 31, 2007 at Rev. 100)

	* Gavin Simpson joined the vegan team.

	* oecosimu: new functions for indices of nestedness of patches or
	islands, and simulation of null communities.
	
	* scores: cca method does now accept display = c("species", "sites").
	Previous fix (1.10-5) was for rda method only. Documentation updated
	to reflect changes.
	
	* biplot.rda: now allows a different type to be specified for each of
	the species and site scores. Function now documented more completely.
	
	* ordixyplot, ordicloud and ordisplom: now have argument 'scaling'.
	
	* orditorp: now handles additional arguments passed as '...' more 
	cleanly. Arguments can be passed to scores() or points/text. This
	should avoid the warning messages of previous versions.

	* sipoo: a new data set on the bird communities in the Sipoo
	(Sibbo) archipelago to demonstrate the oecosimu functions.

Version 1.10-5 (closed Oct 18, 2007 at Rev. 86)

	* biplot.rda: new biplot function for PCA in rda() (Gavin
	Simpson). 

	* scores: cca method accepts now display = c("species", "sites"),
	when it only used to accept c("sp","wa"). More consistent
	arguments in the default method.  
	
	* CCorA: Pierre Legendre submitted code for permutation test of
	Pillai's trace.

	* capscale: negative scaling works now in plot() and scores():
	estimates species  sd() from the 'comm' if 'comm' is known.

Version 1.10-4 (closed Oct 6, 2007 at Rev. 75)

	* anova.cca: failed in anova(object, by = "axis") when the fitted
	model had terms like poly(x, 2) or log(x).

	* ordiresids: new function for plot.lm like diagnostic plots for
	constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals)) ~
	Fitted, and qqmath(~ Residuals) using Lattice graphics.
       
	* fitted.cca, fitted.rda: gained agument type = "working" to get
	the fitted values and residuals used internally in calculation (to
	be used in plot.lm diagnostic plots residuals ~ fitted).
 	
Version 1.10-3 (closed Oct 2, 2007 at Rev. 62)

	* doc: added vignettes intro-vegan on ordination methods and
	diversity-vegan.

	* Trellis graphics for ordination objects with functions
	ordixyplot, ordicloud and ordisplom. These functions are still
	unsatisfactory. In particular, I haven't found a clean way of
	having biplot arrows in the graphs (how do you know the
	coordinates and the axes used?). Contributions are welcome.

	* ordispantree made dysfunctional (deprecated in 1.8-1). 
	
Version 1.10-2 (closed Sep 14, 2007 at Rev. 36)

	* vegandocs: added FAQ-vegan, and renamed the old vegan-FAQ to
	decision-vegan. Only primary sources (texi, Rnw) in the source
	repository: derived files (.tex, .pdf) should be made when package
	is built.
	
	* CCorA: Pierre Legendre's functions for Canonical Correlation
	Analysis. These provide a more robust alternative to the standard
	cancor() in base R. (under work)
		
	* scores.default: handles numeric data frames.
	
Version 1.10-1 (closed Sep 7, 2007 at Rev. 21)

	* taxondive: Fixed dimension checking, matching names and
	non-unique taxon names.
	
Version 1.10-0 (Sep 6, 2007)

	* Moved vegan_1.8-7 (CRAN release) into R-Forge.R-Project.org and
	Subversion SCM. This ChangeLog will only contain most important
	news (and should be renamed to NEWS), and the real ChangeLogs are
	created by the SCM.  The revisions will be numbered as 1.10-1 to
	1.10-x, and the next release will be 1.11-0.

VEGAN RELEASE VERSIONS at http://cran.r-project.org/

Version 1.8-8 (Oct 2, 2007)

	* Minor bugfix release for upcoming R-2.6.0. Based on the
	http://r-forge.r-project.org/projects/vegan/ revision 17 (= 1.8-7)
	with ported bug fix revisions from 1.10-3 (see below for revision
	numbers).
	
	* anova.cca: by = "term" failed in partial model. This was broken
	in 1.8-6 by introducing a test against deficit rank models (r47). 
	
	* cascadeKM: Calinski index works now when the input data is a
	data.frame (r57, 58).

	* flush.console: metaMDSiter and bioenv use now flush.console()
	so that Windows people also see the trace (r56).

	* ordispantree: made defunct, was deprecated in 1.8-1 (r38). 

	* scores: handles now numeric data frames (r25).

	* summary.cca: failed if only one type of scores was requested
	(r50, 52).

	* taxondive: Fixed dim checking and matching species names in
	community data and taxonomic distance data (r21).

	* tweaks to pass --pedantic R CMD check, mainly in formatting
	source files, unused variables in source files and superfluous
	braces in help files (r39, r46, r62).

	* Updated FAQ-vegan.pdf to the current version at R-Forge.
	
Version 1.8-7 (August 24, 2007)

	* Based on devel version 1.9-34.

	* DESCRIPTION: M. Henry H. Stevens (Miami University, Oxford,
	Ohio) joined the vegan team.
	
	* adonis: new function for nonparametric MANOVA that is
	appropriate for even extremely wide matrices sometimes associated
	with gene data and with diverse ecological communities. Author
	Hank Stevens.

	* taxondive: a new function for indices of taxonomic diversity and
	distinctness after Clarke & Warwick (Mar Ecol Prog Ser 216,
	265--278, 2001 and other papers). With a helper function
	'taxa2dist' to turn taxonomies into distances with an option for
	variable step length (Clarke & Warwick, Mar Ecol Prog Ser 184,
	21--29, 1999), and a toy data set on the taxonomy of dune meadow
	species ('dune.taxon'). With a help, testing and pressure from
	Mike Cappo, James Cook Uni, Qld.

	* bgdispersal: previous version was partly garbled (by me), and
	P. Legendre provided a corrected one.

	* designdist: keeps 'dist' attributes even when the 'method'
	function drops them. Swapped the order to (terms, methods) in the
	default name. 

	* metaMDS: issues a warning if data are disconnected. Passes extra
	arguments to other 'distfun' than 'vegdist' so that you can set
	'terms' in 'designdist' etc (metaMDSdist). Can now do trymax=0 or
	skip random starts and give you enhanced 'isoMDS' result
	(metaMDSiter).

	* ordiplot: failed if number of species was equal to number of
	sites (and so did plot.metaMDS and plot.isomap using this).

	* plot.profile.fisherfit: corrected a harmless error detected by
	checkUsagePackage().

	* predict.rda: removed some dead (but heavy) code from type =
        "response".

Version 1.8-6 (May 9, 2007)

	* Based on devel version 1.9-23.

	* as.mlm.cca, as.mlm.rda: new functions to refit constrained
	ordination result (cca, rda, capscale) as a multiple response
	linear model. You can find influence statistics (Cook's distance,
	hat values) from the refitted model. You also can find t-values
	etc., but these have the same bias as in other software and should
	not be used.

	* bgdispersal: a new function for dispersal direction in
	biogeography (Legendre & Legendre 1998, section 13.3.4). Author
	Pierre Legendre.

	* designdist: a new function for defining your own dissimilarity
	index or for estimating beta diversity (Koleff et al.,
	J. Ecol. 72, 367-382; 2003).

	* isomap: a new function for isometric feature mapping of
	Tenenbaum et al. (Science 290, 2319-2323; 2000).

	* screeplot, bstick: new functions to draw screeplots of vegan
	ordination results with brokenstick lines, and alternative
	screeplot functions for prcomp and princomp with brokenstick.
	Author Gavin L. Simpson.

	* swan: a new function for the degree of absence (Swan 1970,
	Ecology 51, 89-102).

	* anova.cca: now refuses to do 'by = "terms"' if the rank of
	constraints is higher than the rank of the community matrix.
	
	* bioenv: gains argument 'partial' to perform partial bioenv.

	* cca, rda, capscale: can now handle longer expression within
	'Condition()' (ordiParseFormula). Used to drop observations with
	missing values in unused variables (ordiGetData).

	* goodness.cca, goodness.rda. 'statistic = "distance"' was wrongly
	implemented. Now refuses to find "distance" in constrained
	analysis: distances of constrained and unconstrained components do
	not add up to to distances in unconstrained ordination.

	* metaMDS (metaMDSdist): gains argument 'distfun' to use other
	dissimilarity functions than vegdist.

	* renyiaccum: used a variable that was not defined as an argument.
	Added support functions persp.renyiaccum and rgl.renyiaccum
	(Roeland Kindt).

	* stressplot: R2's renamed to 'non-metric fit' and 'linear fit'.

	* Doc: Corrected reference to Hurlbert in diversity (thanks to
	Ralph Grundel). Updated references (varpart, renyiaccum). Removed
	discussion on t-values in cca from vignettes, because as.mlm.cca
	now implements those. General cleanup and better utf-8 encoding.
	
Version 1.8-5 (January 11, 2007)

	* Based on devel version 1.9-12.
	
	* no.shared (manifest in metaMDS): prints thousands of lines of
	debugging info that I forgot to deactive in release. Not fatal,
	but extremely annoying.

	* capscale: inertia name as "unknown" if the dissimilarity object
	does not have a "method" name. Suggested by Roeland Kindt.

	* DESCRIPTION: license is now explicitly GPL v2 (but not later).

Version 1.8-4 (January 8, 2007)

	* Based on devel version 1.9-10.

	* cascadeKM: a new function to wrap kmeans and optimality criteria
	for classification (Sebastien Durand, Pierre Legendre & Marie
	Helene Ouellette).

	* renyiaccum: a new function for Renyi (and Hill) accumulation
        curves (Roeland Kindt).

	* bioenv: bioenv.formula uses now "na.action = NULL" in
        'model.frame', and bioenv.default passes arguments to 'cor' which
        means that you can set NA treatment in 'cor' using argument "use".

	* cca, rda: added "..." to formula versions to satisfy tests in
        R-DEVEL. 

	* cca, rda, capscale: used to fail if called within other
	functions.  Now data always evaluated in the environment of
	formula using new internal function ordiGetData.
	
	* anova.cca: checks that the model has both residual and
        constrained components or stops with understandable error message
        (used to stop with incomprehensible error message). 

	* print.summary.cca, print.summary.decorana: have now arguments
        'head' and 'tail' to print only a part of species and site
        scores. Suggested by Gavin Simpson.

	* metaMDS: checks now that the input data ('comm') is not a 'dist'
        object (like many users have had).

	* ordisurf: Does not depend on package 'akima' any longer, but
	directly finds fitted values in a regular grid using
	'predict.gam'.  Added pnpoly.c to find which of these values are
	within the convex hull defined by data.  Results also look neater
	with sparse data now.  Added argument 'labcex' passed to 'contour'
	for changing size of contour labels.  Setting 'labcex = 0' will
	suppress drawing labels (by setting drawlabels = FALSE in
	'contour()').

	* orditorp: handles now vector arguments of 'col', 'pcol', 'cex',
        and 'pch'.

	* rad.zipfbrot: less likely to overflow to NA coefficients during
        iteration. 

	* renyi: added a plot function, and documented together with
        renyiaccum() instead of diversity().

	* scores.default: Knows now about ade4 objects.  Primarily looks
	for scores scaled by eigenvalues both for sites and species.

	* specaccum: Added new conditioned method of Colwell et
        al. with estimated sd based on extrapolated richness (Roeland
        Kindt). 

	* vegdist.c: More informative warnings with 'method' name (useful
	with rankindex).

	* DESCRIPTION: listed 'require()d' packages in the "Suggests:"
	field to satisfy more anal tests in R-DEVEL.  Mention diversity
	analysis in the "Description:".
	
Version 1.8-3 (Sept 29, 2006)

	* Based on devel version 1.9-2.

	* varespec.rda, varechem.rda: saved in binary form, because old
	ascii form gave warning in R-2.4.0-rc.

	* vegdist: added Chao index (of Jaccard type) that should take
        into account missing pairs of species.  Checks that Binomial index
        is non-negative.  Identical sites could have dissimilarity of
        magnitude 1e-17 after some standardizations, but now values <1e-15
        are zapped to zero.

	* estimateR: uses now standard unbiased formulation of Chao. 

	* renyi: should work now (really!).

	* metaMDS: with zero = "add", zeros now replaced with
	min(dis[dis>0])/2 (used to be 1E-4) (metaMDSdist).  Sets number of
	tries also when this was not set previously (metaMDSiter)

Version 1.8-2 (June 13, 2006)

	* version 1.8-1 failed test in Windows because of a wrong encoding
	name.  Explicit \enc added for non-ascii words.  Kurt Hornik and
	Uwe Ligges diagnosed this and led me to see the light.

	* similar to devel version 1.7-97.
	
Version 1.8-1 (June 12, 2006)

	* Based on devel version 1.7-96. 

	* Pierre Legendre joined the vegan team.

	* beals: a new function for Beals smoothing.

	* bioenv: added 'trace' argument.

	* cca/rda/capscale: accept several 'Condition' elements in the
	formula. 

	* capscale: capscale(y ~ ., data=...) or expansion of "." on the
	rhs works now. Documentation recognizes now db-RDA as the real
	mother method.

	* scores.cca, summary.cca etc: rewrite so that is cleaner and
	easier to maintain. User visible changes are scaling by species
	standard deviation (negative scaling) for 'rda', scaling=0
        (no scaling) for all methods and slightly changed output and
	improved user control in summary. These scalings actually were
	documented in 1.6-10, although I dropped them just before the
	release. predict.cca, predict.rda: work now with 'newdata' even
	when not called with formula.

	* anova.cca: new argument 'by' for tests of single terms or axes:
	with by = "terms" performs individual test for constraints, and
	with by = "axis" a separate sequential test for each axis. New
	argument 'first' to analyse only the first axis instead of all
	constrained variation.
	
	* intersetcor: new function for the interset correlation or the
	(weighted) correlation between individual constraints (contrasts)
	and invidual axes in cca/rda/capscale. (Not recommended.)

	* decostand: does not automatically convert matrix to a
	data.frame. NA handling more consistent now (thanks to Tyler Smith
	for diagnosis). Adds attribute 'decostand' giving the "method".

	* linestack: now really uses median as the midpoint with the odd
	number of cases, and does not give superfluous warnings with three
	or less items.  New argument 'labels' to replace the default text
	in plot. The old argument 'label' renamed to 'side'.  However, the
	function still works with the old syntax, but gives a warning if
	the old argument 'label' is used for 'side'. Returns invisibly the
	shifted positions of labels.

	* metaMDS: 'postMDS' sets now attributes similarly when called
        independently or within 'metaMDS'.  'metaMDS' forwards arguments
        to 'postMDS' except 'halfchange'.  Change of phrasing in
        'print'. Added handling of zero dissimilarities into
        'metaMDSdist': either "fail" or "add" 1E-4 into zeros.
	
	* mrpp: new function for the multiresponse permutation procedure
	(MRPP). Code by Henry Stevens (Miami Univ, Oxford, Ohio).

	* ordiarrows: draws arrowhead only in the last segment. New
        argument 'startmark' for marking the starting point of the arrow. 

	* ordisurf: new arguments 'main' for the title and 'nlevels' and
	'levels' for the number of contour or their values.

	* orditorp: arguments for text colour and text character expansion
	changed to standard 'col' and 'cex' from previous 'tcol' and
	'tcex'. 

	* procrustes: 'summary' prints now rotation matrix, translation
        and scale, and honours 'digits'.

	* prc: new functions for Principal Response Curves (PRC) of van
        den Brink and ter Braak (Envir. Toxicol. Chem, 18, 138-148; 1999).
        This is a special rda() model with dedicated summary and plot
        functions. New data set 'pyrifos' to demonstrate 'prc'.

	* radfit: added brokenstick as a null model (rad.null), removed
	rad.veil (as it was a bad idea originally), corrected minor bugs
	in rad.preempt (which did not fail gracefully).  Line colours
	start from the point colour in plot.radfit.frame.  'print' uses
	"g" format for coefficients and adds 'digits' argument. Added
	'summary.radfit.frame' that simply prints each model.

	* rankindex: uses now cluster:::daisy when 'grad' includes
        factors.
	
	* spantree: now a method function with 'plot', 'lines' and
	'cophenetic' methods. 'lines' replaces 'ordispantree'.  The plot
	has a weird, new way of finding configuration for a spanning tree
	from cophenetic distances (unpublished). Documented separately.

	* specaccum: 'plot' honours now 'ylim'.

	* specpool: Chao richness was wrongly defined, but now uses the
	biased formula (error introduced in 1.6-5, correct earlier).
	Failed with zero species or if there were no species that occurred
	exactly one in the 'pool' (thanks to Emmanuel Castella, Geneve CH,
	for the bug report).

	* varpart: new functions for unbiased partitioning of variation by
	two to four explanatory tables in RDA or linear regression.  The
	author of these functions is Pierre Legendre & co (Univ
	Montreal). New data sets 'mite', 'mite.env' and 'mite.pcnm' to
	demonstrate the functions.

	* vegandocs: new function to display *all* pdf documentation and
	ChangeLog. This really should be in base R -- this is a kluge to
	fill the hole.

	* vegemite: added argument to 'select' a subset of sites. Drops
        missing species from the table. Prints number of species and
        number of sites and the used cover scale at the end of the table.
        Passes arguments (i.e., 'maxabund') to coverscale().

	* coverscale: added argument 'maxabund' to 'scale = "log"'.
	Returns the name of the cover scale as an attribute for vegemite()
	to print.

	* vegdist: now first checks input and then transforms (if
	needed). Thanks to Tyler Smith,

	* Internal changes: permuted.index acceptes NULL strata as an
	alternative to missing strata. ordispantreee deprecated.
	spider.cca removed.

	* Documentation: general cleanup in help files. New chapter on
	t-values in cca/rda/capscale in vegan-FAQ. New pdf document on
	partioning with varpart by Pierre Legendre & co. Non-latin
	characters now use UTF-8 in documentation.  R manual says that you
	should not use non-latin characters in help files, but that was
	written by Englishmen. However, this seems to cause distress to
	some users of a US West Coast OS (Windows), but OK with mainstream
	OS's (Linux, MacOS). .
	
Version 1.6-10 (September 26, 2005)

	* Based on devel version 1.7-77.  Checked with R 2.1.1 (stable)
	and R 2.2.0 (alpha).
 	
	* rda: negative scalings explicitly ignored and treated as
	corresponding positive values.  Function summary.rda used to fail
	with NA centroids.

	* permutest.cca & anova.cca: permutation of 'cca' result now
	re-weights environmental data properly with permuted community
	weights (this breaks compliance with popular proprietary
	software).  New default method 'direct' that always permutes the
	data instead of residuals.  Now clearly faster basic routines, but
	re-weighting in 'cca' is costly, and permutations may even be
	slower than earlier in small data sets.  The permutest.cca returns
	more data: constrained and residual total inertia, degrees of
	freedom in the input model, and .Random.seed used in iterations.
	Thanks to Pierre Legendre for pushing me to make this faster.

	* ordination plot functions: obey now xlim and ylim.

	* ordination text and points functions: a new argument 'select'
	that can be used to select a subset of items, and a new argument
	'labels' for text used instead of the default row names.

	* points.cca, text.cca: biplot arrows will be scaled automatically
	to fit the current graph if 'arrow.mul' is not given.  The new
	behaviour is similar to the default in plot.cca and in
	plot.envfit.
	
	* orditorp: a new "ordination text or points" function to add text
	or points to an existing plot: adds text if this can be done
	without overwriting other text labels, and points otherwise.

	* linestack: a new function to draw labelled one-dimensional
	diagrams without overwriting the labels (a primitive one, and
	could easily be improved: submissions are welcome).

	* ordirgl, orgltext: adapted to changes in rgl package version
	0.65.  Workaround for older rgl packages, too.
	
	* decostand: Added Hellinger transformation. Empty columns and
	rows become now 0 instead of NaN in most methods, except when the
	input data contains negative values. Warns on input with negative
	entries or on output containing NaN.  Has now argument
	'range.global' for method 'range' based on the code supplied by
	Tyler Smith.

	* plot.radfit: puts now legend "topright" in R >= 2.1.0 (which has
	this keyword).
	
	* read.cep: issues a warning if vegan was compiled with gfortran,
	which has a bug that may corrupt the result.  The bug concerns
	multiline input with T format modifier, and it was corrected in
	http://gcc.gnu.org/ml/gcc-patches/2005-09/msg00126.html, but still
	bugs most released versions of gcc.

	* vegdist: new indices 'raup' and 'binomial'. Method 'raup'
	implements probabilistic Raup-Crick index and is based on the code
	submitted by Michael Bedward.  Method 'binomial' implements
	Millar's index, officially published as "Binomial deviance as a
	dissimilarity measure" (the C code has been in vegan for about two
	years, but now I tell about it and add the public interface).
	Method 'mountford' will give NA for any comparison involving an
	empty site.  Warns about empty sites or negative entries with all
	methods except 'euclidean' and 'manhattan'.
	
	* Documentation: added documentation of the cca/rda/capscale
	result object. Dontruns used more neatly.
	
Version 1.6-9 (April 22, 2005)

	* Maintenance release: 1.6-8 failed in R 2.1.0 patched and R 2.2.0
	devel (works in R 2.1.0 release) due to problems in
	as.preston. Based on devel version 1.7-62.

	* as.fisher, as.preston: used table() in a way that failed in R
	2.1.0 patched

	* calibrate.cca: new function to predict or calibrate or
	bioindicate the values of environmental constraints from
	community composition (ordination).
	
	* decostand: new argument na.rm (defaults FALSE) for ignoring
	missing values in row, column or matrix standardizations.

	* vegdist: new argument na.rm (defaults FALSE) for pairwise
	deletion of missing vaues in dissimilarity calculation.
		
Version 1.6-8 (April 18, 2005)

	* Based on devel version 1.7-59.  Adapted to R 2.1.0 beta.

	* DESCRIPTION: gives due credit to Roeland Kindt and Bob O'Hara as
	co-authors. 

	* documentation: updates in capscale, vegdist. vegan-FAQ adapted
	to changes in Sweave in R 2.1.0.

	* several methods assumed that input is count data, but silently
	accepted floating point numbers and gave wrong results.  Now they
	stop with error with non-integer input: fisherfit, prestonfit,
	prestondistr, rarefy, fisher.alpha, estimateR.
	
	* bioenv: uses now 'cor' instead of 'cor.test', and does not give
	so many superfluous warnings and is marginally faster.  Changed
	printed output, so that gives 'call' instead of names of community
	and environmental data, since bioenv.formula could not handle
	these cleanly.

	* capscale: has now argument 'add' to use an additive constant to
	all dissimilarities so that all computed eigenvalues are
	non-negative.  This is an argument of underlying 'cmdscale'
	function, which implements the "Correction method 2" of Legendre &
	Legendre (1998), p. 434.   

	* decorana: checks now that there are no negative data entries.

	* dune: cleaner site names.

	* envfit: 'plot' now automatically scales arrows similarly as
	'plot.cca' if 'arrow.mul' is not specified and arrows are added to
	an old plot.  Has now a 'scores' function.
	
	* goodness.cca, predict.cca: documented separately.

	* goodness.metaMDS: new function to assess pointwise goodness of
	fit in metaMDS or isoMDS.

	* humpfit: user can now give starting values of parameters.
	'summary.humpfit' returns 'cov.unscaled' so that users can apply
	'ellipse' function of 'ellipse' package to display approximate
	confidence ellipses for pairs of parameters (with Normal
	assumptions). 

	* make.cepnames: No longer duplicates one component names, but
	'abbreviate's them to eight characters.

	* metaMDS: Split to independent metaunits 'metaMDSdist' and
	'metaMDSiter'.  New function 'metaMDSredist' tries to reconstruct
	dissimilarity matrices and transformations. 'postMDS' skips
	halfchange scaling with too few points (with a warning) instead of
	stopping with an error.  Prints now info about 'postMDS'
	operations.  New 'scores' function.  Improved 'plot' function with
	'display' argument and labelling of axes.  Argument 'shrink' to
	undo expansion of species scores in plot or scores functions.
	Workaround for a future bug in 'isoMDS' which drops names of
	points in R 2.1.0.  Updates number of 'tries' with
	'previous.best'.

	* ordiplot: has now 'display' argument, so that only species or
	sites can be plotted.

	* ordiplot3d: a new function for 3D static ordination diagrams.

	* ordirgl: new function for dynamic 3D graphics of ordination
	results.  With support functions orglpoints, orgltext,
	orglsegments and orglspider to add graphical items to dynamic
	plots. Needs 'rgl' package.

	* predict.cca, predict.rda: type = "wa" with 'newdata' works now
	even when some species were removed from the original fit because
	they were all-zero (missing).  Default now to 'model = "CA"' in
	unconstrained analysis without "CCA" component.

	* predict.decorana: a new function for 'decorana' results. Similar
	to 'predict.cca' (but refuses to give impossible results).

	* procrustes: obeys now 'choices' even when input is a matrix.
	Plots now projections of rotated axes.  New argument 'scores' so
	that can handle other than "site" scores.

	* protest: passes now arguments to 'scores' so that now can handle
	other than "site" scores on more than two dimensions.

	* rda: handles now species with constant values (typically
	missing or all zeros). 

	* spenvcor:  new function to find the "species -- environment
	correlation" in contrained ordination (cca, rda, capscale).

	* stressplot: a new function to plot Shepard diagram for 'metaMDS'
	or 'isoMDS'.

	* summary.cca/summary.rda: print now call.

	* vegemite: can now 'use' 'dendrogram' objects.
	
Version 1.6-7 (Jan 24, 2005)

	* Based on devel version 1.7-42.

	* plot.envfit did not plot vectors.  Thanks to Roeland Kindt and
	Ron E. VanNimwegen for bug reports and fixes. 

	* ordisurf obeys now keyword 'display', and '...' will transfer
	arguments to 'scores'.

	* ordisegments: obeys now keyword 'display'.

        * ordigrid: works now.

        * ordihull, ordiarrows, ordisegments, ordispider, ordiellipse:
        have a new keyword 'show.groups' to show only specified groups.
        With the help of this argument it is possible to use different
        colours and linetypes for each group.  Further, it makes possible
        to plot results of logical comparisons (such as A1 > 4) by setting
        show.groups = T. Two user requests.

	* new diagnostic and helper functions for 'cca', 'rda' and
	'capscale': 'goodness' to estimate the proportion of inertia
	accounted for or residuals for sites or species; 'inertcomp' to
	decompose species and site inertia for conditioned, contrained and
	residual componets; 'vif.cca' to estimate the variance inflation
	factors for constraints and conditions; 'fitted' and 'residuals'
	to approximate data by ordination scores; 'predict' to approximate
	data or find site or species scores, possibly with 'newdata';
	'coef' to find the regression coefficients. 'alias.cca' is now
	similar to 'alias.lm' (simplified version of the latter).


Version 1.6-6 (Jan 7, 2005)

	* Based on version 1.7-34, but without still experimental
	functions predict, fitted, vif & goodness for cca and rda
	objects. 

	* mantel: implemented partial mantel test (function
	'mantel.partial'). Both 'mantel' and 'mantel.partial' should be
	marginally faster and not give so many superfluous warnings.

	* plot.envfit: should be more reliable now. A new keyword 'at' to
	position the bunch of arrows in other places than the origin.
	Thanks to Roeland Kindt for fixes.

	* rankindex: Default correlation now "spearman" since the older
	default ("kendall") was far too slow in large data sets.  Should
	not give so many superfluous warnings.

	* summary.rda: Site scores were wrong with 'scaling = 3'.
	Influences 'plot' and 'scores' commands for 'rda' and 'capscale'
	results with 'scaling = 3'.

	* vegdist: Issues a warning if 'method = "morisita"' is used with
	non-integer data.
	
Version 1.6-5 (Oct 12, 2004) 

	* Based on version 1.7-27. Checked with R-1.9.1 (Linux, MacOS X)
	and R-2.0.0 (Linux, patched version in Windows XP). Passed other
	tests, but some examples in 'humpfit' failed in Windows XP, and
	are not run on that platfrom. General cleanup in documentation.
	Does not 'require(mva)' any longer.

	* anosim: corrected the equation in docs (function was
	correct). Thanks to Yong Cao for notifying this.

	* bioenv.formula: finds now variables from attach'ed data.frames
	and 'data' need not be specified.

	* capscale & deviance.rda: capscale was modified so that its
	result could be handled with step (added a terms component).
	Function deviance.capscale was deleted so that deviance.rda will
	be used. A literature reference to AIC in CCA/RDA was added to the
	documentation.

	* cca/rda/capscale: Small eigenvalues are made to zero and rank
	reduced accordingly. Most often influences 'capscale'.
	
	* cca/rda/capscale: Now alias constraints that are collinear with
	other constraints or conditions in partial analysis. New function
	'alias.cca' to print aliased contrasts. NB this does not influence
	the proper ordination results, but only to the selection of biplot
	scores and centroids displayed. 'summary' no longer gives a
	redundant warning.

	* decorana: removes empty species with a warning instead of
	stopping with error. Still error with empty sites. The behaviour
	is similar to 'cca'.

	* envfit (vectorfit, factorfit): Has now a formula interface.
	Bottlenecks in permutation changed now into C functions. Much
	faster, in particular 'factorfit' which was 25 times faster in my
	tests.  plot.envfit could drop names (dimensions). Now honours
	'scaling' argument in cca/rda/capscale (used to 'scaling = 2'
	always).

	* envfit, ordisurf: have now weights parameter 'w'. Weights are
	used for the results of 'cca' and 'decorana' as default, or they
	can be supplied by the user. In this way, envfit gives equal
	results to biplot scores and centroids in 'cca', and ordisurf is
	consistent with envfit. Both can now access 'lc' scores of 'cca'
	etc. 

	* estimateR:  Abundance-based estimators of extrapolated richness,
	written by Bob O'Hara <bob.ohara@helsinki.fi>. 

	* humpfit: Asesses now the dispersion parameter in non-Poisson
        models (summary.humpfit). Added a profile method that inherits
        from profile.glm, so that you can use plot.profile.glm,
        pairs.profile.glm and confint.profile.glm of MASS for displaying
        profile and finding the confidence intervals from the profile
        likelihood.

	* fisherfit: prints now standard error of the estimate. Added
        'profile' and 'confint' methods.
	
	* metaMDS:  A new function to collect all Peter Minchin's
        recommendations to run nonmetric multidimensional scaling: (1)
        adequate data transformation with Wisconsin double and sqrt if
        needed, (2) use of adequate dissimilarity measure, (3) possible
        stepacross if needed (this Minchin didn't have), (4) run NMDS with
        several random starts and stop after finding two similar
        solutions, (5) scale results with postMDS, and (6) add species
        scores with wascores. Function has print and plot methods.
        Function scores.default changed to understand metaMDS.

	* specpool: Chao is now based on unbiased equation. Standard
	errors now estimated for Chao, 1st-order jackknife and bootstrap
	richness, but SE of 2nd-order jackknife still missing.
	
	* vegdist: an option for binary indices, since some users believed
	these are not in vegan, although you can get them with
	'decostand'.

Version 1.6-4 (June 10, 2004)

	* Based on 1.7-12.

	* anova.cca: Changed defaults to beta=0.01 and perm.max=10000.

	* bioenv: A new function implementing the BIO-ENV procedure of
        Clarke & Ainsworth (Mar. Ecol. Prog. Ser. 92, 205-219; 1993).  The
        function finds the subset of scaled environmental variables with
        maximum (rank) correlation with community data.

	* cca: added ter Braak scaling, a.k.a. Hill scaling, with
	negative values of `scaling'. This scaling should approximate
	Hill's non-linear rescaling of `decorana', but it the scaling is
	linear and does not rescale. The scaling is very simple: the
	results from corresponding positive scaling are multipiled with
	sqrt(1/(1-lambda)). 

	* plot.cca: Better heuristics used for the length of biplot
	arrows, and they are now longer in general. Axes are drawn for
	biplot arrows also with `text.cca' and `points.cca' functions.

	* deviance.cca and extractAIC.cca: auxilliary functions which
	allow automatic model building with `step' or `stepAIC' (MASS)
	functions in cca and rda. Unfortunately, cca and rda do not have
	deviance or AIC, and these functions are certainly wrong and
	dangerous. However, with continuous candidate variables they
	select the variables in the same order as Canoco.

	* humpfit: A new family of functions to fit the no-interaction
	model (Oksanen, J., J. Ecol. 84, 293-295; 1996) to species
	richness -- biomass data.
	
	* vegdist: corrected a bug in Gower index -- range standardization
	was made to sites, but it should be done to species. Thanks to
	Brett Melbourne <bamelbourne@ucdavis.edu> for the bug report.
	
Version 1.6-3 (Mar 22, 2004)

	* Still based on 1.7-3, but ported some changes from version
	1.7-7 (envfit, procrustes). This version was produced to prepare
	for incompatible changes in coming R-1.9.0.

	* vegan-FAQ: Does not show the vegan and R versions the
	documentations were built, because of stupid incompatible change
	in R-1.9.0 of the future.  package.description() function was
	unnecessarily replaced with packageDescription, and to accomodate
	recent, present and future versions of R seemed to be too much
	hassle.
 
        * plot.envfit: Added option 'p.max' to display only environmental
        variables assessed to have P values less or equal to the given
        limit.
         
        * plot.procrustes: added option kind = 0 to draw only axes and
        functions points.procrustes and lines.procrustes to add points and
        line segments or arrows to the plot.
         
	
Version 1.6-2: Based on devel version 1.7-3.

	* renyi: should work now (again?).

	* prestondistr: The truncation level was badly chosen. Now default
	level is set to -1, or log2(-1) = 0.5 which might be the left
	limit of the first octave. This is now a parameter, leaving the
	choice as the responsibility of the user.

	* cca.default: Removes missing species and issues a warning
	instead of stopping with error.  
	
Version 1.6-1: Based on devel version 1.7-1.

	* Minor maintanenance release to satisfy tests in R-devel. There
	was a buglet in ordisegments that caused a warning. I had
	introduced a trick to handle printCoefmat before it was invented
	to replace print.coefmat, but this failed in R-devel.  

	* Vignettes included in this release. These were only in devel
	versions of my web pages previously.

Version 1.6-0 (Fisher)


	* Based on devel version 1.5-58. Passes checks with R-1.8.0 and
	R-1.7.0 and compiles into a Windows binary. Many functions were
	contributed by Roeland Kindt (Nairobi, Kenya).

	* BCI: A new data set on tree counts on 1-ha plots in the Barro
	Colorado Island. Thanks to Roeland Kindt and Richard S. Condit.

	* capscale: A new function for [partial] constrained analysis of
	principal coordinates (CAP).

	* cca, rda: Can now handle cases where the number of constraints
	is higher than the number of species.

	* cca, decorana: Find now if data have empty rows or columns.

	* decostand: Added Chi-square transformation.

	* distconnected: A new function to find if vegetation data are
	disconnected below given threshold dissimilarity level. Utility
	function no.shared gives a logical dissimilarity matrix with
	values TRUE for cases with no shared species.

	* fisher.alpha: Should work with large sample sizes now (bug
	report thanks to Ariel Bergamini).

	* fisherfit, prestonfit, prestondistr: New functions to fit
	Fisher's logarithmic series and Preston's log-normal model.

	* make.cepnames: New utility function to change Latin names into
	4+4 character CEP names.

	* ordicluster, ordispantree: New functions in the ordihull family
	to overlay a cluster dendrogram or a spanning tree onto an
	ordination. Weights are now really used with cca and decorana
	plots.

	* radfit: New function to fit Ranked Abundance Dominance or
	Dominance/ Diversity models with maximum likelihood: Pre-emption,
	log-normal, veiled log-normal, Zipf and Zipf--Mandelbrot models.

	* rankindex: Can now use stepacross and new dissimilarity indices
	of vegdist.

	* rarefy: Can now optionally find SE of rarefied richness.

	* renyi: A new function to find Rényi diversities or Hill numbers
	with any scale (thanks to Roeland Kindt).

	* scores.ordiplot: should be more robust now.

	* spantree: A new function to find a minimum spanning tree using
	only dissimilarities below a threshold or disregarding NA
	dissimilarities.

	* specaccum: A new function for species accumulation
	curves. Thanks to Roeland Kindt.

	* specnumber: A very simple utility function to find species
	richness.

	* specpool: New function for extrapolated species richness in a
	species pool, or for estimating the number of unseen species.

	* stepacross: New function for estimation of dissimilarities
	between sites that have no shared species. Implements both
	flexible shortest paths and their approximation known as extended
	dissimilarities.

	* vegdist: New dissimilarity indices Jaccard (finally), Morisita,
	Horn--Morisita and Mountford.

Version 1.4-4

	* Based on devel version 1.5-35.

	* decorana: Finds now eigenvalues from the final solution as ratio
	of biased weighted variances of site and species scores. The
	values returned by the legacy Fortran function are called
	``decorana values''.

	* downweight: passes the downweighting fraction as an attribute,
	and decorana catches and prints the fraction.

	* wascores: Uses now biased variances for expading WAs and returns
	the shrinkage factors as an attribute "shrinkage".  Shrinkage
	factors are equal to eigenvalues in CCA when only this one
	variable is used as constraint. Function `eigengrad' returns only
	these eigenvalues.

	* rda summary/plot bugfix: Failed with non-default scaling (1 or
	3) when there were no factor constraints. Corrected a statement
	giving a harmless warning in plot.cca.

	* ordiplot knows now option type = "text".  New simpleminded
	functions points.ordiplot and text.ordiplot for adding items in an
	ordiplot graph.

	* ordiarrows, ordisegments could drop dimensions (when will I
	learn!)  and fail if only one arrow or one segment should be
	drawn.  One argument was missing in a `gl' command in `ordigrid'.


Version 1.4-3 (Luova)

	* Based on devel version 1.5-30

	* `cca' and `rda' use canonical expansion of the formula and
	return the `terms' component.  Functions like `terms', `formula'
	and `update' magically started to work with cca and rda (and eight
	lines of code would allow `step' and `stepAIC' to work magically
	in model building... but it's so much magic that I don't trust
	it). Some of the allowed things are now `mod <- cca(dune ~ . -
	Use, dune.env)'
	(all variables but `Use' in dune.env), and `update(mod, . ~ . -
	Manure)' (remove `Manure' from the previous).

	* `cca' and `rda' find centroids of factor levels with factor
	constraints (only with formula interface). These can be accessed
	with `display="cn"' in `scores', `summary' and `plot'.  If
	`display="cn"' is requested in `plot', biplot arrows are still
	drawn unless there is a class centroid with the same name:
	continuous variables are still shown as arrows and ordered factors
	both as arrows as centroids.

	* Enhanced user control of many ordination plots. Some accept more
	graphical parameters (`ordiplot', `plot.procrustes'). New
	functions `points.cca' and `text.cca' to add these items into
	CCA/RDA plots (documented separately).

	* `identify.ordiplot' knows more alternatives, among them
	`plot.procrustes'.  This was helped with new, very generic
	`scores.ordiplot'.

	* New functions to add graphical items in ordination diagrams:
	`ordihull' draws convex hulls for groups, `ordiarrows' draws
	arrows, `ordisegments' segments, `ordigrid' combines points in to
	a grid, `ordispider' combines points to their (weighted) centroids
	or WA scores to the corresponding LC score in cca/rda,
	`ordiellipse' draws dispersion or confidence ellipses for
	points. All these take a groups argument for selecting subsets of
	points. `ordispider' obsoletes `spider.cca' (introduced in the
	previous release).

	* Implemented simple ``deshrinking'' of weighted averages in
	`wascores'.

	* A new diversity function `fisher.alpha' that estimates the
	diversity as the alpha parameter of Fisher's log-series. Thanks to
	Bob O'Hara <bob.ohara@helsinki.fi> for the main code.

	* `summary.decorana' now in canonical form so that printing is
	done by `print.summary.decorana' and user can intercept and catch
	the result.  Several users had been surprised of the earlier
	non-canonical behaviour. `summary' knows again the prior weights
	used in downweighting of rare species (these evaporated in 1.4-0).

	* rda summary/scores/plot bugfix: Scaling of site scores was wrong
	with scaling alternatives 1 and 3.

	* envfit (vectorfit, factorfit) bug fixes: Can now handle single
	vectors (labelling, permutation). Recognize now `choices' so that
	the user can select ordination axes.

	* Checked with released R-1.7.0.

Version 1.4-2


Based on devel version 1.5-18

	* New functions and data sets:

	* dune: A new data set -- the classic Dune Meadow data with the
	environmental data.

	* ordiplot, identify.ordiplot: New functions to plot "any"
	ordination result and identify plotted points. Intended to provide
	similar functionality as `plot', `plotid' and `specid' functions
	in `labdsv' without name clashes. Functions `plot.cca' and
	`plot.decorana' return (invisibly) `ordiplot' objects as well, and
	these can be used by `identify' to label species and sites.

	* rda: Redundancy Analysis, or optionally, yet another PCA. This
	is a spin-off from cca(), and it is documented together with
	cca. The only new functions are rda, rda.default, rda.formula and
	summary.rda. Otherwise rda uses cca methods which were changed to
	be aware of rda.

	* read.cep: A function to read Cornell Ecology Package or CEP
	formatted files into R. This has been in devel versions since
	1.1-1, but it never made to the releases, since this worked only
	in Linux, but crashed R in Windows. It seemed to work in R-1.6.1
	with gcc 3.2
	(MinGW) in Windows, so it is included. Treat with caution.

	* spider.cca: A tiny function that joins each WA score to the
	corresponding LC score in cca/rda plots.

Minor changes:

	* Checked with R-1.7.0 (unstable devel version, snapshot
	2003-02-05) and corrected as needed.

	* Added symmetric scaling (=3) to alternitves in cca and rda.

	* Minor improvements and bug fixes in vegemite.

Version 1.4-1 (Logan)

Based on devel version 1.5-10.

New features:

	* Permutation tests added to envfit (vectorfit, factorfit) and
	procrustes (called protest).

	* All permutation tests take now argument strata: If given,
	permutations made only within strats. Concerns anosim, anova.cca
	(permutest.cca), mantel, envfit (factorfit, envfit) and protest
	(in procrustes).

	* fitted.procrustes(): A new function.

	* rarefy(): A new function for rarefaction species richness.

Other changes:


	* cca.default(): Handles now NULL matrices X and Z: skips them.

	* cca.formula(): Knows now cca(X ~ 1) and permforms unconstrained
	CA, and cca(X ~ ., data) and perfors CCA using all variables in
	`data' as constraints. Has now na.action=na.fail so that cca
	crashes more informatively (used to crash mysteriously). A more
	graceful na.action may come. Assignment "=" corrected to the true
	blue "<-" (used to crash in old R).

	* envfit (factorfit, vectorfit): Use `scores' now. Various
	bugfixes and should work now with single factors or vectors.

	* plot.envfit(): Options `choices' works now like documented.

	* ordisurf(): A new name to surf() to avoid name clash with
	labdsv.
  
	* procrustes(): added option `symmetric' for symmetric rotation
	and goodness of fit statistic.

	* plot.procrustes(): Keyword `axes' changed to `choices' to be
	consistent with other functions.

	* vegemite(): A new name to vegetab. The name was chosen because
	the output is so compact (and to avoid confusion with function
	vegtab in labdsv). Function checks now that the cover codes fit in
	one column and splits the output if it does not fit into used page
	width.

Version 1.4-0

Based on devel version 1.3-19.

New functions:

	* `anosim': Analysis of Similarities.

	* `cca': [Partial] [Constrained] Correspondence Analysis.  This is
	an alternative to Dray's `CAIV' (package `CoCoAn').  Differences
	include formula interface, WA scores in addition to LC scores,
	partial CCA, residual CA after constraints, algorithm based on svd
	(and much faster), more standard support functions (`plot',
	`summary', `print').

	* `anova.cca' and `permutest.cca': Permutation tests for `cca'.

	* `envfit': A new wrapper function which calls either `vectorfit'
	or new `factorfit' function, and `plot.envfit' for easier display
	of results in graphs.  

	* `mantel': Mantel test for two
	dissimilarity matrices.

	* `scores': A generic function to extract scores from `cca',
	`decorana' or even from some common ordination methods in R.

	* `surf': Surface fitting for ordination, intended as an
	alternative to `vectorfit'.

	* `vegetab': Prints a compact, ordered vegetation table, together
	with `coverscale' to transform data into compact format.

Other changes:

	* `downweight': directly callable instead of being embedded in
	`decorana'. Now it can be used with other downweighting thresholds
	or with other CA's than `decorana', e.g., `cca', `ca', `CAIV'.

	* `plot.decorana': new keyword `type', removed keyword `tol'.

	* `vectorfit': centres now ordination before fitting, so it will
	work with other ordinations than MDS.

	* Mainly user invisible changes in `plot.decorana',
	`plot.procrustes', `postMDS', `print.summary.procrustes',
	`vectorfit', `procrustes'.  One of the main changes was that
	`eqscplot' of `MASS' library was replaced with `plot(..., asp=1)'
	of standard R (but this is not S-plus compliant).

	* Edited help files.  More examples run from help files.

	* Tried to improve LabDSV compliance, see
	http://labdsv.nr.usu.edu/.

	* Checked with R-1.5.0.  However, `log' in diversity not changed
	into `logb' (yet), although base is specified, because `logb'
	won't work in R pre-1.5.0.

Version 1.2-1

	* Checked with R-1.4-0 (frozen snapshot) tools: Documentation and
	method consistency corrected (summary.decorana.R, decorana.Rd),
	and file permissions changed.

	* decorana.Rd: removed dependence on package `multiv' in the
	example, since it is not a `recommended package' -- replaced with
	`decorana(..., ira=1)'.

Version 1.2-0


Based on experimental version 1.1-6. Doesn't include read.cep() of the
experimental version, because the function is certainly unportable to
all platforms (works on Red Hat Linux 7.1, but perhaps nowhere else).

Major new feature:

	* decorana(): R port of Mark Hill's DECORANA for Detrended
	correspondence analysis, with methods print(), summary() and
	plot().

Minor changes:

	* postMDS(): finds isoMDS scores and doesn't destroy list
	structure.

	* vectorfit: finds isoMDS scores and decorana row scores (which
	are uncentred, though).

	* Proof reading in documentation.

Version 1.0-3

	*`plot.procrustes': selection of axes plotted, improved scaling in
	graphics, control of axis labels.  

	* `postMDS': added plot to demonstrate half-change scaling.

	* `procrustes': target can now have lower dimensionality than
	rotated matrix.

Version 1.0-2


	* Fixed bugs in documentation.

	* `plot.procrustes': Fixed passing `...' to graphics functions.

Version 1.0-1

	* The first public version.
r-cran-vegan 2.4-2-1 / usr / lib / R / site-library / vegan / OldChangeLog
