/usr/lib/R/site-library/vegan/ONEWS

-*-Text-*-

			VEGAN RELEASE VERSIONS 
		       	======================

		       CHANGES IN VEGAN 1.17-12

    - This is a maintenance release which improves robustness of
      several functions. A major release is expected soon.

    - tolerance.cca: a new function to find the species response
      widths (a.k.a. tolerances) and sample heteregeneities from a
      cca() result.

    - adonis: much faster.

    - betadiver: argument 'index' was renamed to 'method' so that the
      function can be used similarly as dist(), vegdist() and other
      distance functions. This allows using betadiver() as a distance
      function in metaMDS().

    - cca/rda/capscale: handling of aliased and other zero-rank
      components changed in vegan 1.17-11, but not all support
      functions were adapted to these changes in that release. Now the
      following functions cope with the changes and are more robust:
      capscale, anova.cca, bstick.cca, goodness.cca, predict.cca,
      screeplot.cca, calibrate.cca, deviance.cca/rda, ordiplot3d,
      ordiresids, ordirgl, ordixytplot.

    - isomap: text or points are plotted more cleanly, and text uses
      ordilabel(). 

    - make.cepnames: a bit more flexible and robust, with a new
      argument that allows selecting first and second name component
      instead of first and last.

    - metaMDSrotate: rotation could be slightly off with more than two
      dimensions when there are NA scores.

    - ordiellipse, ordihull, ordispider, orditorp: accept NA scores.

    - ordilabel: gained argument 'select'. 

    - ordiplot: better handling of graphical arguments, arg 'cex' can
      be set by the user.

    - swan: gained new argument 'maxit' that allows setting maximum
      number of iterations. Defaults 'maxit = Inf' or the current
      behaviour of continuing as long as there are zeros that can be
      filled. 

                      CHANGES IN VEGAN 1.17-11

    - This is a maintenance release which improves the robustness of
      several functions but introduces no new important features.

    - cca/rda/capscale: handling of aliased and other zero-rank
      components changed. They are no longer made NULL and left
      undisplayed, but now they are shown as zero rank. The general
      output also changed so that proportions of inertia are only
      shown if there are conditions or constraints, but not for
      unconstrained analysis. The capscale() function no longer shows
      species scores if these are unavailable. Several support
      functions more robust.

    - nobs: R 2.13.0 introduced generic function nobs() to find the
      number of observations, and this release provides nobs() for
      several vegan results. (This does not make vegan dependent on R
      2.13.0, but vegan works with older R as well.)

    - prc: allows anova(..., by = "axis") and other 'by' cases for
      prc() results. Some rda() support functions still fail, but now
      they stop informatively.

    - specaccum: gained argument 'groups' which can be used to find
      the number of species in subsets of the data.

		       CHANGES IN VEGAN 1.17-10

    - This is minor revision that mainly fixes vegan with respect to
      changes in the currently released R 2.13.0. Most importantly,
      cmdscale() output changed in R 2.13.0 and because of this
      capscale() could fail in some rare situations with argument 'add
      = TRUE'. This vegan bug made BiodiversityR package fail its
      tests in R 2.13.0. 

    - metaMDSrotate: gained argument na.rm = TRUE.

                       CHANGES IN VEGAN 1.17-9

    - anova of cca/rda/capscale results gave wrong results in partial
      models. The bug was introduced in vegan 1.17-7. 

    - diversity and related functions rarefy, rrarefy and specnumber
      now accept vector input. Earlier a single site had to be
      analysed either as a single-row matrix or using the non-default
      setting MARGIN = 2.

    - drarefy: new function that returns a matrix of probabilities
      that a species occurs in a rarefied sample of a given size.

    - metaMDS: it is possible to supply a starting configuration with
      argument 'previous.best'. A previous metaMDS or isoMDS result can
      also be given as a starting configuration. If the starting
      configuration has a higher number of dimensions than requested,
      the extra ones are dropped, and if the starting configuration
      has fewer dimensions, random scores for extra dimensions will be
      added. This may help in running metaMDS over a range of
      dimensionalities. 

    - metaMDSrotate: can now rotate metaMDS solutions with any number
      of dimensions so that the first axis is parallel to a fitted
      environmental vector. Previously, only two dimensional solutions
      worked.

    - ordilabel: gained argument 'xpd' that allows labels outside the
      plot area. This allows labels above axes, for instance.

    - ordisurf: gained several new arguments to control the mgcv::gam
      fitting. Also gained an argument to suppress plotting, and a new
      plot method. The fitted model can be specified with a formula. 

    - prestonfit and friends: default is now 'tiesplit = TRUE' (which
      was a new feature introduced in vegan 1.17-8).

                       CHANGES IN VEGAN 1.17-8

    - prestonfit: fixed a bug in as.preston(): the largest octave
      could be missing with 'tiesplit = TRUE'.
    
    - decorana: spurious axes scores and eigenvalues could be reported
      when the eigenvalues actually were zero. This was rarely a
      problem with real data, but occurred only in arbitrary examples.

    - procrustes: checks input.

                      CHANGES IN VEGAN 1.17-7

    - anova.cca: more robust when models were fitted without 'data'
      argument, or when 'na.action' or 'subset' was used.

    - capscale: implemented 'subset' in model definition. Additive
      constant with 'add = TRUE' is taken into account in predict()
      and fitted(). Implemented simulate() which returns a
      dissimilarity matrix with random error about predicted values. 

    - eigenvals: can now extract eigenvalues of some ade4 and labdsv
      result objects. 

    - nestednodf: did not use binary data when weighted = FALSE was
      used together with order = FALSE. Reported by Daniel Spitale.

    - prestonfit: gained option to split tied frequencies (1, 2, 4, 8,
      etc.) between adjacent octaves.

    - specaccum: implemented choice of using either "individuals" or
      "sites" as x-axis in plot(). Corrected a typo in the result
      object: now returns indeed "individuals".

 
		       CHANGES IN VEGAN 1.17-6

    - capscale: vegan 1.17-5 defined total inertia as the sum of
      absolute values of eigenvalues which changed the total inertia
      from previous versions. This is changed so that the total
      inertia is the sum of all eigenvalues, i.e., negative
      eigenvalues are subtracted from the total which was the
      definition in 1.17-4 and earlier. The proportions of inertia
      components are now expressed for non-negative eigenvalues only,
      and a new item "Real Total" (sum of positive eigenvalues) is
      added to the output if there are negative eigenvalues
      ("Imaginary" component). The function no longer returns the
      negative eigenvalues.

    - CCorA: scaling of object scores changed: they are no longer
      divided with sqrt(n-1). Minor fixes for improved robustness.

    - metaMDS: automatically changes some arguments to non-default
      values if input data contains negative entries. Help page gives
      advice to do so for non-community data.

    - wascores: checks that input weights are non-negative.

	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-5				   		    	    
    - anova.cca: Empty models with no constrained component have
      correct degrees of freedom. Tests 'by = "axis"' are really
      marginal for all axes (first axis used to be non-marginal to
      latter axes).

    - as.mlm.cca/rda, intersetcor, vif.cca: avoid bug in qr.X in R
      2.12.0 which use wrong variable names in aliased models (fixed
      also in R 2.12.1).

    - betadisper: plot did not allow selecting axes. Reported by Sarah
      Goslee. 

    - capscale: failed with NA action (reported by Nevil Amos). Total
      inertia is defined as the sum of absolute values of all
      eigenvalues consistently with cmdscale (from R 2.12.1) and other
      vegan functions.

    - cca/rda/capscale: print proportions of inertia components. 

    - decorana: Fortran code prints warnings of failed convergence.
      Default plot() uses points if items have no name labels to be
      plotted.

    - deviance.cca/rda: return 0 (instead of NA) for over-paremetrized
      models with no unconstrained component.

    - eigenvals: uses sum of absolute values of eigenvalues in models
      that may have negative eigenvalues (cmdscale, wcmdscale,
      capscale). Can extract eigenvalues of pcnm() and cmdscale() of R
      2.12.1. Uses zapsmall() to print near-zero
      eigenvalues.

    - mantel.correlog: P-values could slightly off. The function uses
      internally mantel() to evaluate the statistic and its
      significance. The mantel() function adds one both to the
      denominator and numerator, but mantel.correlog() did not notice
      this and made the addition for the second time. When the
      mantel.correlog() reported a positive value of the statistic, it
      reversed the direction of the one-sided test of mantel(), but
      did not handle tied values correctly in this reversal.
   
    - nestednodf: Gustavo Carvalho's new version that also implements
      a new quantitative method of Almeida-Neto & Ulrich (Env Mod
      Software, 26, 173-178; 2011).

    - oecosimu: takes care that the statistic is evaluated with binary
      data when null models are binary (regression introduced in vegan
      1.17-0). Can handle NA values in permutations (as na.rm = TRUE).

    - ordilabel: gained new argument 'col' to set the text colour of
      the labels separately from 'border'. Function ordiellipse() uses
      this in filled polygons to set the colour of labels to that of
      borders or foreground instead of the colour of the fill.

    - ordiR2step: new function to model selection in rda() and
      capscale() based on adjusted R2 following the recommendations of
      Blanchet, Legendre & Borcard (Ecology 89, 2623-2632; 2008).

    - ordistep: correct a name clash when the fitted model had term or
      item called 'mod'. Reported by Richard Telford (Bergen, Norway).

    - pcnm: returns the truncated distanced matrix with argument
      'dist.ret'.
      
    - prc: rewritten by Cajo ter Braak with a fix to scaling of
      coefficients for full compatibility with Canoco. 

    - procrustes: Fixed translation following the report and fix by
      Christian Dudel (Bochum, Germany). New predict() method to
      rotate 'newdata' points to the target. Graphics with plot()
      select the direction of arrows with new argument 'to.target',
      and use ordilabel() to display the labels with 'type = "t"'.

    - rankindex: can take a list of dissimilarity functions as the
      argument to allow the use of other dissimilarity functions than
      vegdist() of vegan.
 
    - rda/capscale: the scores() can take two scaling constants
      ('const'). One is used for species, second for WA and LC scores
      of sites. This allows using scalings of prcomp(), princomp() or
      Canoco (like documented in the design decisions vignette).

    - swan: disconnected data caused infinite loop. Now zeros are left
      to the result with disconnected data.

    - treedist: can handle empty or one-node trees. Gained new
      argument 'relative' (defaults TRUE): if FALSE, finds raw
      dissimilarities of tree heights.  Help page tells that relative
      tree distances are in range 0..2 instead of 0..1, since
      combining two trees may add a new common root.

    - treedive: handles trivial cases of zero (diversity NA) or one
      species (diversity 0).

    - vegdist: help page gives now binary variants of the indices
      using designdist() notation.

    - vif.cca: can handle models with aliased terms.

    - wcmdscale: returns goodness of fit statistic (item GOF) and
      handles negative eigenvalues consistently with cmdscale() and
      capscale().

	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-4

    - MOStest: a new set of functions to implement generalized
      Mitchell-Olds & Shaw test for the location of the quadratic
      extreme in a given interval. The test can also be used for the
      location of the optimum of the Gaussian response model. In
      addition to the basic test, there are Fieller and deviance
      profile methods for the confidence interval of the location of
      the quadratic extreme or Gaussian optimum.

    - mrpp & meandist: mrpp() does not evaluate the Classification
      Strength (CS) of Van Sickle & Hughes (J. N. Am. Benthol. Soc.,
      19: 370-384; 2000) any longer. The old version misinterpreted
      the weighting scheme of CS, and with correct scheme there is no
      exact relationship between CS and the corresponding MRPP
      statistic and therefore permutation tests are not available. CS
      is still evaluated in meandist(), but with corrected weighting
      scheme, and no tests are performed. Reported by Dr John Van
      Sickle (Corvallis OR). 

    - msoplot: legend text was in a wrong order. Reported by Daniel
      Borcard. 

    - vegdist: Marti Anderson variant of the Gower distance (method =
      "altGower") should be without range standardization. Reported by
      Sergio Garcia. 

    - ordiellipse: labels disappeared in their background with 'draw =
      "polygon"'. 

    - predict.cca and predict.rda: gained argument 'newdata' for 'type
      = "response"' and 'type = "working"'.  These return estimates
      of the response data, or dissimilarities in capscale().
  

	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-3

    - adonis: handles ties correctly.

    - anova.cca and permutest.cca: permutations of cca result is
      faster and now nearly equally fast (or slow) in rda and cca. 

    - betadisper: 'type = "median"' (the default) was not computing
      the spatial median on the real and imaginary axes separately.
      Reported by Marek Omelka.

    - cca, rda and capscale failed when Condition() was a factor, but
      the constraints had only continuous variables.

    - envfit: defaults to use 999 permutations instead of skipping
      permutations. 

    - mantel and mantel.partial: faster permutation.

    - mantel.correlog: upgraded and faster.

    - ordiarrows, ordisegments and ordispider gained argument 'label'
      to label the groups corresponding to drawn arrows or lines.

    - ordiresids: de-weights residuals and fitted values in CCA so
      that these are identical to the values shuffled in simulate.cca.

    - permutest.cca: adds observed statistic among permutations when
      printing the result (does not influence anova.cca or
      calculations).

    - RsquareAdj: The 'rda' method used wrong number of degrees of
      freedom in rank deficit models (number of dependent variables
      was lower than the rank of constraints and conditions). Default
      method handles vector input.

    - scores: default method works with one row of scores. The scores
      of "cca" and "rda" methods always have names, even if there are
      no names in the input data.

    - Permutation tests: The available permutation tests are described
      in a new help files accessed via ?permutations.

		     NEW FEATURES IN VEGAN 1.17-2

    - permutest.betadisper: printed P-values in a wrong order in
      displaying the the matrix of pairwise tests (the values were
      correct, but formatting failed). Reported by Dan O'Shea.

    - nesteddisc: failed if the most species rich sites were tied. The
      function is now much faster (though still slow), but the price
      is that it does not try as hard to find the optimal ordering.

    - screeplot.cca & friends: new argument 'legend' for all methods
      (except 'decorana') to draw a legend if the observed and broken
      stick distribution are both plotted. 

    - ordistep: adds an 'anova' item to the final model similarly as
      the standard step(). You can suppress the tracing ('trace =
      FALSE'), and find the model build history save in 'anova' in a
      compact form.

    - densityplot.oecosimu: gave warnings when there was only one
      statistic and hence one lattice panel. 

    - predict functions for cca and rda objects match 'newdata' by
      dimension names instead of index.

    - simulate.rda and simulate.cca have new argument 'rank' which
      allows using lower rank presentation of fitted values
      (including rank = 0). 

    - treedist: new function to find dissimilarities of species
      property trees of communities. The property trees can be, e.g.,
      functional diversity trees, taxonomies or phylogenies. Similar
      in spirit to UniFrac distance (C. Lozupone & R. Knight, Appl
      Environ Microbiol 71:8225-8235; 2005), but completely different
      in design and works only with binary data.

		NEW FEATURES AND FIXES IN VEGAN 1.17-1

    - multipart: new functions for multiplicative partionining of
      gamma diversity into alpha and beta diversity components. 

    - CCorA: Fixed choice of scores in biplots -- Used PC scores
      instead of observed scores in the right-hand-side biplot
      panel. The biplot function has several new and enhanched
      alternatives of plots.

    - envfit: ignored weights in cca() results for factors or a single
      continuous variable.  The bug was introduced with NA handling
      upgrade in vegan 1.17-0. The problem with fitted vectors was
      reported by Richard Telford (Bergen, Norway).


	       CHANGES AND NEW FEATURES IN VEGAN 1.17-0

    - Guillaume Blanchet joined the vegan team.

    - New function to partition data-set diversity (gamma) into
      within-plot (alpha) and between-plot (beta) diversity
      components. Function adipart performs additive
      partitioning (gamma = alpha + beta). Function hiersimu performs
      hierarchical null model testing similar to adipart but by using
      custom function to calculate statistics for levels of a hierarchy.

    - Subsets and missing value handling added to constrained
      ordination methods cca(), rda() and capscale(). The missing
      values (NA) can be handled with setting na.action (defaults
      na.fail). With na.action = na.omit, observations with missing
      values are removed, and with na.action = na.exclude they are
      kept, but scores may be NA. However, the WA scores for sites are
      available in non-partial models with na.action = na.exclude.
      The 'subset' can be defined using any variable in the
      constraining data set or species in the dependent data.

    - Functions for fitting environmental variables onto ordination
      (envfit, ordisurf) are aware of missing values in constraints or
      NA values in scores. The ordination plot functions also can
      handle NA scores.

    - New and upgraded quantitative null models. In particular,
      quantitative swap models (function abuswap) allows generetating
      null matrices where marginal totals and fill are fixed, or row
      and column fills are fixed, or row and column fills and either
      row or column totals are fixed.

    - oecosimu: rewritten to handle quantitative null models. Gained
      keyword 'alternative' for "two-sided", or "less" and "greater"
      one-sided tests. More robust with degenerate solutions. The
      'method' can now be a user-supplied function. New support
      functions as.ts() and as.mcmc which transform sequential models
      into form that can be analysed using tools for time-series
      (as.ts()) or MCMC sequences of the 'coda' package (as.mcmc).

    - calibrate: calibrate is now a generic function with a new method
      calibrate.ordisurf() in addition to the old calibrate.cca. These
      find the estimates of environmental variables from ordination.

    - ordistep: stepwise selection of terms in constrained ordination
      (cca, rda and capscale) using permutation tests instead of
      pseudo-AIC that is used by the standard step() function.

    - pcnm: new function to find weighted principal coordinates of
      neighbour matrix (PCNM) from distances between points. These are
      typically used for spatial filtering in constrained
      ordination. The function uses weighted analysis and can
      therefore produce PCNM for correspondence analysis in addition
      to PCA and RDA.

    - betadisper: can use spatial medians which are now the default
      method. Preliminary tests indicate that spatial medians correct
      the anti-conservative Type I errors reported by Stewart
      Schultz. 

    - decostand & vegdist: new transformation 'log' which implements
      Marti Anderson's scaling log(x) + 1 for x>0 (which is not at all
      the same as log(x+1)), and vegdist has alternative Gower
      function that skips double zeros. Together these implement the
      "modified Gower" distance of Anderson et al. (Ecology Letters 9,
      683-693; 2006).  Feature request #473 by Etienne Laliberte in
      vegan.r-forge.r-project.org.

    - model.matrix.cca & model.frame.cca: new functions to reconstruct
      the model frame and model matrix (model matrices in partial
      models) of constraints used in ordination methods cca(), rda()
      and capscale().

    - simulate.cca & simulate.cca: simulate the community (response)
      data from the result of cca() or rda() under alternative
      hypothesis. Error is added to the fitted values from
      ordination. The function uses either Gaussian error or permutes
      residuals and adds these to fitted values. 

    - spandepth: a new function to find the depth of each node in the
      minimum spanning tree produced by spantree(). Feature request by
      W. E. Sharp. 

    - alias.cca: gained argument names.only.

    - metaMDSrotate: a new function to rotate metaMDS so that first
      axis is parallel to an environmental variable. 

    - msoplot: uses standard legend. 

    - nesteddisc: new method that tries to find the smallest possible
      value of the statistic in tied data. Slow, but fixes the
      problems of the published method. The problem with tied values
      in nesteddisc was found with Carsten Dormann. 

    - contribdiv: gained a plot method. 

    - rarefy: failed with one site and many sample sizes like
      rarefy(rpois(10, 2), sample=2:3).

    - meandist: plot can draw histograms as an alternative to
      dendrograms. 

    - plot functions for 'decorana' and 'cca' and friends and
      'ordiplot' use 'linestack' if only one axis was requested.


		       CHANGES IN VEGAN 1.15-4

    - Changed package dependence: vegan does not depend on 'ellipse'.

    - anosim: user interface identical to 'mrpp'. Accepts now data
      matrix and finds dissimilarities internally.

    - betadisper: fix removal of zero eigenvalues with non-Euclidean
      distances. This may change the results slightly, but in most
      cases the effects are minor or none.

    - capscale: has now 'fitted' and 'residual' methods, and 'predict'
      works with 'type = "response"'. These return dissimilarities
      that produce the same ordination as the original data. 

    - indpower: new function to find the indicator power of species to
      predict presence of other species (Halme et al., Conservation
      Biology 23, 1008-1016; 2009). Closely related to the the power
      to predict probabilities in beals().

    - mantel.correlog: new functions to produce multivariate Mantel
      correlograms (Legendre & Legendre, Numerical Ecology, section
      13.1.5; 1998). 

    - metaMDS: accepts user-supplied dissimilarities. Species scores,
      data transformation, step-across and half-change scaling are
      unavailable with user-supplied dissimilarities, but random
      starts, PC rotation and scaling to original range of input
      dissimilarities work.

    - nestedtemp: row and column labels can be turned on/off
      independently in plots.

    - ordihull & ordiellipse: new argument 'label' to plot group names
      for hulls or ellipses. Return (invisibly) the data for plotted
      convex hulls or ellipses. In 'ordihull' this is a list of hull
      vertices, and in 'ordiellipse' a list of (scaled) covariance and
      centre data for ellipses. New 'summary' methods find the centres
      and areas of plotted hulls or ellipses. Argument 'draw' has new
      option "none" that suppresses all drawing so that only the data
      for summary can be extracted without plotting.

    - orditorp: works with reversed axes, like with 'xlim = c(3, -3)'.

    - ordixyplot: has a panel function for arrows: a lattice variant
      of ordiarrows.

    - poolaccum, estaccumR: new functions to find the specpool() or
      estimateR() estimates of extrapolated species richness in random
      accumulations of sites. These have 'plot' and 'summary' methods.

    - scores: functions biplot, points, text, ordilabel, ordiplot3d,
      ordixyplot and spantreee did not pass all arguments to scores()
      function. In particular, this concerned rda where 'scaling' and
      'const' arguments could not be used within these functions.

    - radfit: new function 'radlattice' for a lattice plots of fitted
      models for a single site.

    - rrarefy: a new function to generate random rarefied communities.

    - RsquareAdj: now a generic function to find adjusted R squared
      with special cases to 'rda', 'cca', 'lm' and 'glm'. 

    - summary.cca: cleaner output.

    - wcmdscale: returns scaled scores for axes with negative
      eigenvalues. 
    

			CHANGES IN VEGAN 1.15-3

    - anosim, mantel, mrpp, protest, envfit: did not include the
      observed statistic among permutations. Functions adonis and
      permutest.cca did this correctly, but did not print results
      neatly. 
      
    - anova.cca: name clash if data were indexed with 'i'.

    - capscale: fixed handling of negative eigenvalues with
      non-Euclidean distances. The total inertia is the sum of all
      eigenvalues so that negative eigenvalues are subtracted from the
      total. The total inertia of negative components and their rank
      (number) is given as 'Imaginary' component, and the negative
      eigenvalues are listed after unconstrained positive eigenvalues.
      The procedure is based on Gower, Linear Algebra and its
      Applications 67, 81-97 (1985).  New argument 'sqrt.dist' takes
      square root of the internally calculated dissimilarities and
      avoids negative eigenvalues with some indices, such as vegan
      Jaccard and Bray-Curtis. The adjustment is corrected for indices
      with upper limit of one, and the reported eigenvalues and
      inertia components are reduced by a factor of sqrt(n-1) and are
      similar to those reported by 'cmdscale' or 'wcmdscale'.

    - eigenvals: a new function to extract eigenvalues from rda, cca,
      capscale, wcmdscale, prcomp, princomp, svd or eigen. If the
      result object contains squareroots of eigenvalues, they are
      squared. The summary method also finds proportions and
      cumulative proportions explained. Function summary.cca now uses
      this to display eigenvalues.

    - kendall.global: could get wrong counts of ties in large data
      sets. 

    - meandist: new sister function to 'mrpp' that finds mean
      within-group and between-group dissimilarities. The summary
      function finds overall averages of these, and returns all three
      MRPP variants plus classification strength. The plot method
      draws a dendrogram based on the mean dissimilarity matrix, with
      leaves hanging to within-groups dissimilarity. The functions
      follow Sickle, J. Agric. Biol. Envir. Stat. 2, 370-388 (1997). 

    - ordisurf: fits now linear or quadratic trend surfaces if 
      'knots' argument is set to 0, 1, or 2. 

    - orditkplot: copes with NA and NaN scores.

    - ordixyplot: mixed x and y axes for biplot arrows and class
      centroids. Function failed in constrained ordination. 

    - tsallis: gained argument 'hill' to find results analogous to
      Hill numbers in renyi(), or the species number equivalents of
      indices.  

    - wcmdscale: removes now zero eigenvalues instead of the last
      eigenvalue. The bug was copied from cmdscale(), which still has
      the bug in R 2.9.0 (plus another that was not copied to
      wcmdscale).


		       CHANGES IN VEGAN 1.15-2
    
    - adonis: adds one to numerator and denominator of permutation
      tests, the default number of iterations was raised from 5 to
      999, and the result object got a 'terms' component. Uses much 
      less memory  allowing analysis of larger problems.

    - anova.cca: anova(..., by = "axis") gained new keyword 'cutoff'
      to stop permutation tests after exceeding the given cut off
      level of significance. The second term of anova(..., by =
      "margin") used different random numbers than other terms.
    
    - beals: Completely rewritten by Miquel de Caceres.  Knows now
      also the cross validated version of Beals smoothing and other
      choices described by De Caceres & Legendre, Oecologia 156,
      657-669; 2008.

    - betadisper: handles missing values both in dissimilarities and
      grouping. 

    - cca/rda: cleaner output of summary() in unconstrained models.

    - commsimulator: simulated result retains original row and column
      names. 

    - contribdiv: new function for contribution diversity (Lu et al.,
      Basic and Applied Ecology 8, 1-12; 2007).

    - decostand: gained dots in argument list, so that
      stressplot(metaMDS(x, dist = "gower", trymax = 40)) works.

    - dispindmorisita: new function for the Morisita index of
      dispersion. See Krebs, Ecological Methodology; 1999.

    - kendall.global and kendall.post: new functions for Kendall's
      coefficient of concordance. In ecology these can be used to
      identify significant species associations (Legendre, J Agric
      Biol Environm Stat 10, 226-245; 2005).

    - metaMDS: more robust with distances like Euclidean and Manhattan
      which have no upper limit. The stepacross works correctly for
      these, but gives a warning that its use may not be sensible.
      There is a better heuristics to avoid half-change scaling with
      these indices. The 'halfchange' argument is now honoured when
      given in metaMDS() call.

    - mrpp: returns within-class dissimilarities. Evaluates
      classification strength (Van Sickle, Biological and
      Environmental Statistics, 2, 370-388; 1997) if weight.type = 3
      was used.

    - nestednodf: new nestedness function of overlap and decreasing
      fill (Almeida-Neto et al., Oikos 117, 1227-1239; 2008). Coding
      by Gustava Carvalho.

    - ordirgl: no more superfluous warnings with type = "t". 

    - ordisurf: gained an argument 'bubble' to draw bubble plots, or
      vary point sizes according the value of the observed variable.
      The (invisible) return object now has an item 'grid' for the
      fitted value and grid values.

    - orditkplot: can produce TIFF graphics, if installed R has this
      capability.

    - procrustes: new text() function.

    - radfit: broken-stick model (function rad.null) failed with
      Gaussian and Gamma error families. The plot.radfit command
      gains argument log = "y", which allows using arithmetic scales
      or log-log scales where Zipf model is a straight line.

    - spantree: retains names and uses labels in plot.

    - datasets: Oribatid mites (data 'mite') got taxon names.

    - help files updated, and do not raise errors or warnings with the
      Rd parser version 2 in R 2.9.0.

		       CHANGES IN VEGAN 1.15-1

    - betadisper and related functions now work when the 'group'
      argument represents a single group/level.

    - decorana: 'text' function failed.

    - cca/rda/capscale: cleaner handling of results with missing
      (NULL) row or column names, also in plots.

    - cca/rda/capscale: new functions 'head' and 'tail' for 'summary'
      of cca results to show only some rows of the scores.

    - nestedness: method nesteddisc was found to be strongly dependent
      on the ordering of tied column (species) frequencies. A warning
      is now issued, and development version of vegan in
      http://vegan.r-forge.r-project.org/ has an experimental function
      that tries to find the optimal ordering.

    - permatfull: 'row'/'column' arguments were mixed.

    - radfit: all methods work consistently for communities of 0, 1 or
      2 species.

    - wcmdscale: typo in the result object items corrected.

		       CHANGES IN VEGAN 1.15-0

GENERAL

    - Peter Solymos joined the vegan development team.

NEW FUNCTIONS

    - add1.cca and drop1.cca: functions to implement permutation tests
      with argument test = "permutation". Function drop1.cca uses
      anova.cca(..., by = "margin") and add1.cca implements a new type
      of analysis for single term additions.

    - ordilabel: new alternative for cluttered ordination plots.  Text
      is written on opaque labels. The texts still cover each other,
      but at least the uppermost are readable, and the ordering can be
      controlled by 'priority' argument. Similar to 's.label' in ade4
      package.

    - ordipointlabel: new alternative for cluttered ordination plots.
      Points are in fixed positions, but their text labels are
      located to avoid overplotting. The optimization uses simulated
      annealing of 'optim' function. Returns an "orditkplot" object so
      that the results can be edited with 'orditkplot'. Similar to
      'pointLabel' function in maptools package. 

    - permatfull, permatswap: functions to permute quantitative count
      data.

    - treedive: estimation of functional diversity defined as the
      height of the dendrogram of species properties (Petchey & Gaston,
      Ecology Letters 9, 741-758; 2006). With a helper function
      'treeheight' to find the height of a 'hclust' dendrogram.

    - tsallis: Tsallis entropy family as an alternative to 'renyi'. 

    - wcmdscale: weighted metric scaling a.k.a. weighted principal
      coordinates analysis; only uses row weights.  

NEW FEATURES AND FIXES

    - anova.cca: default permutation model changed from "direct" to
      "reduced" after Pierre Legendre demonstrated that model
      "reduced" was superior in term of Type I error.

    - anova.cca: handles smoothly models where constrained or
      unconstrained models are NULL and the tests are impossible (used
      to stop with error). 

    - anova.cca(..., by = "margin") was handling wrongly 'x' in
      '~Condition(x) + x + z', or model formulae where same variables
      where used both as conditions and (aliased) constraints.

    - cca/rda/capscale: improved robustness in the formula
      interface. Partial handling of "cca" objects produced by
      ade4:::cca. 

    - commsimulator: swap, trial swap and quasiswap written in C and
      *much* faster (100x in some tests). 

    - oecosimu: accepts now a vector of statistics, and the user can
      give the name of the statistic in the function call.

    - ordiplot: did not use partial matching for "sites" and
      "species". 

    - orditkplot: Improved user interface. Improved zooming into
      graphs. Imitates R plotting characters ('pch'). Label font
      family, size and font type can be vectors.

    - permuted.index2 and associated functions allow for restricted
      permutations of strata (i.e., restricted shuffling of blocks). 

    - specaccum: removes missing (all zero) species which gave sd = NA
      with method = "exact".

		       CHANGES IN VEGAN 1.13-2

    - anova.cca (and permutest.cca) now calculate the residual df as
      (number of rows) - (rank of constraints and conditions) - 1
      instead of using the rank of the residual ordination.  With
      single response variable in 'rda' the degrees of freedom and
      F-values are now identical to those in 'lm' (linear
      model). However, the change does not influence significances
      (P-values), because these have been always found by permutation,
      and this change does not influence the order statistic used in
      permutations.

    - oecosimu: always estimates the original statistic with binary
      data even when the user supplies quantitative data.

    - orditkplot: no superfluous pointer lines when moving labels. 

    - procrustes plot failed if two configurations were exactly
      identical. 

    - rda (and capscale) use internal scaling constant so that the
      returned site and species scores with scalings 1, 2 or 3
      together provide a biplot approximation of the original
      data. This scaling constant is calculated internally, but now
      its numerical value is returned as an attribute of 'scores.rda',
      and 'summary' displays its value. Vignette on "Design decisions
      and implementation" in vegan explains the calculation of the
      internal scaling constant.

    - summary of capscale identical to the summary of rda.

    - scores of rda and capscale with scaling = 0 really return the
      unmodified scores without the scaling constant.

		       CHANGES IN VEGAN 1.13-1

GENERAL

    - Helene Wagner joined the vegan team.

FIXES FOR HANDLING RANKS IN CONSTRAINED ORDINATION

    - cca, rda and capscale had only known one kind of rank: the rank
      of the ordination result (= number of axes). In fact there are
      two other types of ranks: the rank of constraints after removing
      conditions, and the rank of constraints + conditions, where
      conditions refer to terms "partialled out". This hit those that
      tried to use rda with single response variable instead of
      community matrix, and also some partial models were handled
      wrongly. The changes mainly concern cases where the rank of
      constraints is higher than the rank of the ordination (more
      constraints than ordination axes).  The changes have visible
      effects in following support functions:
      	  
    - alias: no superfluous aliasing of terms, partial models aliased
      correctly.

    - anova: always uses rank of the constraints which also fixes
      anova(..., by = "terms") when single response variable was used.

    - calibrate.cca: identifies cases when the rank of constraints is
      higher than the rank of ordination and refuses to analyse these.

    - extractAIC: uses rank of constraints for degrees of freedom.

    - predict: predict(..., type = "lc", newdata = somedata) works in
      partial analysis.

OTHER FIXES

    - adonis: faster and improved documentation.

    - intersetcor and inertcomp now check that input really is from
      constrained ordination instead of giving obscure error messages.

    - lines.spantree knows again graphical arguments such as 'col',
      'lty'.

    - mite.xy: new data set on the spatial coordinates of sample sites
      of Oribatid mites.

    - mso: plot.mso replaced with msoplot, and plot function now
      displays the ordination scatter plot. Function msoplot collapses
      distances larger than half of the maximum distance into a single
      distance class. Printed result shows the variogram data.

    - ordicluster, ordiellipse, ordispider, orglspider, ordisurf,
      factorfit and vectorfit could fail with non-vegan ordination
      objects in R 2.7.0 whose weights.default function gave error if
      object had no weights (these worked in R 2.6.2 and earlier).

    - taxa2dist: has a "method" name for distances.


		       CHANGES IN VEGAN 1.13-0

GENERAL

    - Based on development version 1.12-15 (revision 354 at
      http://vegan.r-forge.r-project.org) 

NEW FUNCTIONS

    - betadiver: beta diversity functions as reviewed by Patricia
      Koleff et al.  (J. Anim. Ecol., 72, 367-382; 2003), with a plot
      function to produce triangular plots.

    - mso: Helene Wagner's multiscale ordination or spatial
      partitioning of cca and rda. This is taken from the Ecological
      Archives with minimal edition with the permission of Helene
      Wagner.

    - nestedtemp: matrix temperature method for oecosimu following
      Rodriguez-Girones & Santamaria (J. Biogeogr. 33, 924-935; 2006),
      but still without iterative optimization of row and column
      ordering.

    - TukeyHSD.betadisper: pairwise comparisons for betadisper.

NEW FEATURES AND FIXES

    - adonis: returns both species and site scores.

    - betadisper: was not calculating distance to centroid correctly
      for observations where the imaginary distance to centroid was
      greater than the real distance. Now takes the absolute value of
      the combined distance before taking the square root. This is
      in-line with Marti Anderson's PERMDISP2.

    - BCI: example has spatial coordinates of plots.

    - biplot.rda: argument for arrow col.

    - capscale: accepts other distance functions than vegdist, and can
      use metaMDSdist for extended dissimilarites & "metaPCoA".

    - designdist: knows 2x2 contingency table notation with a, b, c,
      and d.

    - metaMDS: transforms data like with distances for species WA.

    - orditkplot: allows editing labels and zooming into plot.

    - permDisper: renamed to permutest.betadisper.

    - permutest: now a generic function, currently with methods
      'cca' and 'permDisper'.

    - rarefy: accepts vectors of sample sizes.

    - rgl.isomap: dynamic rgl plots for isomap.

    - screeplot.cca etc: return invisibly xycoords.

    - specaccum: returns numbers of individuals with method = "rarefaction".

    - summary.cca: returns more statistics on "variance explained by axes".

    - zzz: vegan got startup message.


		   CHANGES IN VEGAN VERSION 1.11-4

    - A critical bug fix in adonis: there was a critical bug in adonis
      code, and inconsistent statistics were used in permutations so
      that P-values were grossly wrong in multi-variables models
      (single variable models were OK). In addition, df were wrong in
      deficit rank models, and unused factor levels were not dropped.
      All adonis users should upgrade and rerun their analyses.

		   CHANGES IN VEGAN VERSION 1.11-3

GENERAL

    - Bug fixes from Rev. 305 on http://r-forge.r-project.org/.

FIXES

    - anova.cca: number of permutations could exceed perm.max.

    - permuted.index2: updated to the version in devel branch. This
      means bugfixes in permCheck, numPerms and permuted.index2. It
      also adds allPerms to get all possible permutations when
      complete enumeration is feasible. In addition, there is now a
      function permuplot to graphically show the current permutation
      scheme.

    - plot.cca, plot.envfit and associates: automatic scaling of
      biplot arrows and fitted vectors was wrong when axes were
      reversed (like 'xlim = c(1,-1)') or the origin was shifted in
      plot.envfit (like 'at = c(1,1)'). Added internal function
      'ordiArrowMul'.

    - plot.procrustes: failed if two configurations were identical.

    - varpart4: sum of squares was wrong if called directly instead of
      being called via varpart(). Reported by Guillaume Blanchet.

		   CHANGES IN VEGAN VERSION 1.11-2

GENERAL

    - minor bug fixes and documentation updates from the devel trunk.

    - version 1.11-1 was made but never released to CRAN, and this is
      the first minor release of the 1.11 series.

FIXES AND UPDATES

    - bstick.princomp: works now.

    - numPerms: was returning incorrect number of permutations
      when type = "strata" selected.

    - permuted.index2: was permuting samples within levels of strata
      as well as permuting the levels themselves if type = "strata"
      selected.
 
    - Documentation: diversity-vegan gains discussion on taxonomic
      diversity and using designdist for analysing beta diversity.
      Proof-reading and updates in diversity-vegan and FAQ-vegan.

	
		   CHANGES IN VEGAN VERSION 1.11-0

GENERAL

    - Based on devel version 1.10-13 (rev. 205 at R-Forge).

    - Gavin Simpson joined the vegan team.

    - Suggests now 'tcltk' (for orditkplot).

NEW FUNCTIONS

    - anova.cca gained a new support function to analyse marginal
      effects of individual terms (which are similar to Type III
      effects). Defined with argument 'by = "margin"'.

    - betadisper: new functions for Marti Anderson's analysis of
      homogeneity of multivariate dispersions.

    - biplot.rda: biplot function for PCA run with rda. Arrows are
      used instead of points.

    - CCorA: Canonical correlation analysis with a robust algorithm,
      with permutation test and plot function.

    - oecosimu: functions to analyse nestedness of communities (such
      as on islands or patches). Function oecosimu is a general
      wrapper, and commsimulator generates null-communities of various
      types (r00, r0, r1, r2, c0, swap, trial swap, backtracking,
      quasiswap). The nestedness can be analysed with functions like
      nestedchecker (number of checkerboard units), nestedn0 (measure
      N0), nesteddisc (discrepancy), but users can supply their own
      functions or even use some standard R functions such as
      chisq.test.

    - ordiresids: similar diagnostic plots as in plot.lm for
      constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals))
      ~ Fitted, and qqmath(~ Residuals) using Lattice graphics.

    - orditkplot: interactive and editable plotting function. Function
      displays one set of points (species, sites) using both points
      and labels (text). The points are fixed, but labels can be
      dragged to better positions with mouse. The edited plots can be
      saved as EPS, exported to various graphical formats (EPS, PDF,
      PNG, JPEG, BMP, XFIG depending on the system) or dumped back to
      the R session for plotting and further processing.

    - ordixyplot: a set of functions for Lattice graphics of
      ordination results. Includes ordixyplot for 2D graphics,
      ordisplom for pairs plots, and ordicloud for 3D graphics. All
      can be subsetted and formatted in the usual Lattice way.

    - permuted.index2: New version of permuted.index() that now allows
      restricted permutations. Can produce permutations for
      time-series or line transects and for spatial grids. These can
      also be nested within 'strata'. permuted.series() and
      permuted.grid() are the relevant workhorse
      functions. Permutation options are set by new function
      permControl(). Currently used only in betadisper, but we plan to
      migrate vegan functions to permuted.index2() in the devel
      version, and will eventually replace the current
      permuted.index().  With support function permCheck for checking
      permutation schemes.

NEW DATA SETS

    - sipoo: birds in the Sipoo archipelago (Finland, too close to
      Helsinki).

NEW FEATURES AND FIXES

    - adonis: accepts any 'dist' object as input.

    - as.mlm.cca, as.mlm.rda use now correct names for variables in
      aliased models. The data were pivoted correctly in R, but the
      labels were not.

    - anova.cca assesses now P value as (hits+1)/(tries+1).

    - anova.cca: anova(..., by = "axis") failed when fitted model had
      terms like poly(x,2) or log(x).

    - bgdispersal uses now a more powerful statistic for the McNemar
      test (in terms of Type 1 error rate).

    - calibrate.cca does correct pivoting in aliased models.

    - capscale: negative scaling in plot works similarly as in rda.

    - decorana does not crash R when called with NULL row data, such
      as decorana(dune[FALSE,]). Method predict(..., type="sites")
      works correctly with downweighted analysis.

    - fitted.cca, fitted.rda gained argument type = "working" to get
      the fitted values and residuals used internally in calculation
      (in cca() these are weigthed and Chi-square standardized
      values).

    - isomap checks that input data are dissimilarities or can be
      changed into dissimilarities without warnings.

    - metaMDS gains argument wascores (defaults TRUE) to suppress
      calculation of species scores.

    - orditorp now handles "..." more cleanly.

    - scores.cca, scores.rda accept display = c("species", "sites").

    - summary.prc honours argument 'axis'.

    - taxa2dist issues now a warning if called with 'check = FALSE'
      and some distances == 0, typically meaning that basal taxa
      (species) were not coded.

    - varpart failed if there were unused levels in factors.

    - wascores returns now NA for missing (all zero) species instead
      of failing.

DOCUMENTS

    - new documents: FAQ, a simple introduction to ordination in
      vegan, a detailed explanation of diversity methods. New
      formatting.

    - Added these NEWS.

			 OLDER VEGAN VERSIONS

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.
r-cran-vegan 2.4-6-1 / usr / lib / R / site-library / vegan / ONEWS
