[Vegan-commits] r2031 - branches/2.0/inst

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 20 12:35:16 CET 2011


Author: jarioksa
Date: 2011-12-20 12:35:15 +0100 (Tue, 20 Dec 2011)
New Revision: 2031

Modified:
   branches/2.0/inst/ChangeLog
Log:
merge r2030: resurrect old ChangeLog entries

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2011-12-20 09:29:27 UTC (rev 2030)
+++ branches/2.0/inst/ChangeLog	2011-12-20 11:35:15 UTC (rev 2031)
@@ -4,6 +4,7 @@
 
 Version 2.0-3 (opened November 13, 2011)
 
+	* merge r2030: resurrect old ChangeLog entries.
 	* merge r2018,19,21: add nestedbetasor() & nestedbetajac().
 	* merge r2016: empty factor levels in betadisper() fixed in
 	ordimedian(). 
@@ -2869,4 +2870,1285 @@
 	(species) were not coded. Also explained in the help.
 
 	* varpart: failed if there were unused levels in factors (reported
-	by Cl
+	by Clément Tisseuil, Toulouse). 
+
+	* adonis: loses argument 'distfun'. Instead accepts now any 'dist'
+	object as input instead of a data frame or a matrix.
+	
+Version 1.10-7 (closed Nov 18, 2007 at Rev. 119)
+
+	* adonis: gains argument 'distfun' (default 'vegdist') so that
+	other standard conforming dissimilarity functions than vegdist can
+	be used (a user request).
+	
+	* decorana: does not crash R when called with NULL row data such
+	as decorana(dune[FALSE,]) (reported by Richard Tellford, Bergen,
+	Norway), and predict(..., type="sites") works correctly with
+	downweighted analysis (reported by Colin Beale, Aberdeen,
+	Scotland).
+
+	* isomap: checks now that input data are dissimilarities or can be
+	changed into dissimilarities without warnings.
+
+	* ordixyplot: can now display biplot arrows and factor centroids
+	in constrained ordination or from envfit (ordisplom and ordicloud
+	cannot display these).
+	
+	* ordixyplot, ordicloud and ordisplom: no longer have explicit scaling
+	argument, but can now pass arguments to scores() as well as to the
+	plotting functions.
+
+	* oecosimu: evaluates now two-sided P-value of the statistic from
+	simulations. Doc updates.
+
+	* vignettes: use all similar style (amsart, a4paper, sidecap,
+	date style).
+
+	* FAQ: tell about docs added to R-Forge versions of vegan. Tell
+	about predict() for having "passive" points.
+	
+Version 1.10-6 (closed Oct 31, 2007 at Rev. 100)
+
+	* Gavin Simpson joined the vegan team.
+
+	* oecosimu: new functions for indices of nestedness of patches or
+	islands, and simulation of null communities.
+	
+	* scores: cca method does now accept display = c("species", "sites").
+	Previous fix (1.10-5) was for rda method only. Documentation updated
+	to reflect changes.
+	
+	* biplot.rda: now allows a different type to be specified for each of
+	the species and site scores. Function now documented more completely.
+	
+	* ordixyplot, ordicloud and ordisplom: now have argument 'scaling'.
+	
+	* orditorp: now handles additional arguments passed as '...' more 
+	cleanly. Arguments can be passed to scores() or points/text. This
+	should avoid the warning messages of previous versions.
+
+	* sipoo: a new data set on the bird communities in the Sipoo
+	(Sibbo) archipelago to demonstrate the oecosimu functions.
+
+Version 1.10-5 (closed Oct 18, 2007 at Rev. 86)
+
+	* biplot.rda: new biplot function for PCA in rda() (Gavin
+	Simpson). 
+
+	* scores: cca method accepts now display = c("species", "sites"),
+	when it only used to accept c("sp","wa"). More consistent
+	arguments in the default method.  
+	
+	* CCorA: Pierre Legendre submitted code for permutation test of
+	Pillai's trace.
+
+	* capscale: negative scaling works now in plot() and scores():
+	estimates species  sd() from the 'comm' if 'comm' is known.
+
+Version 1.10-4 (closed Oct 6, 2007 at Rev. 75)
+
+	* anova.cca: failed in anova(object, by = "axis") when the fitted
+	model had terms like poly(x, 2) or log(x).
+
+	* ordiresids: new function for plot.lm like diagnostic plots for
+	constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals)) ~
+	Fitted, and qqmath(~ Residuals) using Lattice graphics.
+       
+	* fitted.cca, fitted.rda: gained agument type = "working" to get
+	the fitted values and residuals used internally in calculation (to
+	be used in plot.lm diagnostic plots residuals ~ fitted).
+ 	
+Version 1.10-3 (closed Oct 2, 2007 at Rev. 62)
+
+	* doc: added vignettes intro-vegan on ordination methods and
+	diversity-vegan.
+
+	* Trellis graphics for ordination objects with functions
+	ordixyplot, ordicloud and ordisplom. These functions are still
+	unsatisfactory. In particular, I haven't found a clean way of
+	having biplot arrows in the graphs (how do you know the
+	coordinates and the axes used?). Contributions are welcome.
+
+	* ordispantree made dysfunctional (deprecated in 1.8-1). 
+	
+Version 1.10-2 (closed Sep 14, 2007 at Rev. 36)
+
+	* vegandocs: added FAQ-vegan, and renamed the old vegan-FAQ to
+	decision-vegan. Only primary sources (texi, Rnw) in the source
+	repository: derived files (.tex, .pdf) should be made when package
+	is built.
+	
+	* CCorA: Pierre Legendre's functions for Canonical Correlation
+	Analysis. These provide a more robust alternative to the standard
+	cancor() in base R. (under work)
+		
+	* scores.default: handles numeric data frames.
+	
+Version 1.10-1 (closed Sep 7, 2007 at Rev. 21)
+
+	* taxondive: Fixed dimension checking, matching names and
+	non-unique taxon names.
+	
+Version 1.10-0 (Sep 6, 2007)
+
+	* Moved vegan_1.8-7 (CRAN release) into R-Forge.R-Project.org and
+	Subversion SCM. This ChangeLog will only contain most important
+	news (and should be renamed to NEWS), and the real ChangeLogs are
+	created by the SCM.  The revisions will be numbered as 1.10-1 to
+	1.10-x, and the next release will be 1.11-0.
+
+VEGAN RELEASE VERSIONS at http://cran.r-project.org/
+
+Version 1.8-8 (Oct 2, 2007)
+
+	* Minor bugfix release for upcoming R-2.6.0. Based on the
+	http://r-forge.r-project.org/projects/vegan/ revision 17 (= 1.8-7)
+	with ported bug fix revisions from 1.10-3 (see below for revision
+	numbers).
+	
+	* anova.cca: by = "term" failed in partial model. This was broken
+	in 1.8-6 by introducing a test against deficit rank models (r47). 
+	
+	* cascadeKM: Calinski index works now when the input data is a
+	data.frame (r57, 58).
+
+	* flush.console: metaMDSiter and bioenv use now flush.console()
+	so that Windows people also see the trace (r56).
+
+	* ordispantree: made defunct, was deprecated in 1.8-1 (r38). 
+
+	* scores: handles now numeric data frames (r25).
+
+	* summary.cca: failed if only one type of scores was requested
+	(r50, 52).
+
+	* taxondive: Fixed dim checking and matching species names in
+	community data and taxonomic distance data (r21).
+
+	* tweaks to pass --pedantic R CMD check, mainly in formatting
+	source files, unused variables in source files and superfluous
+	braces in help files (r39, r46, r62).
+
+	* Updated FAQ-vegan.pdf to the current version at R-Forge.
+	
+Version 1.8-7 (August 24, 2007)
+
+	* Based on devel version 1.9-34.
+
+	* DESCRIPTION: M. Henry H. Stevens (Miami University, Oxford,
+	Ohio) joined the vegan team.
+	
+	* adonis: new function for nonparametric MANOVA that is
+	appropriate for even extremely wide matrices sometimes associated
+	with gene data and with diverse ecological communities. Author
+	Hank Stevens.
+
+	* taxondive: a new function for indices of taxonomic diversity and
+	distinctness after Clarke & Warwick (Mar Ecol Prog Ser 216,
+	265--278, 2001 and other papers). With a helper function
+	'taxa2dist' to turn taxonomies into distances with an option for
+	variable step length (Clarke & Warwick, Mar Ecol Prog Ser 184,
+	21--29, 1999), and a toy data set on the taxonomy of dune meadow
+	species ('dune.taxon'). With a help, testing and pressure from
+	Mike Cappo, James Cook Uni, Qld.
+
+	* bgdispersal: previous version was partly garbled (by me), and
+	P. Legendre provided a corrected one.
+
+	* designdist: keeps 'dist' attributes even when the 'method'
+	function drops them. Swapped the order to (terms, methods) in the
+	default name. 
+
+	* metaMDS: issues a warning if data are disconnected. Passes extra
+	arguments to other 'distfun' than 'vegdist' so that you can set
+	'terms' in 'designdist' etc (metaMDSdist). Can now do trymax=0 or
+	skip random starts and give you enhanced 'isoMDS' result
+	(metaMDSiter).
+
+	* ordiplot: failed if number of species was equal to number of
+	sites (and so did plot.metaMDS and plot.isomap using this).
+
+	* plot.profile.fisherfit: corrected a harmless error detected by
+	checkUsagePackage().
+
+	* predict.rda: removed some dead (but heavy) code from type =
+        "response".
+
+Version 1.8-6 (May 9, 2007)
+
+	* Based on devel version 1.9-23.
+
+	* as.mlm.cca, as.mlm.rda: new functions to refit constrained
+	ordination result (cca, rda, capscale) as a multiple response
+	linear model. You can find influence statistics (Cook's distance,
+	hat values) from the refitted model. You also can find t-values
+	etc., but these have the same bias as in other software and should
+	not be used.
+
+	* bgdispersal: a new function for dispersal direction in
+	biogeography (Legendre & Legendre 1998, section 13.3.4). Author
+	Pierre Legendre.
+
+	* designdist: a new function for defining your own dissimilarity
+	index or for estimating beta diversity (Koleff et al.,
+	J. Ecol. 72, 367-382; 2003).
+
+	* isomap: a new function for isometric feature mapping of
+	Tenenbaum et al. (Science 290, 2319-2323; 2000).
+
+	* screeplot, bstick: new functions to draw screeplots of vegan
+	ordination results with brokenstick lines, and alternative
+	screeplot functions for prcomp and princomp with brokenstick.
+	Author Gavin L. Simpson.
+
+	* swan: a new function for the degree of absence (Swan 1970,
+	Ecology 51, 89-102).
+
+	* anova.cca: now refuses to do 'by = "terms"' if the rank of
+	constraints is higher than the rank of the community matrix.
+	
+	* bioenv: gains argument 'partial' to perform partial bioenv.
+
+	* cca, rda, capscale: can now handle longer expression within
+	'Condition()' (ordiParseFormula). Used to drop observations with
+	missing values in unused variables (ordiGetData).
+
+	* goodness.cca, goodness.rda. 'statistic = "distance"' was wrongly
+	implemented. Now refuses to find "distance" in constrained
+	analysis: distances of constrained and unconstrained components do
+	not add up to to distances in unconstrained ordination.
+
+	* metaMDS (metaMDSdist): gains argument 'distfun' to use other
+	dissimilarity functions than vegdist.
+
+	* renyiaccum: used a variable that was not defined as an argument.
+	Added support functions persp.renyiaccum and rgl.renyiaccum
+	(Roeland Kindt).
+
+	* stressplot: R2's renamed to 'non-metric fit' and 'linear fit'.
+
+	* Doc: Corrected reference to Hurlbert in diversity (thanks to
+	Ralph Grundel). Updated references (varpart, renyiaccum). Removed
+	discussion on t-values in cca from vignettes, because as.mlm.cca
+	now implements those. General cleanup and better utf-8 encoding.
+	
+Version 1.8-5 (January 11, 2007)
+
+	* Based on devel version 1.9-12.
+	
+	* no.shared (manifest in metaMDS): prints thousands of lines of
+	debugging info that I forgot to deactive in release. Not fatal,
+	but extremely annoying.
+
+	* capscale: inertia name as "unknown" if the dissimilarity object
+	does not have a "method" name. Suggested by Roeland Kindt.
+
+	* DESCRIPTION: license is now explicitly GPL v2 (but not later).
+
+Version 1.8-4 (January 8, 2007)
+
+	* Based on devel version 1.9-10.
+
+	* cascadeKM: a new function to wrap kmeans and optimality criteria
+	for classification (Sebastien Durand, Pierre Legendre & Marie
+	Helene Ouellette).
+
+	* renyiaccum: a new function for Renyi (and Hill) accumulation
+        curves (Roeland Kindt).
+
+	* bioenv: bioenv.formula uses now "na.action = NULL" in
+        'model.frame', and bioenv.default passes arguments to 'cor' which
+        means that you can set NA treatment in 'cor' using argument "use".
+
+	* cca, rda: added "..." to formula versions to satisfy tests in
+        R-DEVEL. 
+
+	* cca, rda, capscale: used to fail if called within other
+	functions.  Now data always evaluated in the environment of
+	formula using new internal function ordiGetData.
+	
+	* anova.cca: checks that the model has both residual and
+        constrained components or stops with understandable error message
+        (used to stop with incomprehensible error message). 
+
+	* print.summary.cca, print.summary.decorana: have now arguments
+        'head' and 'tail' to print only a part of species and site
+        scores. Suggested by Gavin Simpson.
+
+	* metaMDS: checks now that the input data ('comm') is not a 'dist'
+        object (like many users have had).
+
+	* ordisurf: Does not depend on package 'akima' any longer, but
+	directly finds fitted values in a regular grid using
+	'predict.gam'.  Added pnpoly.c to find which of these values are
+	within the convex hull defined by data.  Results also look neater
+	with sparse data now.  Added argument 'labcex' passed to 'contour'
+	for changing size of contour labels.  Setting 'labcex = 0' will
+	suppress drawing labels (by setting drawlabels = FALSE in
+	'contour()').
+
+	* orditorp: handles now vector arguments of 'col', 'pcol', 'cex',
+        and 'pch'.
+
+	* rad.zipfbrot: less likely to overflow to NA coefficients during
+        iteration. 
+
+	* renyi: added a plot function, and documented together with
+        renyiaccum() instead of diversity().
+
+	* scores.default: Knows now about ade4 objects.  Primarily looks
+	for scores scaled by eigenvalues both for sites and species.
+
+	* specaccum: Added new conditioned method of Colwell et
+        al. with estimated sd based on extrapolated richness (Roeland
+        Kindt). 
+
+	* vegdist.c: More informative warnings with 'method' name (useful
+	with rankindex).
+
+	* DESCRIPTION: listed 'require()d' packages in the "Suggests:"
+	field to satisfy more anal tests in R-DEVEL.  Mention diversity
+	analysis in the "Description:".
+	
+Version 1.8-3 (Sept 29, 2006)
+
+	* Based on devel version 1.9-2.
+
+	* varespec.rda, varechem.rda: saved in binary form, because old
+	ascii form gave warning in R-2.4.0-rc.
+
+	* vegdist: added Chao index (of Jaccard type) that should take
+        into account missing pairs of species.  Checks that Binomial index
+        is non-negative.  Identical sites could have dissimilarity of
+        magnitude 1e-17 after some standardizations, but now values <1e-15
+        are zapped to zero.
+
+	* estimateR: uses now standard unbiased formulation of Chao. 
+
+	* renyi: should work now (really!).
+
+	* metaMDS: with zero = "add", zeros now replaced with
+	min(dis[dis>0])/2 (used to be 1E-4) (metaMDSdist).  Sets number of
+	tries also when this was not set previously (metaMDSiter)
+
+Version 1.8-2 (June 13, 2006)
+
+	* version 1.8-1 failed test in Windows because of a wrong encoding
+	name.  Explicit \enc added for non-ascii words.  Kurt Hornik and
+	Uwe Ligges diagnosed this and led me to see the light.
+
+	* similar to devel version 1.7-97.
+	
+Version 1.8-1 (June 12, 2006)
+
+	* Based on devel version 1.7-96. 
+
+	* Pierre Legendre joined the vegan team.
+
+	* beals: a new function for Beals smoothing.
+
+	* bioenv: added 'trace' argument.
+
+	* cca/rda/capscale: accept several 'Condition' elements in the
+	formula. 
+
+	* capscale: capscale(y ~ ., data=...) or expansion of "." on the
+	rhs works now. Documentation recognizes now db-RDA as the real
+	mother method.
+
+	* scores.cca, summary.cca etc: rewrite so that is cleaner and
+	easier to maintain. User visible changes are scaling by species
+	standard deviation (negative scaling) for 'rda', scaling=0
+        (no scaling) for all methods and slightly changed output and
+	improved user control in summary. These scalings actually were
+	documented in 1.6-10, although I dropped them just before the
+	release. predict.cca, predict.rda: work now with 'newdata' even
+	when not called with formula.
+
+	* anova.cca: new argument 'by' for tests of single terms or axes:
+	with by = "terms" performs individual test for constraints, and
+	with by = "axis" a separate sequential test for each axis. New
+	argument 'first' to analyse only the first axis instead of all
+	constrained variation.
+	
+	* intersetcor: new function for the interset correlation or the
+	(weighted) correlation between individual constraints (contrasts)
+	and invidual axes in cca/rda/capscale. (Not recommended.)
+
+	* decostand: does not automatically convert matrix to a
+	data.frame. NA handling more consistent now (thanks to Tyler Smith
+	for diagnosis). Adds attribute 'decostand' giving the "method".
+
+	* linestack: now really uses median as the midpoint with the odd
+	number of cases, and does not give superfluous warnings with three
+	or less items.  New argument 'labels' to replace the default text
+	in plot. The old argument 'label' renamed to 'side'.  However, the
+	function still works with the old syntax, but gives a warning if
+	the old argument 'label' is used for 'side'. Returns invisibly the
+	shifted positions of labels.
+
+	* metaMDS: 'postMDS' sets now attributes similarly when called
+        independently or within 'metaMDS'.  'metaMDS' forwards arguments
+        to 'postMDS' except 'halfchange'.  Change of phrasing in
+        'print'. Added handling of zero dissimilarities into
+        'metaMDSdist': either "fail" or "add" 1E-4 into zeros.
+	
+	* mrpp: new function for the multiresponse permutation procedure
+	(MRPP). Code by Henry Stevens (Miami Univ, Oxford, Ohio).
+
+	* ordiarrows: draws arrowhead only in the last segment. New
+        argument 'startmark' for marking the starting point of the arrow. 
+
+	* ordisurf: new arguments 'main' for the title and 'nlevels' and
+	'levels' for the number of contour or their values.
+
+	* orditorp: arguments for text colour and text character expansion
+	changed to standard 'col' and 'cex' from previous 'tcol' and
+	'tcex'. 
+
+	* procrustes: 'summary' prints now rotation matrix, translation
+        and scale, and honours 'digits'.
+
+	* prc: new functions for Principal Response Curves (PRC) of van
+        den Brink and ter Braak (Envir. Toxicol. Chem, 18, 138-148; 1999).
+        This is a special rda() model with dedicated summary and plot
+        functions. New data set 'pyrifos' to demonstrate 'prc'.
+
+	* radfit: added brokenstick as a null model (rad.null), removed
+	rad.veil (as it was a bad idea originally), corrected minor bugs
+	in rad.preempt (which did not fail gracefully).  Line colours
+	start from the point colour in plot.radfit.frame.  'print' uses
+	"g" format for coefficients and adds 'digits' argument. Added
+	'summary.radfit.frame' that simply prints each model.
+
+	* rankindex: uses now cluster:::daisy when 'grad' includes
+        factors.
+	
+	* spantree: now a method function with 'plot', 'lines' and
+	'cophenetic' methods. 'lines' replaces 'ordispantree'.  The plot
+	has a weird, new way of finding configuration for a spanning tree
+	from cophenetic distances (unpublished). Documented separately.
+
+	* specaccum: 'plot' honours now 'ylim'.
+
+	* specpool: Chao richness was wrongly defined, but now uses the
+	biased formula (error introduced in 1.6-5, correct earlier).
+	Failed with zero species or if there were no species that occurred
+	exactly one in the 'pool' (thanks to Emmanuel Castella, Geneve CH,
+	for the bug report).
+
+	* varpart: new functions for unbiased partitioning of variation by
+	two to four explanatory tables in RDA or linear regression.  The
+	author of these functions is Pierre Legendre & co (Univ
+	Montreal). New data sets 'mite', 'mite.env' and 'mite.pcnm' to
+	demonstrate the functions.
+
+	* vegandocs: new function to display *all* pdf documentation and
+	ChangeLog. This really should be in base R -- this is a kluge to
+	fill the hole.
+
+	* vegemite: added argument to 'select' a subset of sites. Drops
+        missing species from the table. Prints number of species and
+        number of sites and the used cover scale at the end of the table.
+        Passes arguments (i.e., 'maxabund') to coverscale().
+
+	* coverscale: added argument 'maxabund' to 'scale = "log"'.
+	Returns the name of the cover scale as an attribute for vegemite()
+	to print.
+
+	* vegdist: now first checks input and then transforms (if
+	needed). Thanks to Tyler Smith,
+
+	* Internal changes: permuted.index acceptes NULL strata as an
+	alternative to missing strata. ordispantreee deprecated.
+	spider.cca removed.
+
+	* Documentation: general cleanup in help files. New chapter on
+	t-values in cca/rda/capscale in vegan-FAQ. New pdf document on
+	partioning with varpart by Pierre Legendre & co. Non-latin
+	characters now use UTF-8 in documentation.  R manual says that you
+	should not use non-latin characters in help files, but that was
+	written by Englishmen. However, this seems to cause distress to
+	some users of a US West Coast OS (Windows), but OK with mainstream
+	OS's (Linux, MacOS). .
+	
+Version 1.6-10 (September 26, 2005)
+
+	* Based on devel version 1.7-77.  Checked with R 2.1.1 (stable)
+	and R 2.2.0 (alpha).
+ 	
+	* rda: negative scalings explicitly ignored and treated as
+	corresponding positive values.  Function summary.rda used to fail
+	with NA centroids.
+
+	* permutest.cca & anova.cca: permutation of 'cca' result now
+	re-weights environmental data properly with permuted community
+	weights (this breaks compliance with popular proprietary
+	software).  New default method 'direct' that always permutes the
+	data instead of residuals.  Now clearly faster basic routines, but
+	re-weighting in 'cca' is costly, and permutations may even be
+	slower than earlier in small data sets.  The permutest.cca returns
+	more data: constrained and residual total inertia, degrees of
+	freedom in the input model, and .Random.seed used in iterations.
+	Thanks to Pierre Legendre for pushing me to make this faster.
+
+	* ordination plot functions: obey now xlim and ylim.
+
+	* ordination text and points functions: a new argument 'select'
+	that can be used to select a subset of items, and a new argument
+	'labels' for text used instead of the default row names.
+
+	* points.cca, text.cca: biplot arrows will be scaled automatically
+	to fit the current graph if 'arrow.mul' is not given.  The new
+	behaviour is similar to the default in plot.cca and in
+	plot.envfit.
+	
+	* orditorp: a new "ordination text or points" function to add text
+	or points to an existing plot: adds text if this can be done
+	without overwriting other text labels, and points otherwise.
+
+	* linestack: a new function to draw labelled one-dimensional
+	diagrams without overwriting the labels (a primitive one, and
+	could easily be improved: submissions are welcome).
+
+	* ordirgl, orgltext: adapted to changes in rgl package version
+	0.65.  Workaround for older rgl packages, too.
+	
+	* decostand: Added Hellinger transformation. Empty columns and
+	rows become now 0 instead of NaN in most methods, except when the
+	input data contains negative values. Warns on input with negative
+	entries or on output containing NaN.  Has now argument
+	'range.global' for method 'range' based on the code supplied by
+	Tyler Smith.
+
+	* plot.radfit: puts now legend "topright" in R >= 2.1.0 (which has
+	this keyword).
+	
+	* read.cep: issues a warning if vegan was compiled with gfortran,
+	which has a bug that may corrupt the result.  The bug concerns
+	multiline input with T format modifier, and it was corrected in
+	http://gcc.gnu.org/ml/gcc-patches/2005-09/msg00126.html, but still
+	bugs most released versions of gcc.
+
+	* vegdist: new indices 'raup' and 'binomial'. Method 'raup'
+	implements probabilistic Raup-Crick index and is based on the code
+	submitted by Michael Bedward.  Method 'binomial' implements
+	Millar's index, officially published as "Binomial deviance as a
+	dissimilarity measure" (the C code has been in vegan for about two
+	years, but now I tell about it and add the public interface).
+	Method 'mountford' will give NA for any comparison involving an
+	empty site.  Warns about empty sites or negative entries with all
+	methods except 'euclidean' and 'manhattan'.
+	
+	* Documentation: added documentation of the cca/rda/capscale
+	result object. Dontruns used more neatly.
+	
+Version 1.6-9 (April 22, 2005)
+
+	* Maintenance release: 1.6-8 failed in R 2.1.0 patched and R 2.2.0
+	devel (works in R 2.1.0 release) due to problems in
+	as.preston. Based on devel version 1.7-62.
+
+	* as.fisher, as.preston: used table() in a way that failed in R
+	2.1.0 patched
+
+	* calibrate.cca: new function to predict or calibrate or
+	bioindicate the values of environmental constraints from
+	community composition (ordination).
+	
+	* decostand: new argument na.rm (defaults FALSE) for ignoring
+	missing values in row, column or matrix standardizations.
+
+	* vegdist: new argument na.rm (defaults FALSE) for pairwise
+	deletion of missing vaues in dissimilarity calculation.
+		
+Version 1.6-8 (April 18, 2005)
+
+	* Based on devel version 1.7-59.  Adapted to R 2.1.0 beta.
+
+	* DESCRIPTION: gives due credit to Roeland Kindt and Bob O'Hara as
+	co-authors. 
+
+	* documentation: updates in capscale, vegdist. vegan-FAQ adapted
+	to changes in Sweave in R 2.1.0.
+
+	* several methods assumed that input is count data, but silently
+	accepted floating point numbers and gave wrong results.  Now they
+	stop with error with non-integer input: fisherfit, prestonfit,
+	prestondistr, rarefy, fisher.alpha, estimateR.
+	
+	* bioenv: uses now 'cor' instead of 'cor.test', and does not give
+	so many superfluous warnings and is marginally faster.  Changed
+	printed output, so that gives 'call' instead of names of community
+	and environmental data, since bioenv.formula could not handle
+	these cleanly.
+
+	* capscale: has now argument 'add' to use an additive constant to
+	all dissimilarities so that all computed eigenvalues are
+	non-negative.  This is an argument of underlying 'cmdscale'
+	function, which implements the "Correction method 2" of Legendre &
+	Legendre (1998), p. 434.   
+
+	* decorana: checks now that there are no negative data entries.
+
+	* dune: cleaner site names.
+
+	* envfit: 'plot' now automatically scales arrows similarly as
+	'plot.cca' if 'arrow.mul' is not specified and arrows are added to
+	an old plot.  Has now a 'scores' function.
+	
+	* goodness.cca, predict.cca: documented separately.
+
+	* goodness.metaMDS: new function to assess pointwise goodness of
+	fit in metaMDS or isoMDS.
+
+	* humpfit: user can now give starting values of parameters.
+	'summary.humpfit' returns 'cov.unscaled' so that users can apply
+	'ellipse' function of 'ellipse' package to display approximate
+	confidence ellipses for pairs of parameters (with Normal
+	assumptions). 
+
+	* make.cepnames: No longer duplicates one component names, but
+	'abbreviate's them to eight characters.
+
+	* metaMDS: Split to independent metaunits 'metaMDSdist' and
+	'metaMDSiter'.  New function 'metaMDSredist' tries to reconstruct
+	dissimilarity matrices and transformations. 'postMDS' skips
+	halfchange scaling with too few points (with a warning) instead of
+	stopping with an error.  Prints now info about 'postMDS'
+	operations.  New 'scores' function.  Improved 'plot' function with
+	'display' argument and labelling of axes.  Argument 'shrink' to
+	undo expansion of species scores in plot or scores functions.
+	Workaround for a future bug in 'isoMDS' which drops names of
+	points in R 2.1.0.  Updates number of 'tries' with
+	'previous.best'.
+
+	* ordiplot: has now 'display' argument, so that only species or
+	sites can be plotted.
+
+	* ordiplot3d: a new function for 3D static ordination diagrams.
+
+	* ordirgl: new function for dynamic 3D graphics of ordination
+	results.  With support functions orglpoints, orgltext,
+	orglsegments and orglspider to add graphical items to dynamic
+	plots. Needs 'rgl' package.
+
+	* predict.cca, predict.rda: type = "wa" with 'newdata' works now
+	even when some species were removed from the original fit because
+	they were all-zero (missing).  Default now to 'model = "CA"' in
+	unconstrained analysis without "CCA" component.
+
+	* predict.decorana: a new function for 'decorana' results. Similar
+	to 'predict.cca' (but refuses to give impossible results).
+
+	* procrustes: obeys now 'choices' even when input is a matrix.
+	Plots now projections of rotated axes.  New argument 'scores' so
+	that can handle other than "site" scores.
+
+	* protest: passes now arguments to 'scores' so that now can handle
+	other than "site" scores on more than two dimensions.
+
+	* rda: handles now species with constant values (typically
+	missing or all zeros). 
+
+	* spenvcor:  new function to find the "species -- environment
+	correlation" in contrained ordination (cca, rda, capscale).
+
+	* stressplot: a new function to plot Shepard diagram for 'metaMDS'
+	or 'isoMDS'.
+
+	* summary.cca/summary.rda: print now call.
+
+	* vegemite: can now 'use' 'dendrogram' objects.
+	
+Version 1.6-7 (Jan 24, 2005)
+
+	* Based on devel version 1.7-42.
+
+	* plot.envfit did not plot vectors.  Thanks to Roeland Kindt and
+	Ron E. VanNimwegen for bug reports and fixes. 
+
+	* ordisurf obeys now keyword 'display', and '...' will transfer
+	arguments to 'scores'.
+
+	* ordisegments: obeys now keyword 'display'.
+
+        * ordigrid: works now.
+
+        * ordihull, ordiarrows, ordisegments, ordispider, ordiellipse:
+        have a new keyword 'show.groups' to show only specified groups.
+        With the help of this argument it is possible to use different
+        colours and linetypes for each group.  Further, it makes possible
+        to plot results of logical comparisons (such as A1 > 4) by setting
+        show.groups = T. Two user requests.
+
+	* new diagnostic and helper functions for 'cca', 'rda' and
+	'capscale': 'goodness' to estimate the proportion of inertia
+	accounted for or residuals for sites or species; 'inertcomp' to
+	decompose species and site inertia for conditioned, contrained and
+	residual componets; 'vif.cca' to estimate the variance inflation
+	factors for constraints and conditions; 'fitted' and 'residuals'
+	to approximate data by ordination scores; 'predict' to approximate
+	data or find site or species scores, possibly with 'newdata';
+	'coef' to find the regression coefficients. 'alias.cca' is now
+	similar to 'alias.lm' (simplified version of the latter).
+
+
+Version 1.6-6 (Jan 7, 2005)
+
+	* Based on version 1.7-34, but without still experimental
+	functions predict, fitted, vif & goodness for cca and rda
+	objects. 
+
+	* mantel: implemented partial mantel test (function
+	'mantel.partial'). Both 'mantel' and 'mantel.partial' should be
+	marginally faster and not give so many superfluous warnings.
+
+	* plot.envfit: should be more reliable now. A new keyword 'at' to
+	position the bunch of arrows in other places than the origin.
+	Thanks to Roeland Kindt for fixes.
+
+	* rankindex: Default correlation now "spearman" since the older
+	default ("kendall") was far too slow in large data sets.  Should
+	not give so many superfluous warnings.
+
+	* summary.rda: Site scores were wrong with 'scaling = 3'.
+	Influences 'plot' and 'scores' commands for 'rda' and 'capscale'
+	results with 'scaling = 3'.
+
+	* vegdist: Issues a warning if 'method = "morisita"' is used with
+	non-integer data.
+	
+Version 1.6-5 (Oct 12, 2004) 
+
+	* Based on version 1.7-27. Checked with R-1.9.1 (Linux, MacOS X)
+	and R-2.0.0 (Linux, patched version in Windows XP). Passed other
+	tests, but some examples in 'humpfit' failed in Windows XP, and
+	are not run on that platfrom. General cleanup in documentation.
+	Does not 'require(mva)' any longer.
+
+	* anosim: corrected the equation in docs (function was
+	correct). Thanks to Yong Cao for notifying this.
+
+	* bioenv.formula: finds now variables from attach'ed data.frames
+	and 'data' need not be specified.
+
+	* capscale & deviance.rda: capscale was modified so that its
+	result could be handled with step (added a terms component).
+	Function deviance.capscale was deleted so that deviance.rda will
+	be used. A literature reference to AIC in CCA/RDA was added to the
+	documentation.
+
+	* cca/rda/capscale: Small eigenvalues are made to zero and rank
+	reduced accordingly. Most often influences 'capscale'.
+	
+	* cca/rda/capscale: Now alias constraints that are collinear with
+	other constraints or conditions in partial analysis. New function
+	'alias.cca' to print aliased contrasts. NB this does not influence
+	the proper ordination results, but only to the selection of biplot
+	scores and centroids displayed. 'summary' no longer gives a
+	redundant warning.
+
+	* decorana: removes empty species with a warning instead of
+	stopping with error. Still error with empty sites. The behaviour
+	is similar to 'cca'.
+
+	* envfit (vectorfit, factorfit): Has now a formula interface.
+	Bottlenecks in permutation changed now into C functions. Much
+	faster, in particular 'factorfit' which was 25 times faster in my
+	tests.  plot.envfit could drop names (dimensions). Now honours
+	'scaling' argument in cca/rda/capscale (used to 'scaling = 2'
+	always).
+
+	* envfit, ordisurf: have now weights parameter 'w'. Weights are
+	used for the results of 'cca' and 'decorana' as default, or they
+	can be supplied by the user. In this way, envfit gives equal
+	results to biplot scores and centroids in 'cca', and ordisurf is
+	consistent with envfit. Both can now access 'lc' scores of 'cca'
+	etc. 
+
+	* estimateR:  Abundance-based estimators of extrapolated richness,
[TRUNCATED]

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