$Date: 2011-10-19 22:06:33 +0300 (Wed, 19 Oct 2011) $

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

Version 2.0-1 (released October 20, 2011)

	* merge r1945: add plot & lines for as.preston & as.fisher.
	* merge r1944: R 2.14.0 (r52709) gives a message() when sd() is
	used for matrices -- now fixed for rda.default, capscale and
	simulate.rda/cca/capscale. 
	* merge r1939: slacker and faster nesteddisc.
	* merge r1928: permutest.cca result could not be update()d.
 	* merge r1927: reset 'tries' when 'previous.best' was a different
	model.
	* merge r1916: ordisurf.Rd references.
	* merge r1914: example speed-up.
	* r1897, 1840, 1825, 1823: copy clamtest (at r1897),
	summary.clamtest, print.summary.clamtest, plot.clamtest (all at
	r1823) and clamtest.Rd (at r1897)
	* merge r1872: raupcrick doc fixes.
	* merge r1869: meandist re-ordering bug fix.
	* merge r1846: tweak speed (a bit).
	* merge r1845: faster centroids.cca.
	* merge r1843: tiny speed-up in permutest.cca(..., first=TRUE) 
	* merge r1838: a bit faster example(MDSrotate).
	* merge r1835: add raupcrick.
	* merge r1811: permatswap bug fix in nestedness.c.
	* merge r1810: -pedatic -Wall fixes in monoMDS.f, ordering.f
	
Version 2.0-0 (released September 8, 2011)

	* opened the release candidate of vegan_2.0-0 on September 3,
	2011 in the devel branch pkg/vegan at r1785.
	* Release: Copied the devel pkg/vegan branch to release
	branches/2.0 at r1796 (inst/doc/vegan.bib at r1798), and removed
	tests/ directory.
	* merge r1800: Abstract to diversity-vegan.Rnw.
	* 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. 

VEGAN DEVEL VERSIONS at http://vegan.r-forge.r-project.org/

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 Cl
