[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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svnlook diff /svnroot/vegan -r 2031
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