
$Date: 2008-09-30 10:04:55 +0300 (Tue, 30 Sep 2008) $

VEGAN STABLE VERSIONS

Version 1.15-0 (released September 30, 2008)

	* based on rev506 at http://r-forge.r-project.org/

	* removed MOStest.

	* removed adipart.

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

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. 
	
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
