VEGAN STABLE VERSIONS 
$Date: 2007-10-03 10:10:09 +0300 (Wed, 03 Oct 2007) $
	
Version 1.8-8 (Oct 2, 2007)

	* Minor bugfix release for upcoming R-2.6.0. Based on the
	http://r-forge.r-project.org/projects/vegan/ revision 17 (= 1.8-7)
	with ported bug fix revisions (see below for revision numbers).

	* anova.cca: by = "term" failed in partial model. This was broken
	in 1.8-6 by introducing a test against deficit rank models (r47). 
	
	* cascadeKM: Calinski index works now when the input data is a
	data.frame (r57:58).

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

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

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

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

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

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

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

	* Based on devel version 1.9-34.

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

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

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

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

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

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

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

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

Version 1.8-6 (May 9, 2007)

	* Based on devel version 1.9-23.

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

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

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

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

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

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

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

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

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

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

	* renyiaccum: used a variable that was not defined as an argument.
	Added support functions persp.renyiaccum and rgl.renyiaccum
	(Roeland Kindt).

	* stressplot: R2's renamed to 'non-metric fit' and 'linear fit'.

	* Doc: Corrected reference to Hurlbert in diversity (thanks to
	Ralph Grundel). Updated references (varpart, renyiaccum). Removed
	discussion on t-values in cca from vignettes, because as.mlm.cca
	now implements those. General cleanup and better utf-8 encoding.
	
Version 1.8-5 (January 11, 2007)

	* Based on devel version 1.9-12.
	
	* no.shared (manifest in metaMDS): prints thousands of lines of
	debugging info that I forgot to deactive in release. Not fatal,
	but extremely annoying.

	* capscale: inertia name as "unknown" if the dissimilarity object
	does not have a "method" name. Suggested by Roeland Kindt.

	* DESCRIPTION: license is now explicitly GPL v2 (but not later).

Version 1.8-4 (January 8, 2007)

	* Based on devel version 1.9-10.

	* cascadeKM: a new function to wrap kmeans and optimality criteria
	for classification (Sebastien Durand, Pierre Legendre & Marie
	Helene Ouellette).

	* renyiaccum: a new function for Renyi (and Hill) accumulation
        curves (Roeland Kindt).

	* bioenv: bioenv.formula uses now "na.action = NULL" in
        'model.frame', and bioenv.default passes arguments to 'cor' which
        means that you can set NA treatment in 'cor' using argument "use".

	* cca, rda: added "..." to formula versions to satisfy tests in
        R-DEVEL. 

	* cca, rda, capscale: used to fail if called within other
	functions.  Now data always evaluated in the environment of
	formula using new internal function ordiGetData.
	
	* anova.cca: checks that the model has both residual and
        constrained components or stops with understandable error message
        (used to stop with incomprehensible error message). 

	* print.summary.cca, print.summary.decorana: have now arguments
        'head' and 'tail' to print only a part of species and site
        scores. Suggested by Gavin Simpson.

	* metaMDS: checks now that the input data ('comm') is not a 'dist'
        object (like many users have had).

	* ordisurf: Does not depend on package 'akima' any longer, but
	directly finds fitted values in a regular grid using
	'predict.gam'.  Added pnpoly.c to find which of these values are
	within the convex hull defined by data.  Results also look neater
	with sparse data now.  Added argument 'labcex' passed to 'contour'
	for changing size of contour labels.  Setting 'labcex = 0' will
	suppress drawing labels (by setting drawlabels = FALSE in
	'contour()').

	* orditorp: handles now vector arguments of 'col', 'pcol', 'cex',
        and 'pch'.

	* rad.zipfbrot: less likely to overflow to NA coefficients during
        iteration. 

	* renyi: added a plot function, and documented together with
        renyiaccum() instead of diversity().

	* scores.default: Knows now about ade4 objects.  Primarily looks
	for scores scaled by eigenvalues both for sites and species.

	* specaccum: Added new conditioned method of Colwell et
        al. with estimated sd based on extrapolated richness (Roeland
        Kindt). 

	* vegdist.c: More informative warnings with 'method' name (useful
	with rankindex).

	* DESCRIPTION: listed 'require()d' packages in the "Suggests:"
	field to satisfy more anal tests in R-DEVEL.  Mention diversity
	analysis in the "Description:".
	
Version 1.8-3 (Sept 29, 2006)

	* Based on devel version 1.9-2.

	* varespec.rda, varechem.rda: saved in binary form, because old
	ascii form gave warning in R-2.4.0-rc.

	* vegdist: added Chao index (of Jaccard type) that should take
        into account missing pairs of species.  Checks that Binomial index
        is non-negative.  Identical sites could have dissimilarity of
        magnitude 1e-17 after some standardizations, but now values <1e-15
        are zapped to zero.

	* estimateR: uses now standard unbiased formulation of Chao. 

	* renyi: should work now (really!).

	* metaMDS: with zero = "add", zeros now replaced with
	min(dis[dis>0])/2 (used to be 1E-4) (metaMDSdist).  Sets number of
	tries also when this was not set previously (metaMDSiter)

Version 1.8-2 (June 13, 2006)

	* version 1.8-1 failed test in Windows because of a wrong encoding
	name.  Explicit \enc added for non-ascii words.  Kurt Hornik and
	Uwe Ligges diagnosed this and led me to see the light.

	* similar to devel version 1.7-97.
	
Version 1.8-1 (June 12, 2006)

	* Based on devel version 1.7-96. 

	* Pierre Legendre joined the vegan team.

	* beals: a new function for Beals smoothing.

	* bioenv: added 'trace' argument.

	* cca/rda/capscale: accept several 'Condition' elements in the
	formula. 

	* capscale: capscale(y ~ ., data=...) or expansion of "." on the
	rhs works now. Documentation recognizes now db-RDA as the real
	mother method.

	* scores.cca, summary.cca etc: rewrite so that is cleaner and
	easier to maintain. User visible changes are scaling by species
	standard deviation (negative scaling) for 'rda', scaling=0
        (no scaling) for all methods and slightly changed output and
	improved user control in summary. These scalings actually were
	documented in 1.6-10, although I dropped them just before the
	release. predict.cca, predict.rda: work now with 'newdata' even
	when not called with formula.

	* anova.cca: new argument 'by' for tests of single terms or axes:
	with by = "terms" performs individual test for constraints, and
	with by = "axis" a separate sequential test for each axis. New
	argument 'first' to analyse only the first axis instead of all
	constrained variation.
	
	* intersetcor: new function for the interset correlation or the
	(weighted) correlation between individual constraints (contrasts)
	and invidual axes in cca/rda/capscale. (Not recommended.)

	* decostand: does not automatically convert matrix to a
	data.frame. NA handling more consistent now (thanks to Tyler Smith
	for diagnosis). Adds attribute 'decostand' giving the "method".

	* linestack: now really uses median as the midpoint with the odd
	number of cases, and does not give superfluous warnings with three
	or less items.  New argument 'labels' to replace the default text
	in plot. The old argument 'label' renamed to 'side'.  However, the
	function still works with the old syntax, but gives a warning if
	the old argument 'label' is used for 'side'. Returns invisibly the
	shifted positions of labels.

	* metaMDS: 'postMDS' sets now attributes similarly when called
        independently or within 'metaMDS'.  'metaMDS' forwards arguments
        to 'postMDS' except 'halfchange'.  Change of phrasing in
        'print'. Added handling of zero dissimilarities into
        'metaMDSdist': either "fail" or "add" 1E-4 into zeros.
	
	* mrpp: new function for the multiresponse permutation procedure
	(MRPP). Code by Henry Stevens (Miami Univ, Oxford, Ohio).

	* ordiarrows: draws arrowhead only in the last segment. New
        argument 'startmark' for marking the starting point of the arrow. 

	* ordisurf: new arguments 'main' for the title and 'nlevels' and
	'levels' for the number of contour or their values.

	* orditorp: arguments for text colour and text character expansion
	changed to standard 'col' and 'cex' from previous 'tcol' and
	'tcex'. 

	* procrustes: 'summary' prints now rotation matrix, translation
        and scale, and honours 'digits'.

	* prc: new functions for Principal Response Curves (PRC) of van
        den Brink and ter Braak (Envir. Toxicol. Chem, 18, 138-148; 1999).
        This is a special rda() model with dedicated summary and plot
        functions. New data set 'pyrifos' to demonstrate 'prc'.

	* radfit: added brokenstick as a null model (rad.null), removed
	rad.veil (as it was a bad idea originally), corrected minor bugs
	in rad.preempt (which did not fail gracefully).  Line colours
	start from the point colour in plot.radfit.frame.  'print' uses
	"g" format for coefficients and adds 'digits' argument. Added
	'summary.radfit.frame' that simply prints each model.

	* rankindex: uses now cluster:::daisy when 'grad' includes
        factors.
	
	* spantree: now a method function with 'plot', 'lines' and
	'cophenetic' methods. 'lines' replaces 'ordispantree'.  The plot
	has a weird, new way of finding configuration for a spanning tree
	from cophenetic distances (unpublished). Documented separately.

	* specaccum: 'plot' honours now 'ylim'.

	* specpool: Chao richness was wrongly defined, but now uses the
	biased formula (error introduced in 1.6-5, correct earlier).
	Failed with zero species or if there were no species that occurred
	exactly one in the 'pool' (thanks to Emmanuel Castella, Geneve CH,
	for the bug report).

	* varpart: new functions for unbiased partitioning of variation by
	two to four explanatory tables in RDA or linear regression.  The
	author of these functions is Pierre Legendre & co (Univ
	Montreal). New data sets 'mite', 'mite.env' and 'mite.pcnm' to
	demonstrate the functions.

	* vegandocs: new function to display *all* pdf documentation and
	ChangeLog. This really should be in base R -- this is a kluge to
	fill the hole.

	* vegemite: added argument to 'select' a subset of sites. Drops
        missing species from the table. Prints number of species and
        number of sites and the used cover scale at the end of the table.
        Passes arguments (i.e., 'maxabund') to coverscale().

	* coverscale: added argument 'maxabund' to 'scale = "log"'.
	Returns the name of the cover scale as an attribute for vegemite()
	to print.

	* vegdist: now first checks input and then transforms (if
	needed). Thanks to Tyler Smith,

	* Internal changes: permuted.index acceptes NULL strata as an
	alternative to missing strata. ordispantreee deprecated.
	spider.cca removed.

	* Documentation: general cleanup in help files. New chapter on
	t-values in cca/rda/capscale in vegan-FAQ. New pdf document on
	partioning with varpart by Pierre Legendre & co. Non-latin
	characters now use UTF-8 in documentation.  R manual says that you
	should not use non-latin characters in help files, but that was
	written by Englishmen. However, this seems to cause distress to
	some users of a US West Coast OS (Windows), but OK with mainstream
	OS's (Linux, MacOS). .
	
Version 1.6-10 (September 26, 2005)

	* Based on devel version 1.7-77.  Checked with R 2.1.1 (stable)
	and R 2.2.0 (alpha).
 	
	* rda: negative scalings explicitly ignored and treated as
	corresponding positive values.  Function summary.rda used to fail
	with NA centroids.

	* permutest.cca & anova.cca: permutation of 'cca' result now
	re-weights environmental data properly with permuted community
	weights (this breaks compliance with popular proprietary
	software).  New default method 'direct' that always permutes the
	data instead of residuals.  Now clearly faster basic routines, but
	re-weighting in 'cca' is costly, and permutations may even be
	slower than earlier in small data sets.  The permutest.cca returns
	more data: constrained and residual total inertia, degrees of
	freedom in the input model, and .Random.seed used in iterations.
	Thanks to Pierre Legendre for pushing me to make this faster.

	* ordination plot functions: obey now xlim and ylim.

	* ordination text and points functions: a new argument 'select'
	that can be used to select a subset of items, and a new argument
	'labels' for text used instead of the default row names.

	* points.cca, text.cca: biplot arrows will be scaled automatically
	to fit the current graph if 'arrow.mul' is not given.  The new
	behaviour is similar to the default in plot.cca and in
	plot.envfit.
	
	* orditorp: a new "ordination text or points" function to add text
	or points to an existing plot: adds text if this can be done
	without overwriting other text labels, and points otherwise.

	* linestack: a new function to draw labelled one-dimensional
	diagrams without overwriting the labels (a primitive one, and
	could easily be improved: submissions are welcome).

	* ordirgl, orgltext: adapted to changes in rgl package version
	0.65.  Workaround for older rgl packages, too.
	
	* decostand: Added Hellinger transformation. Empty columns and
	rows become now 0 instead of NaN in most methods, except when the
	input data contains negative values. Warns on input with negative
	entries or on output containing NaN.  Has now argument
	'range.global' for method 'range' based on the code supplied by
	Tyler Smith.

	* plot.radfit: puts now legend "topright" in R >= 2.1.0 (which has
	this keyword).
	
	* read.cep: issues a warning if vegan was compiled with gfortran,
	which has a bug that may corrupt the result.  The bug concerns
	multiline input with T format modifier, and it was corrected in
	http://gcc.gnu.org/ml/gcc-patches/2005-09/msg00126.html, but still
	bugs most released versions of gcc.

	* vegdist: new indices 'raup' and 'binomial'. Method 'raup'
	implements probabilistic Raup-Crick index and is based on the code
	submitted by Michael Bedward.  Method 'binomial' implements
	Millar's index, officially published as "Binomial deviance as a
	dissimilarity measure" (the C code has been in vegan for about two
	years, but now I tell about it and add the public interface).
	Method 'mountford' will give NA for any comparison involving an
	empty site.  Warns about empty sites or negative entries with all
	methods except 'euclidean' and 'manhattan'.
	
	* Documentation: added documentation of the cca/rda/capscale
	result object. Dontruns used more neatly.
	
Version 1.6-9 (April 22, 2005)

	* Maintenance release: 1.6-8 failed in R 2.1.0 patched and R 2.2.0
	devel (works in R 2.1.0 release) due to problems in
	as.preston. Based on devel version 1.7-62.

	* as.fisher, as.preston: used table() in a way that failed in R
	2.1.0 patched

	* calibrate.cca: new function to predict or calibrate or
	bioindicate the values of environmental constraints from
	community composition (ordination).
	
	* decostand: new argument na.rm (defaults FALSE) for ignoring
	missing values in row, column or matrix standardizations.

	* vegdist: new argument na.rm (defaults FALSE) for pairwise
	deletion of missing vaues in dissimilarity calculation.
		
Version 1.6-8 (April 18, 2005)

	* Based on devel version 1.7-59.  Adapted to R 2.1.0 beta.

	* DESCRIPTION: gives due credit to Roeland Kindt and Bob O'Hara as
	co-authors. 

	* documentation: updates in capscale, vegdist. vegan-FAQ adapted
	to changes in Sweave in R 2.1.0.

	* several methods assumed that input is count data, but silently
	accepted floating point numbers and gave wrong results.  Now they
	stop with error with non-integer input: fisherfit, prestonfit,
	prestondistr, rarefy, fisher.alpha, estimateR.
	
	* bioenv: uses now 'cor' instead of 'cor.test', and does not give
	so many superfluous warnings and is marginally faster.  Changed
	printed output, so that gives 'call' instead of names of community
	and environmental data, since bioenv.formula could not handle
	these cleanly.

	* capscale: has now argument 'add' to use an additive constant to
	all dissimilarities so that all computed eigenvalues are
	non-negative.  This is an argument of underlying 'cmdscale'
	function, which implements the "Correction method 2" of Legendre &
	Legendre (1998), p. 434.   

	* decorana: checks now that there are no negative data entries.

	* dune: cleaner site names.

	* envfit: 'plot' now automatically scales arrows similarly as
	'plot.cca' if 'arrow.mul' is not specified and arrows are added to
	an old plot.  Has now a 'scores' function.
	
	* goodness.cca, predict.cca: documented separately.

	* goodness.metaMDS: new function to assess pointwise goodness of
	fit in metaMDS or isoMDS.

	* humpfit: user can now give starting values of parameters.
	'summary.humpfit' returns 'cov.unscaled' so that users can apply
	'ellipse' function of 'ellipse' package to display approximate
	confidence ellipses for pairs of parameters (with Normal
	assumptions). 

	* make.cepnames: No longer duplicates one component names, but
	'abbreviate's them to eight characters.

	* metaMDS: Split to independent metaunits 'metaMDSdist' and
	'metaMDSiter'.  New function 'metaMDSredist' tries to reconstruct
	dissimilarity matrices and transformations. 'postMDS' skips
	halfchange scaling with too few points (with a warning) instead of
	stopping with an error.  Prints now info about 'postMDS'
	operations.  New 'scores' function.  Improved 'plot' function with
	'display' argument and labelling of axes.  Argument 'shrink' to
	undo expansion of species scores in plot or scores functions.
	Workaround for a future bug in 'isoMDS' which drops names of
	points in R 2.1.0.  Updates number of 'tries' with
	'previous.best'.

	* ordiplot: has now 'display' argument, so that only species or
	sites can be plotted.

	* ordiplot3d: a new function for 3D static ordination diagrams.

	* ordirgl: new function for dynamic 3D graphics of ordination
	results.  With support functions orglpoints, orgltext,
	orglsegments and orglspider to add graphical items to dynamic
	plots. Needs 'rgl' package.

	* predict.cca, predict.rda: type = "wa" with 'newdata' works now
	even when some species were removed from the original fit because
	they were all-zero (missing).  Default now to 'model = "CA"' in
	unconstrained analysis without "CCA" component.

	* predict.decorana: a new function for 'decorana' results. Similar
	to 'predict.cca' (but refuses to give impossible results).

	* procrustes: obeys now 'choices' even when input is a matrix.
	Plots now projections of rotated axes.  New argument 'scores' so
	that can handle other than "site" scores.

	* protest: passes now arguments to 'scores' so that now can handle
	other than "site" scores on more than two dimensions.

	* rda: handles now species with constant values (typically
	missing or all zeros). 

	* spenvcor:  new function to find the "species -- environment
	correlation" in contrained ordination (cca, rda, capscale).

	* stressplot: a new function to plot Shepard diagram for 'metaMDS'
	or 'isoMDS'.

	* summary.cca/summary.rda: print now call.

	* vegemite: can now 'use' 'dendrogram' objects.
	
Version 1.6-7 (Jan 24, 2005)

	* Based on devel version 1.7-42.

	* plot.envfit did not plot vectors.  Thanks to Roeland Kindt and
	Ron E. VanNimwegen for bug reports and fixes. 

	* ordisurf obeys now keyword 'display', and '...' will transfer
	arguments to 'scores'.

	* ordisegments: obeys now keyword 'display'.

        * ordigrid: works now.

        * ordihull, ordiarrows, ordisegments, ordispider, ordiellipse:
        have a new keyword 'show.groups' to show only specified groups.
        With the help of this argument it is possible to use different
        colours and linetypes for each group.  Further, it makes possible
        to plot results of logical comparisons (such as A1 > 4) by setting
        show.groups = T. Two user requests.

	* new diagnostic and helper functions for 'cca', 'rda' and
	'capscale': 'goodness' to estimate the proportion of inertia
	accounted for or residuals for sites or species; 'inertcomp' to
	decompose species and site inertia for conditioned, contrained and
	residual componets; 'vif.cca' to estimate the variance inflation
	factors for constraints and conditions; 'fitted' and 'residuals'
	to approximate data by ordination scores; 'predict' to approximate
	data or find site or species scores, possibly with 'newdata';
	'coef' to find the regression coefficients. 'alias.cca' is now
	similar to 'alias.lm' (simplified version of the latter).


Version 1.6-6 (Jan 7, 2005)

	* Based on version 1.7-34, but without still experimental
	functions predict, fitted, vif & goodness for cca and rda
	objects. 

	* mantel: implemented partial mantel test (function
	'mantel.partial'). Both 'mantel' and 'mantel.partial' should be
	marginally faster and not give so many superfluous warnings.

	* plot.envfit: should be more reliable now. A new keyword 'at' to
	position the bunch of arrows in other places than the origin.
	Thanks to Roeland Kindt for fixes.

	* rankindex: Default correlation now "spearman" since the older
	default ("kendall") was far too slow in large data sets.  Should
	not give so many superfluous warnings.

	* summary.rda: Site scores were wrong with 'scaling = 3'.
	Influences 'plot' and 'scores' commands for 'rda' and 'capscale'
	results with 'scaling = 3'.

	* vegdist: Issues a warning if 'method = "morisita"' is used with
	non-integer data.
	
Version 1.6-5 (Oct 12, 2004) 

	* Based on version 1.7-27. Checked with R-1.9.1 (Linux, MacOS X)
	and R-2.0.0 (Linux, patched version in Windows XP). Passed other
	tests, but some examples in 'humpfit' failed in Windows XP, and
	are not run on that platfrom. General cleanup in documentation.
	Does not 'require(mva)' any longer.

	* anosim: corrected the equation in docs (function was
	correct). Thanks to Yong Cao for notifying this.

	* bioenv.formula: finds now variables from attach'ed data.frames
	and 'data' need not be specified.

	* capscale & deviance.rda: capscale was modified so that its
	result could be handled with step (added a terms component).
	Function deviance.capscale was deleted so that deviance.rda will
	be used. A literature reference to AIC in CCA/RDA was added to the
	documentation.

	* cca/rda/capscale: Small eigenvalues are made to zero and rank
	reduced accordingly. Most often influences 'capscale'.
	
	* cca/rda/capscale: Now alias constraints that are collinear with
	other constraints or conditions in partial analysis. New function
	'alias.cca' to print aliased contrasts. NB this does not influence
	the proper ordination results, but only to the selection of biplot
	scores and centroids displayed. 'summary' no longer gives a
	redundant warning.

	* decorana: removes empty species with a warning instead of
	stopping with error. Still error with empty sites. The behaviour
	is similar to 'cca'.

	* envfit (vectorfit, factorfit): Has now a formula interface.
	Bottlenecks in permutation changed now into C functions. Much
	faster, in particular 'factorfit' which was 25 times faster in my
	tests.  plot.envfit could drop names (dimensions). Now honours
	'scaling' argument in cca/rda/capscale (used to 'scaling = 2'
	always).

	* envfit, ordisurf: have now weights parameter 'w'. Weights are
	used for the results of 'cca' and 'decorana' as default, or they
	can be supplied by the user. In this way, envfit gives equal
	results to biplot scores and centroids in 'cca', and ordisurf is
	consistent with envfit. Both can now access 'lc' scores of 'cca'
	etc. 

	* estimateR:  Abundance-based estimators of extrapolated richness,
	written by Bob O'Hara <bob.ohara@helsinki.fi>. 

	* humpfit: Asesses now the dispersion parameter in non-Poisson
        models (summary.humpfit). Added a profile method that inherits
        from profile.glm, so that you can use plot.profile.glm,
        pairs.profile.glm and confint.profile.glm of MASS for displaying
        profile and finding the confidence intervals from the profile
        likelihood.

	* fisherfit: prints now standard error of the estimate. Added
        'profile' and 'confint' methods.
	
	* metaMDS:  A new function to collect all Peter Minchin's
        recommendations to run nonmetric multidimensional scaling: (1)
        adequate data transformation with Wisconsin double and sqrt if
        needed, (2) use of adequate dissimilarity measure, (3) possible
        stepacross if needed (this Minchin didn't have), (4) run NMDS with
        several random starts and stop after finding two similar
        solutions, (5) scale results with postMDS, and (6) add species
        scores with wascores. Function has print and plot methods.
        Function scores.default changed to understand metaMDS.

	* specpool: Chao is now based on unbiased equation. Standard
	errors now estimated for Chao, 1st-order jackknife and bootstrap
	richness, but SE of 2nd-order jackknife still missing.
	
	* vegdist: an option for binary indices, since some users believed
	these are not in vegan, although you can get them with
	'decostand'.

Version 1.6-4 (June 10, 2004)

	* Based on 1.7-12.

	* anova.cca: Changed defaults to beta=0.01 and perm.max=10000.

	* bioenv: A new function implementing the BIO-ENV procedure of
        Clarke & Ainsworth (Mar. Ecol. Prog. Ser. 92, 205-219; 1993).  The
        function finds the subset of scaled environmental variables with
        maximum (rank) correlation with community data.

	* cca: added ter Braak scaling, a.k.a. Hill scaling, with
	negative values of `scaling'. This scaling should approximate
	Hill's non-linear rescaling of `decorana', but it the scaling is
	linear and does not rescale. The scaling is very simple: the
	results from corresponding positive scaling are multipiled with
	sqrt(1/(1-lambda)). 

	* plot.cca: Better heuristics used for the length of biplot
	arrows, and they are now longer in general. Axes are drawn for
	biplot arrows also with `text.cca' and `points.cca' functions.

	* deviance.cca and extractAIC.cca: auxilliary functions which
	allow automatic model building with `step' or `stepAIC' (MASS)
	functions in cca and rda. Unfortunately, cca and rda do not have
	deviance or AIC, and these functions are certainly wrong and
	dangerous. However, with continuous candidate variables they
	select the variables in the same order as Canoco.

	* humpfit: A new family of functions to fit the no-interaction
	model (Oksanen, J., J. Ecol. 84, 293-295; 1996) to species
	richness -- biomass data.
	
	* vegdist: corrected a bug in Gower index -- range standardization
	was made to sites, but it should be done to species. Thanks to
	Brett Melbourne <bamelbourne@ucdavis.edu> for the bug report.
	
Version 1.6-3 (Mar 22, 2004)

	* Still based on 1.7-3, but ported some changes from version
	1.7-7 (envfit, procrustes). This version was produced to prepare
	for incompatible changes in coming R-1.9.0.

	* vegan-FAQ: Does not show the vegan and R versions the
	documentations were built, because of stupid incompatible change
	in R-1.9.0 of the future.  package.description() function was
	unnecessarily replaced with packageDescription, and to accomodate
	recent, present and future versions of R seemed to be too much
	hassle.
 
        * plot.envfit: Added option 'p.max' to display only environmental
        variables assessed to have P values less or equal to the given
        limit.
         
        * plot.procrustes: added option kind = 0 to draw only axes and
        functions points.procrustes and lines.procrustes to add points and
        line segments or arrows to the plot.
         
	
Version 1.6-2: Based on devel version 1.7-3.

	* renyi: should work now (again?).

	* prestondistr: The truncation level was badly chosen. Now default
	level is set to -1, or log2(-1) = 0.5 which might be the left
	limit of the first octave. This is now a parameter, leaving the
	choice as the responsibility of the user.

	* cca.default: Removes missing species and issues a warning
	instead of stopping with error.  
	
Version 1.6-1: Based on devel version 1.7-1.

	* Minor maintanenance release to satisfy tests in R-devel. There
	was a buglet in ordisegments that caused a warning. I had
	introduced a trick to handle printCoefmat before it was invented
	to replace print.coefmat, but this failed in R-devel.  

	* Vignettes included in this release. These were only in devel
	versions of my web pages previously.

Version 1.6-0 (Fisher)


	* Based on devel version 1.5-58. Passes checks with R-1.8.0 and
	R-1.7.0 and compiles into a Windows binary. Many functions were
	contributed by Roeland Kindt (Nairobi, Kenya).

	* BCI: A new data set on tree counts on 1-ha plots in the Barro
	Colorado Island. Thanks to Roeland Kindt and Richard S. Condit.

	* capscale: A new function for [partial] constrained analysis of
	principal coordinates (CAP).

	* cca, rda: Can now handle cases where the number of constraints
	is higher than the number of species.

	* cca, decorana: Find now if data have empty rows or columns.

	* decostand: Added Chi-square transformation.

	* distconnected: A new function to find if vegetation data are
	disconnected below given threshold dissimilarity level. Utility
	function no.shared gives a logical dissimilarity matrix with
	values TRUE for cases with no shared species.

	* fisher.alpha: Should work with large sample sizes now (bug
	report thanks to Ariel Bergamini).

	* fisherfit, prestonfit, prestondistr: New functions to fit
	Fisher's logarithmic series and Preston's log-normal model.

	* make.cepnames: New utility function to change Latin names into
	4+4 character CEP names.

	* ordicluster, ordispantree: New functions in the ordihull family
	to overlay a cluster dendrogram or a spanning tree onto an
	ordination. Weights are now really used with cca and decorana
	plots.

	* radfit: New function to fit Ranked Abundance Dominance or
	Dominance/ Diversity models with maximum likelihood: Pre-emption,
	log-normal, veiled log-normal, Zipf and Zipf--Mandelbrot models.

	* rankindex: Can now use stepacross and new dissimilarity indices
	of vegdist.

	* rarefy: Can now optionally find SE of rarefied richness.

	* renyi: A new function to find Rényi diversities or Hill numbers
	with any scale (thanks to Roeland Kindt).

	* scores.ordiplot: should be more robust now.

	* spantree: A new function to find a minimum spanning tree using
	only dissimilarities below a threshold or disregarding NA
	dissimilarities.

	* specaccum: A new function for species accumulation
	curves. Thanks to Roeland Kindt.

	* specnumber: A very simple utility function to find species
	richness.

	* specpool: New function for extrapolated species richness in a
	species pool, or for estimating the number of unseen species.

	* stepacross: New function for estimation of dissimilarities
	between sites that have no shared species. Implements both
	flexible shortest paths and their approximation known as extended
	dissimilarities.

	* vegdist: New dissimilarity indices Jaccard (finally), Morisita,
	Horn--Morisita and Mountford.

Version 1.4-4

	* Based on devel version 1.5-35.

	* decorana: Finds now eigenvalues from the final solution as ratio
	of biased weighted variances of site and species scores. The
	values returned by the legacy Fortran function are called
	``decorana values''.

	* downweight: passes the downweighting fraction as an attribute,
	and decorana catches and prints the fraction.

	* wascores: Uses now biased variances for expading WAs and returns
	the shrinkage factors as an attribute "shrinkage".  Shrinkage
	factors are equal to eigenvalues in CCA when only this one
	variable is used as constraint. Function `eigengrad' returns only
	these eigenvalues.

	* rda summary/plot bugfix: Failed with non-default scaling (1 or
	3) when there were no factor constraints. Corrected a statement
	giving a harmless warning in plot.cca.

	* ordiplot knows now option type = "text".  New simpleminded
	functions points.ordiplot and text.ordiplot for adding items in an
	ordiplot graph.

	* ordiarrows, ordisegments could drop dimensions (when will I
	learn!)  and fail if only one arrow or one segment should be
	drawn.  One argument was missing in a `gl' command in `ordigrid'.


Version 1.4-3 (Luova)

	* Based on devel version 1.5-30

	* `cca' and `rda' use canonical expansion of the formula and
	return the `terms' component.  Functions like `terms', `formula'
	and `update' magically started to work with cca and rda (and eight
	lines of code would allow `step' and `stepAIC' to work magically
	in model building... but it's so much magic that I don't trust
	it). Some of the allowed things are now `mod <- cca(dune ~ . -
	Use, dune.env)'
	(all variables but `Use' in dune.env), and `update(mod, . ~ . -
	Manure)' (remove `Manure' from the previous).

	* `cca' and `rda' find centroids of factor levels with factor
	constraints (only with formula interface). These can be accessed
	with `display="cn"' in `scores', `summary' and `plot'.  If
	`display="cn"' is requested in `plot', biplot arrows are still
	drawn unless there is a class centroid with the same name:
	continuous variables are still shown as arrows and ordered factors
	both as arrows as centroids.

	* Enhanced user control of many ordination plots. Some accept more
	graphical parameters (`ordiplot', `plot.procrustes'). New
	functions `points.cca' and `text.cca' to add these items into
	CCA/RDA plots (documented separately).

	* `identify.ordiplot' knows more alternatives, among them
	`plot.procrustes'.  This was helped with new, very generic
	`scores.ordiplot'.

	* New functions to add graphical items in ordination diagrams:
	`ordihull' draws convex hulls for groups, `ordiarrows' draws
	arrows, `ordisegments' segments, `ordigrid' combines points in to
	a grid, `ordispider' combines points to their (weighted) centroids
	or WA scores to the corresponding LC score in cca/rda,
	`ordiellipse' draws dispersion or confidence ellipses for
	points. All these take a groups argument for selecting subsets of
	points. `ordispider' obsoletes `spider.cca' (introduced in the
	previous release).

	* Implemented simple ``deshrinking'' of weighted averages in
	`wascores'.

	* A new diversity function `fisher.alpha' that estimates the
	diversity as the alpha parameter of Fisher's log-series. Thanks to
	Bob O'Hara <bob.ohara@helsinki.fi> for the main code.

	* `summary.decorana' now in canonical form so that printing is
	done by `print.summary.decorana' and user can intercept and catch
	the result.  Several users had been surprised of the earlier
	non-canonical behaviour. `summary' knows again the prior weights
	used in downweighting of rare species (these evaporated in 1.4-0).

	* rda summary/scores/plot bugfix: Scaling of site scores was wrong
	with scaling alternatives 1 and 3.

	* envfit (vectorfit, factorfit) bug fixes: Can now handle single
	vectors (labelling, permutation). Recognize now `choices' so that
	the user can select ordination axes.

	* Checked with released R-1.7.0.

Version 1.4-2


Based on devel version 1.5-18

	* New functions and data sets:

	* dune: A new data set -- the classic Dune Meadow data with the
	environmental data.

	* ordiplot, identify.ordiplot: New functions to plot "any"
	ordination result and identify plotted points. Intended to provide
	similar functionality as `plot', `plotid' and `specid' functions
	in `labdsv' without name clashes. Functions `plot.cca' and
	`plot.decorana' return (invisibly) `ordiplot' objects as well, and
	these can be used by `identify' to label species and sites.

	* rda: Redundancy Analysis, or optionally, yet another PCA. This
	is a spin-off from cca(), and it is documented together with
	cca. The only new functions are rda, rda.default, rda.formula and
	summary.rda. Otherwise rda uses cca methods which were changed to
	be aware of rda.

	* read.cep: A function to read Cornell Ecology Package or CEP
	formatted files into R. This has been in devel versions since
	1.1-1, but it never made to the releases, since this worked only
	in Linux, but crashed R in Windows. It seemed to work in R-1.6.1
	with gcc 3.2
	(MinGW) in Windows, so it is included. Treat with caution.

	* spider.cca: A tiny function that joins each WA score to the
	corresponding LC score in cca/rda plots.

Minor changes:

	* Checked with R-1.7.0 (unstable devel version, snapshot
	2003-02-05) and corrected as needed.

	* Added symmetric scaling (=3) to alternitves in cca and rda.

	* Minor improvements and bug fixes in vegemite.

Version 1.4-1 (Logan)

Based on devel version 1.5-10.

New features:

	* Permutation tests added to envfit (vectorfit, factorfit) and
	procrustes (called protest).

	* All permutation tests take now argument strata: If given,
	permutations made only within strats. Concerns anosim, anova.cca
	(permutest.cca), mantel, envfit (factorfit, envfit) and protest
	(in procrustes).

	* fitted.procrustes(): A new function.

	* rarefy(): A new function for rarefaction species richness.

Other changes:


	* cca.default(): Handles now NULL matrices X and Z: skips them.

	* cca.formula(): Knows now cca(X ~ 1) and permforms unconstrained
	CA, and cca(X ~ ., data) and perfors CCA using all variables in
	`data' as constraints. Has now na.action=na.fail so that cca
	crashes more informatively (used to crash mysteriously). A more
	graceful na.action may come. Assignment "=" corrected to the true
	blue "<-" (used to crash in old R).

	* envfit (factorfit, vectorfit): Use `scores' now. Various
	bugfixes and should work now with single factors or vectors.

	* plot.envfit(): Options `choices' works now like documented.

	* ordisurf(): A new name to surf() to avoid name clash with
	labdsv.
  
	* procrustes(): added option `symmetric' for symmetric rotation
	and goodness of fit statistic.

	* plot.procrustes(): Keyword `axes' changed to `choices' to be
	consistent with other functions.

	* vegemite(): A new name to vegetab. The name was chosen because
	the output is so compact (and to avoid confusion with function
	vegtab in labdsv). Function checks now that the cover codes fit in
	one column and splits the output if it does not fit into used page
	width.

Version 1.4-0

Based on devel version 1.3-19.

New functions:

	* `anosim': Analysis of Similarities.

	* `cca': [Partial] [Constrained] Correspondence Analysis.  This is
	an alternative to Dray's `CAIV' (package `CoCoAn').  Differences
	include formula interface, WA scores in addition to LC scores,
	partial CCA, residual CA after constraints, algorithm based on svd
	(and much faster), more standard support functions (`plot',
	`summary', `print').

	* `anova.cca' and `permutest.cca': Permutation tests for `cca'.

	* `envfit': A new wrapper function which calls either `vectorfit'
	or new `factorfit' function, and `plot.envfit' for easier display
	of results in graphs.  

	* `mantel': Mantel test for two
	dissimilarity matrices.

	* `scores': A generic function to extract scores from `cca',
	`decorana' or even from some common ordination methods in R.

	* `surf': Surface fitting for ordination, intended as an
	alternative to `vectorfit'.

	* `vegetab': Prints a compact, ordered vegetation table, together
	with `coverscale' to transform data into compact format.

Other changes:

	* `downweight': directly callable instead of being embedded in
	`decorana'. Now it can be used with other downweighting thresholds
	or with other CA's than `decorana', e.g., `cca', `ca', `CAIV'.

	* `plot.decorana': new keyword `type', removed keyword `tol'.

	* `vectorfit': centres now ordination before fitting, so it will
	work with other ordinations than MDS.

	* Mainly user invisible changes in `plot.decorana',
	`plot.procrustes', `postMDS', `print.summary.procrustes',
	`vectorfit', `procrustes'.  One of the main changes was that
	`eqscplot' of `MASS' library was replaced with `plot(..., asp=1)'
	of standard R (but this is not S-plus compliant).

	* Edited help files.  More examples run from help files.

	* Tried to improve LabDSV compliance, see
	http://labdsv.nr.usu.edu/.

	* Checked with R-1.5.0.  However, `log' in diversity not changed
	into `logb' (yet), although base is specified, because `logb'
	won't work in R pre-1.5.0.

Version 1.2-1

	* Checked with R-1.4-0 (frozen snapshot) tools: Documentation and
	method consistency corrected (summary.decorana.R, decorana.Rd),
	and file permissions changed.

	* decorana.Rd: removed dependence on package `multiv' in the
	example, since it is not a `recommended package' -- replaced with
	`decorana(..., ira=1)'.

Version 1.2-0


Based on experimental version 1.1-6. Doesn't include read.cep() of the
experimental version, because the function is certainly unportable to
all platforms (works on Red Hat Linux 7.1, but perhaps nowhere else).

Major new feature:

	* decorana(): R port of Mark Hill's DECORANA for Detrended
	correspondence analysis, with methods print(), summary() and
	plot().

Minor changes:

	* postMDS(): finds isoMDS scores and doesn't destroy list
	structure.

	* vectorfit: finds isoMDS scores and decorana row scores (which
	are uncentred, though).

	* Proof reading in documentation.

Version 1.0-3

	*`plot.procrustes': selection of axes plotted, improved scaling in
	graphics, control of axis labels.  

	* `postMDS': added plot to demonstrate half-change scaling.

	* `procrustes': target can now have lower dimensionality than
	rotated matrix.

Version 1.0-2


	* Fixed bugs in documentation.

	* `plot.procrustes': Fixed passing `...' to graphics functions.

Version 1.0-1

	* The first public version.
