\name{NEWS}
\title{vegan News}
\encoding{UTF-8}

\section{Changes in version 2.5-1}{

  \subsection{GENERAL}{
    \itemize{

      \item This is a major new release with changes all over the
      package: Nearly 40\% of program files were changed from the
      previous release. Please report regressions and other issues in
      \href{https://github.com/vegandevs/vegan/issues/}{https://github.com/vegandevs/vegan/issues/}.

      \item Compiled code is used much more extensively, and most
      compiled functions use \code{.Call} interface. This gives smaller
      memory footprint and is also faster. In wall clock time, the
      greatest gains are in permutation tests for constrained ordination
      methods (\code{anova.cca}) and binary null models
      (\code{nullmodel}).

      \item Constrained ordination functions (\code{cca}, \code{rda},
      \code{dbrda}, \code{capscale}) are completely rewritten and share
      most of their code. This makes them more consistent with each
      other and more robust. The internal structure changed in
      constrained ordination objects, and scripts may fail if they try
      to access the result object directly. There never was a guarantee
      for unchanged internal structure, and such scripts should be
      changed and they should use the provided support functions to
      access the result object (see documentation of \code{cca.object}
      and github issue
      \href{https://github.com/vegandevs/vegan/issues/262}{#262}).  Some
      support and analysis functions may no longer work with result
      objects created in previous \pkg{vegan} versions. You should use
      \code{update(old.result.object)} to fix these old result
      objects. See github issues
      \href{https://github.com/vegandevs/vegan/issues/218}{#218},
      \href{https://github.com/vegandevs/vegan/issues/227}{#227}.

      \item \pkg{vegan} includes some tests that are run when checking
      the package installation. See github issues
      \href{https://github.com/vegandevs/vegan/issues/181}{#181},
      \href{https://github.com/vegandevs/vegan/issues/271}{#271}.

      \item The informative messages (warnings, notes and error
      messages) are cleaned and unified which also makes possible to
      provide translations.

    } %itemize
  } % general

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item \code{avgdist}: new function to find averaged
      dissimilarities from several random rarefactions of
      communities. Code by Geoffrey Hannigan. See github issues
      \href{https://github.com/vegandevs/vegan/issues/242}{#242},
      \href{https://github.com/vegandevs/vegan/issues/243}{#243},
      \href{https://github.com/vegandevs/vegan/issues/246}{#246}.

      \item \code{chaodist}: new function that is similar to
      \code{designdist}, but uses Chao terms that are supposed to take
      into account the effects of unseen species (Chao et al.,
      \emph{Ecology Letters} \bold{8,} 148-159; 2005). Earlier we had
      Jaccard-type Chao dissimilarity in \code{vegdist}, but the new
      code allows defining any kind of Chao dissimilarity.

      \item New functions to find influence statistics of constrained
      ordination objects: \code{hatvalues}, \code{sigma},
      \code{rstandard}, \code{rstudent}, \code{cooks.distance},
      \code{SSD}, \code{vcov}, \code{df.residual}. Some of these could
      be earlier found via \code{as.mlm} function which is 
      deprecated. See github issue
      \href{https://github.com/vegandevs/vegan/issues/234}{#234}.

      \item \code{boxplot} was added for \code{permustats} results to
      display the (standardized) effect sizes.

      \item \code{sppscores}: new function to add or replace species
      scores in distance-based ordination such as \code{dbrda},
      \code{capscale} and \code{metaMDS}. Earlier \code{dbrda} did not
      have species scores, and species scores in \code{capscale} and
      \code{metaMDS} were based on raw input data which may not be
      consistent with the used dissimilarity measure. See github issue
      \href{https://github.com/vegandevs/vegan/issues/254}{#254}.

      \item \code{cutreeord}: new function that is similar to
      \code{stats::cutree}, but numbers the cluster in the order they
      appear in the dendrogram (left to right) instead of labelling them
      in the order they appeared in the data.

      \item \code{sipoo.map}: a new data set of locations and sizes of
      the islands in the Sipoo archipelago bird data set \code{sipoo}.

    } %itemize
  } % new functions

  \subsection{NEW FEATURES IN CONSTRAINED ORDINATION}{
    \itemize{

      \item The inertia of Correspondence Analysis (\code{cca}) is 
      called \dQuote{scaled Chi-square} instead of using a name of a
      little known statistic.

      \item If elements for Constraints and Conditions are data frames
      in non-formula call of \code{rda} or \code{cca}, these are
      automatically expanded to model matrices and can contain factor
      variables. Earlier they had to be numerical model matrices and
      factors could only be used with the formula interface.

      \item Regression scores for constraints can  be extracted and
      plotted for constrained ordination methods. See github issue
      \href{https://github.com/vegandevs/vegan/issues/226}{#226}.

      \item Full model (\code{model = "full"}) is again enabled in
      permutations tests for constrained ordination results in
      \code{anova.cca} and \code{permutest.cca}.

      \item \code{permutest.cca} gained a new option \code{by = "onedf"} to
      perform tests by sequential one degree-of-freedom contrasts of
      factors. This option is not (yet) enabled in \code{anova.cca}.

      \item The permutation tests are more robust, and most scoping issues
      should have been fixed.

      \item Permutation tests use  compiled C code and they are much
      faster. See github issue
      \href{https://github.com/vegandevs/vegan/issues/211}{#211}.

      \item \code{permutest} printed layout is similar to \code{anova.cca}.

      \item \code{eigenvals} gained a new argument (\code{model}) to
      select either constrained or unconstrained scores. The old
      argument (\code{constrained}) is deprecated. See github issue
      \href{https://github.com/vegandevs/vegan/issues/207}{#207}.

      \item \code{summary.eigenvals} returns a matrix instead of a
      list containing only that matrix.

      \item Adjusted \eqn{R^2}{R-squared} is not calculated for partial
      ordination, because it is unclear how this should be done
      (function \code{RsquareAdj}).

      \item \code{ordiresids} can display standardized and studentized
      residuals.

      \item Function to construct \code{model.frame} and
      \code{model.matrix} for constrained ordination are more robust
      and fail in fewer cases.

      \item \code{goodness} and \code{inertcomp} for constrained
      ordination result object no longer has an option to find
      distances: only explained variation is available.

      \item \code{inertcomp} gained argument \code{unity}. This will
      give \dQuote{local contributions to beta-diversity} (LCBD) and
      \dQuote{species contribution to beta-diversity} (SCBD) of Legendre
      & De \enc{Cáceres}{Caceres} (\emph{Ecology Letters} \bold{16,}
      951-963; 2012).

      \item \code{goodness} is disabled for \code{capscale}.

      \item \code{prc} gained argument \code{const} for general
      scaling of results similarly as in \code{rda}.

      \item \code{prc} uses  regression scores for Canoco-compatibility.

    } %itemae
  } % constrained ordination

  \subsection{NEW FEATURES IN NULL MODEL COMMUNITIES}{
    \itemize{

      \item The C code for swap-based binary null models was made more
      efficients, and the models are  all faster. Many of these
      models selected a \eqn{2 \times 2}{2x2} submatrix, and for this
      they generated four random numbers (two rows, two columns). Now we
      skip selecting third or fourth random number if it is obvious that
      the matrix cannot be swapped. Since most of time was used in
      generating random numbers in these functions, and most candidates
      were rejected, this speeds up functions. However, this also means
      that random number sequences change from previous \pkg{vegan}
      versions, and old binary model results cannot be replicated
      exactly. See github issues
      \href{https://github.com/vegandevs/vegan/issues/197}{#197},
      \href{https://github.com/vegandevs/vegan/issues/255}{#255} for
      details and timing.

      \item Ecological null models (\code{nullmodel}, \code{simulate},
      \code{make.commsim}, \code{oecosimu}) gained new null model
      \code{"greedyqswap"} which can radically speed up quasi-swap
      models with minimal risk of introducing bias.

      \item Backtracking is written in C and it is  much faster. However,
      backtracking models are biased, and they are provided only
      because they are classic legacy models.

    } %itemize
  } % nullmodel

  \subsection{NEW FEATURES IN OTHER FUNCTIONS}{
    \itemize{

      \item \code{adonis2} gained a column of \eqn{R^2}{R-squared}
      similarly as old \code{adonis}.

      \item Great part of \R{} code for \code{decorana} is written in C
      which makes it faster and reduces the memory footprint.

      \item \code{metaMDS} results gained new \code{points} and
      \code{text} methods.

      \item \code{ordiplot} and other ordination \code{plot} functions
      can  be chained with their \code{points} and \code{text}
      functions allowing the use of \pkg{magrittr} pipes.  The
      \code{points} and \code{text} functions gained argument to draw
      arrows allowing their use in drawing biplots or adding vectors of
      environmental variables with \code{ordiplot}.  Since many
      ordination \code{plot} methods return an invisible
      \code{"ordiplot"} object, these \code{points} and \code{text}
      methods also work with them. See github issue
      \href{https://github.com/vegandevs/vegan/issues/257}{#257}.

      \item Lattice graphics (\code{ordixyplot}) for ordination can
       add polygons that enclose all points in the panel and
      complete data.

      \item \code{ordicluster} gained option to suppress drawing in
      plots so that it can be more easily embedded in other functions
      for calculations.

      \item \code{as.rad} returns the index of included taxa as an
      attribute.

      \item Random rarefaction (function \code{rrarefy}) uses compiled
      C code and is much faster.

      \item \code{plot} of \code{specaccum} can  draw short
      horizontal bars to vertical error bars. See StackOverflow
      question
      \href{https://stackoverflow.com/questions/45378751}{45378751}.

      \item \code{decostand} gained new standardization methods
      \code{rank} and \code{rrank} which replace abundance values by
      their ranks or relative ranks. See github issue
      \href{https://github.com/vegandevs/vegan/issues/225}{#225}.

      \item Clark dissimilarity was added to \code{vegdist} (this cannot
      be calculated with \code{designdist}).

      \item \code{designdist} evaluates minimum terms in compiled code,
      and the function is faster than \code{vegdist} also for
      dissimilarities using minimum terms. Although \code{designdist} is
      usually faster than \code{vegdist}, it is numerically less stable,
      in particular with large data sets.

      \item \code{swan} passes \code{type} argument to \code{beals}.

      \item \code{tabasco} can use traditional cover scale values from
      function \code{coverscale}. Function \code{coverscale} can return
      scaled values as integers for numerical analysis instead of
      returning characters for printing.

      \item \code{varpart} can partition \eqn{\chi^2}{Chi-squared}
      inertia of correspondence analysis with new argument
      \code{chisquare}. The adjusted \eqn{R^2}{R-squared} is based on
      permutation tests, and the replicate analysis will have random
      variation.

      \item The explanatory tables can be data frames with factors or
      single factors in \code{varpart} and these will be automatically
      expanded to model matrices. Earlier factors could only be used
      with one-sided model formulae. Based on the code suggested by
      Daniel Borcard, Univ. \enc{Montréal}{Montreal}.

    } % itemize
  } % new features

  \subsection{BUG FIXES}{
    \itemize{

      \item Very long \code{Condition()} statements (> 500 characters)
      failed in partial constrained ordination models (\code{cca},
      \code{rda}, \code{dbrda}, \code{capscale}). The problem was
      detected in StackOverflow question
      \href{https://stackoverflow.com/questions/49249816}{49249816}.

      \item Labels were not adjusted when arrows were rescaled in
      \code{envfit} plots. See StackOverflow question
      \href{https://stackoverflow.com/questions/49259747}{49259747}.

      \item \code{ordiArrowMul} failed if there was only one arrow to
      be plotted in \code{envfit}.

    } % itemize
  } % bug fixes

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{

      \item \code{as.mlm} function for constrained correspondence
      analysis is deprecated in favour of new functions that directly
      give the influence statistics. See github issue
      \href{https://github.com/vegandevs/vegan/issues/234}{#234}.

      \item \code{commsimulator} is now defunct: use \code{simulate}
      for \code{nullmodel} objects.

      \item \pkg{ade4} \code{cca} objects are no longer handled in
      \pkg{vegan}: \pkg{ade4} has had no \code{cca} since version
      1.7-8 (August 9, 2017).

    } %itemize
  } % deprecated & defunct

} % 2.5-0

\section{Changes in version 2.4-6}{

  \subsection{INSTALLATION AND BUILDING}{
    \itemize{

      \item CRAN packages are no longer allowed to use FORTRAN input,
      but \code{read.cep} function used FORTRAN format to read legacy
      CEP and Canoco files. To avoid NOTEs and WARNINGs, the function
      was re-written in \R. The new \code{read.cep} is less powerful and
      more fragile, and can only read data in \dQuote{condensed} format,
      and it can fail in several cases that were successful with the old
      code. The old FORTRAN-based function is still available in CRAN
      package
      \href{https://CRAN.R-project.org/package=cepreader}{cepreader}.
      See github issue
      \href{https://github.com/vegandevs/vegan/issues/263}{#263}. The
      \pkg{cepreader} package is developed in
      \href{https://github.com/vegandevs/cepreader}{https://github.com/vegandevs/cepreader}.

    } %itemize
  } % general

  \subsection{BUG FIXES}{
    \itemize{

      \item Some functions for rarefaction (\code{rrarefy}), species
      abundance distribution (\code{preston}) and species pool
      (\code{estimateR}) need exact integer data, but the test allowed
      small fuzz. The functions worked correctly with original data, but
      if data were transformed and then back-transformed, they would
      pass the integer test with fuzz and give wrong results. For
      instance, \code{sqrt(3)^2} would pass the test as 3, but was
      interpreted strictly as integer 2. See github issue
      \href{https://github.com/vegandevs/vegan/issues/259}{#259}.

    } % itemize
  } % bugs

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{ordiresids} uses now weighted residuals for
      \code{cca} results.

    } %itemize
  } % features

} % 2.4-6

\section{Changes in version 2.4-5}{

  \subsection{BUG FIXES}{
    \itemize{

      \item Several \dQuote{Swap & Shuffle} null models generated wrong
      number of initial matrices. Usually they generated too many, which
      was not dangerous, but it was slow. However, random sequences will
      change with this fix.

      \item Lattice graphics for ordination (\code{ordixyplot} and
      friends) colour the arrows by \code{groups} instead of randomly
      mixed colours.

      \item Information on constant or mirrored permutations was
      omitted when reporting permutation tests (e.g., in \code{anova}
      for constrained ordination).

    } % itemize
  } % bug fixes 

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{ordistep} has improved interpretation of
      \code{scope}: if the lower scope is missing, the formula of the
      starting solution is taken as the lower scope instead of using
      an empty model. See Stackoverflow question
      \href{https://stackoverflow.com/questions/46985029/}{46985029}.

      \item \code{fitspecaccum} gained new support functions \code{nobs}
      and \code{logLik} which allow better co-operation with other
      packages and functions. See GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/250}{#250}.

      \item The \dQuote{backtracking} null model for community
      simulation is faster. However, \dQuote{backtracking} is a biased
      legacy model that should not be used except in comparative
      studies.

    } %itemize
  } % new features


} % 2.4-5

\section{Changes in version 2.4-4}{

  \subsection{INSTALLATION AND BUILDING}{
    \itemize{

      \item \code{orditkplot} should no longer give warnings in CRAN
      tests.

    } %itemize
  } % installatin and building
  
  \subsection{BUG FIXES}{
    \itemize{

      \item \code{anova(..., by = "axis")} for constrained ordination
      (\code{cca}, \code{rda}, \code{dbrda}) ignored partial terms in
      \code{Condition()}.
      
      \item \code{inertcomp} and \code{summary.cca} failed if the
      constrained component was defined, but explained nothing and had
      zero rank. See StackOverflow:
      \href{https://stackoverflow.com/questions/43683699/}{R - Error
      message in doing RDA analysis - vegan package}.

      \item Labels are no longer cropped in the \code{meandist} plots.


    } % itemize
  } % bug fixes
  
  \subsection{NEW FEATURES}{
    \itemize{

      \item The significance tests for the axes of constrained
      ordination use now forward testing strategy. More extensive
      analysis indicated that the previous marginal tests were biased.
      This is in conflict with Legendre, Oksanen & ter Braak,
      \emph{Methods Ecol Evol} \strong{2,} 269--277 (2011) who regarded
      marginal tests as unbiased.

      \item Canberra distance in \code{vegdist} can now handle negative
      input entries similarly as latest versions of \R.

    } %itemize
  } % new features
} % v2.4-4

\section{Changes in version 2.4-3}{

  \subsection{INSTALLATION AND BUILDING}{
    \itemize{

      \item \pkg{vegan} registers native \bold{C} and \bold{Fortran}
      routines. This avoids warnings in model checking, and may also
      give a small gain in speed.

      \item Future versions of \pkg{vegan} will deprecate and remove
      elements \code{pCCA$Fit}, \code{CCA$Xbar}, and \code{CA$Xbar}
      from \code{cca} result objects. This release provides a new
      function \code{ordiYbar} which is able to construct these
      elements both from the current and future releases. Scripts and
      functions directly accessing these elements should switch to
      \code{ordiYbar} for smooth transition.

    } % itemize
  } % installation

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{as.mlm} methods for constrained ordination include
      zero intercept to give the correct residual degrees of freedom for
      derived statistics.

      \item \code{biplot} method for \code{rda} passes
      \code{correlation} argument to the scaling algorithm.

      \item Biplot scores were wrongly centred in \code{cca} which
      caused a small error in their values.

      \item Weighting and centring were corrected in \code{intersetcor}
      and \code{spenvcor}. The fix can make a small difference when
      analysing \code{cca} results.

      Partial models were not correctly handled in \code{intersetcor}.

      \item \code{envfit} and \code{ordisurf} functions failed when
      applied to species scores.

      \item Non-standard variable names can be used within
      \code{Condition()} in partial ordination.  Partial models are used
      internally within several functions, and a problem was reported by
      Albin Meyer (Univ Lorraine, Metz, France) in \code{ordiR2step}
      when using a variable name that contained a hyphen (which was
      wrongly interpreted as a minus sign in partial ordination).

      \item \code{ordispider} did not pass graphical arguments when
      used to show the difference of LC and WA scores in constrained
      ordination.

      \item \code{ordiR2step} uses only \code{forward} selection to
      avoid several problems in model evaluation.

      \item \code{tolerance} function could return \code{NaN} in some
      cases when it should have returned \eqn{0}. Partial models were
      not correctly analysed. Misleading (non-zero) tolerances were
      sometimes given for species that occurred only once or sampling
      units that had only one species.

    } %itemize
  } % bug fixes

} % 2.4-3

\section{Changes in version 2.4-2}{
  \subsection{BUG FIXES}{
    \itemize{

      \item Permutation tests (\code{permutests}, \code{anova}) for the
      first axis failed in constrained distance-based ordination
      (\code{dbrda}, \code{capscale}). Now \code{capscale} will also
      throw away negative eigenvalues when first eigenvalues are
      tested. All permutation tests for the first axis are now
      faster. The problem was reported by Cleo Tebby and the fixes are
      discussed in GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/198}{#198} and
      pull request
      \href{https://github.com/vegandevs/vegan/pull/199}{#199}.

      \item Some support functions for \code{dbrda} or \code{capscale}
      gave results or some of their components in wrong scale. Fixes in
      \code{stressplot}, \code{simulate}, \code{predict} and
      \code{fitted} functions.

      \item \code{intersetcor} did not use correct weighting for
      \code{cca} and the results were slightly off.

      \item \code{anova} and \code{permutest} failed when
      \code{betadisper} was fitted with argument
      \code{bias.adjust = TRUE}. Fixes Github issue
      \href{https://github.com/vegandevs/vegan/issues/219}{#219}
      reported by Ross Cunning, O'ahu, Hawaii.

      \item \code{ordicluster} should return invisibly only the
      coordinates of internal points (where clusters or points are
      joined), but last rows contained coordinates of external points
      (ordination scores of points).

      \item The \code{cca} method of \code{tolerance} was returning
      incorrect values for all but the second axis for sample
      heterogeneities and species tolerances. See issue 
      \href{https://github.com/vegandevs/vegan/issues/216}{#216} for
      details.

    } %itemize
  } % bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item Biplot scores are scaled similarly as site scores in
      constrained ordination methods \code{cca}, \code{rda},
      \code{capscale} and \code{dbrda}. Earlier they were unscaled (or
      more technically, had equal scaling on all axes).

      \item \code{tabasco} adds argument to \code{scale} the colours
      by rows or columns in addition to the old equal scale over the
      whole plot. New arguments \code{labRow} and \code{labCex} can be
      used to change the column or row labels. Function also takes
      care that only above-zero observations are coloured: earlier
      tiny observed values were merged to zeros and were not distinct
      in the plots.

      \item Sequential null models are somewhat faster (up to
      10\%). Non-sequential null models may be marginally faster. These
      null models are generated by function \code{nullmodel} and also
      used in \code{oecosimu}.

      \item \code{vegdist} is much faster. It used to be clearly slower
      than \code{stats::dist}, but now it is nearly equally fast for the
      same dissimilarity measure.

      \item Handling of \code{data=} in formula interface is more
      robust, and messages on user errors are improved. This fixes
      points raised in Github issue
      \href{https://github.com/vegandevs/vegan/issues/200}{#200}.

      \item The families and orders in \code{dune.taxon} were updated to
      APG IV (\emph{Bot J Linnean Soc} \strong{181,} 1--20; 2016) and a
      corresponding classification for higher levels (Chase & Reveal,
      \emph{Bot J Linnean Soc} \strong{161,} 122-127; 2009).

    } %itemize
  } % features


} % 2.4-2

\section{Changes in version 2.4-1}{
  \subsection{INSTALLATION}{
    \itemize{

      \item Fortran code was modernized to avoid warnings in latest
      \R. The modernization should have no visible effect in
      functions. Please report all suspect cases as
      \href{https://github.com/vegandevs/vegan/issues/}{vegan issues}.

    } %itemize
  } % installation

  
  \subsection{BUG FIXES}{
    \itemize{

      \item Several support functions for ordination methods failed if
      the solution had only one ordination axis, for instance, if
      there was only one constraining variable in CCA, RDA and
      friends. This concerned \code{goodness} for constrained
      ordination, \code{inertcomp}, \code{fitted} for
      \code{capscale}, \code{stressplot} for RDA, CCA (GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/189}{#189}).

      \item \code{goodness} for CCA & friends ignored \code{choices}
      argument (GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/190}{#190}).

      \item \code{goodness} function did not consider negative
      eigenvalues of db-RDA (function \code{dbrda}).

      \item Function \code{meandist} failed in some cases when one of
      the groups had only one observation.

      \item \code{linestack} could not handle expressions in
      \code{labels}. This regression is discussed in GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/195}{#195}.

      \item Nestedness measures \code{nestedbetajac} and
      \code{nestedbetasor} expecting binary data did not cope with
      quantitative input in evaluating Baselga's matrix-wide Jaccard
      or Sørensen dissimilarity indices.

      \item Function \code{as.mcmc} to cast \code{oecosimu} result to an
      MCMC object (\pkg{coda} package) failed if there was only one
      chain.

    } % itemize
  } % bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{diversity} function returns now \code{NA} if the
      observation had \code{NA} values instead of returning
      \code{0}. The function also checks the input and refuses to
      handle data with negative values.  GitHub issue
      \href{https://github.com/vegandevs/vegan/issues/187}{#187}.

      \item \code{rarefy} function will work more robustly in marginal
      case when the user asks for only one individual which can only
      be one species with zero variance.

      \item Several functions are more robust if their factor arguments
      contain missing values (\code{NA}): \code{betadisper},
      \code{adipart}, \code{multipart}, \code{hiersimu}, \code{envfit}
      and constrained ordination methods \code{cca}, \code{rda},
      \code{capscale} and \code{dbrda}. GitHub issues
      \href{https://github.com/vegandevs/vegan/issues/192}{#192} and
      \href{https://github.com/vegandevs/vegan/issues/193}{#193}.

    } % itemize
  } % new features

} % 2.4-1

\section{Changes in version 2.4-0}{
  \subsection{DISTANCE-BASED ANALYSIS}{
     \itemize{

       \item Distance-based methods were redesigned and made
       consistent for ordination (\code{capscale}, new \code{dbrda}),
       permutational ANOVA (\code{adonis}, new \code{adonis2}),
       multivariate dispersion (\code{betadisper}) and variation
       partitioning (\code{varpart}).  These methods can produce
       negative eigenvalues with several popular semimetric
       dissimilarity indices, and they were not handled similarly by
       all functions. Now all functions are designed after McArdle &
       Anderson (\emph{Ecology} 82, 290--297; 2001).

       \item \code{dbrda} is a new function for distance-based
       Redundancy Analysis following McArdle & Anderson
       (\emph{Ecology} 82, 290--297; 2001). With metric
       dissimilarities, the function is equivalent to old
       \code{capscale}, but negative eigenvalues of semimetric indices
       are handled differently. In \code{dbrda} the dissimilarities
       are decomposed directly into conditions, constraints and
       residuals with their negative eigenvalues, and any of the
       components can have imaginary dimensions. Function is mostly
       compatible with \code{capscale} and other constrained
       ordination methods, but full compatibility cannot be achieved
       (see issue
       \href{https://github.com/vegandevs/vegan/issues/140}{#140} in
       Github). The function is based on the code by Pierre Legendre.

       \item The old \code{capscale} function for constrained
       ordination is still based only on real components, but the
       total inertia of the components is assessed similarly as in
       \code{dbrda}.

       The significance tests will differ from the previous version,
       but function \code{oldCapscale} will cast the \code{capscale}
       result to a similar form as previously.

       \item \code{adonis2} is a new function for permutational ANOVA
       of dissimilarities. It is based on the same algorithm as the
       \code{dbrda}. The function can perform overall tests of all
       independent variables as well as sequential and marginal tests
       of each term. The old \code{adonis} is still available, but it
       can only perform sequential tests. With same settings,
       \code{adonis} and \code{adonis2} give identical results (but
       see Github issue
       \href{https://github.com/vegandevs/vegan/issues/156}{#156} for
       differences).

       \item Function \code{varpart} can partition dissimilarities
       using the same algorithm as \code{dbrda}.

       \item Argument \code{sqrt.dist} takes square roots of
       dissimilarities and these can change many popular semimetric
       indices to metric distances in \code{capscale}, \code{dbrda},
       \code{wcmdscale}, \code{adonis2}, \code{varpart} and
       \code{betadisper} (issue
       \href{https://github.com/vegandevs/vegan/issues/179}{#179} in
       Github).

       \item Lingoes and Cailliez adjustments change any dissimilarity
       into metric distance in \code{capscale}, \code{dbrda},
       \code{adonis2}, \code{varpart}, \code{betadisper} and
       \code{wcmdscale}.  Earlier we had only Cailliez adjustment in
       \code{capscale} (issue
       \href{https://github.com/vegandevs/vegan/issues/179}{#179} in
       Github).

       \item \code{RsquareAdj} works with \code{capscale} and
       \code{dbrda} and this allows using \code{ordiR2step} in model
       building.

     } % itemize
  } % distance-based

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{specaccum}: \code{plot} failed if line type
      (\code{lty}) was given. Reported by Lila Nath Sharma (Univ
      Bergen, Norway)

    } %itemize
  } %bug fixes

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item \code{ordibar} is a new function to draw crosses of
      standard deviations or standard errors in ordination diagrams
      instead of corresponding ellipses.

      \item Several \code{permustats} results can be combined with a
      new \code{c()} function.

      \item New function \code{smbind} binds together null models by
      row, column or replication. If sequential models are bound
      together, they can be treated as parallel chains in subsequent
      analysis (e.g., after \code{as.mcmc}). See issue
      \href{https://github.com/vegandevs/vegan/issues/164}{#164} in
      Github.

    } %itemize
  } % new functions
  
  \subsection{NEW FEATURES}{
    \itemize{

      \item Null model analysis was upgraded:

      New \code{"curveball"} algorithm provides a fast null model with
      fixed row and column sums for binary matrices after Strona et
      al. (\emph{Nature Commun.} 5: 4114; 2014).

      The \code{"quasiswap"} algorithm gained argument \code{thin}
      which can reduce the bias of null models.

      \code{"backtracking"} is now much faster, but it is still very
      slow, and provided mainly to allow comparison against better and
      faster methods.

      Compiled code can now be interrupted in null model simulations.

      \item \code{designdist} can now use beta diversity notation
      (\code{gamma}, \code{alpha}) for easier definition of beta
      diversity indices.

      \item \code{metaMDS} has new iteration strategy: Argument
      \code{try} gives the minimum number of random starts, and
      \code{trymax} the maximum number. Earlier we only hand
      \code{try} which gave the maximum number, but now we run at
      least \code{try} times. This reduces the risk of being trapped
      in a local optimum (issue
      \href{https://github.com/vegandevs/vegan/issues/154}{#154} in
      Github).

      If there were no convergent solutions, \code{metaMDS} will now
      tabulate stopping criteria (if \code{trace = TRUE}).  This can
      help in deciding if any of the criteria should be made more
      stringent or the number of iterations increased. The
      documentation for \code{monoMDS} and \code{metaMDS} give more
      detailed information on convergence criteria.

      \item The \code{summary} of \code{permustats} prints now
      \emph{P}-values, and the test direction (\code{alternative}) can
      be changed.

      The \code{qqmath} function of \code{permustats} can now plot
      standardized statistics. This is a partial solution to issue
      \href{https://github.com/vegandevs/vegan/issues/172}{#172} in
      Github.

      \item \code{MDSrotate} can rotate ordination to show maximum
      separation of factor levels (classes) using linear discriminant
      analysis (\code{lda} in \pkg{MASS} package).

      \item \code{adipart}, \code{hiersimu} and \code{multipart}
      expose argument \code{method} to specify the null model.

      \item \code{RsquareAdj} works with \code{cca} and this allows
      using \code{ordiR2step} in model building. The code was
      developed by Dan McGlinn (issue
      \href{https://github.com/vegandevs/vegan/issues/161}{#161} in
      Github). However, \code{cca} still cannot be used in
      \code{varpart}.

      \item \code{ordiellipse} and \code{ordihull} allow setting
      colours, line types and other graphical parameters.

      The alpha channel can now be given also as a real number in 0 \dots 1
      in addition to integer 0 \dots 255.

      \item \code{ordiellipse} can now draw ellipsoid hulls that
      enclose points in a group.
      
      \item \code{ordicluster}, \code{ordisegments}, \code{ordispider}
      and \code{lines} and \code{plot} functions for \code{isomap} and
      \code{spantree} can use a mixture of colours of connected
      points. Their behaviour is similar as in analogous functions in
      the the \pkg{vegan3d} package.

      \item \code{plot} of \code{betadisper} is more configurable. See
      issues
      \href{https://github.com/vegandevs/vegan/issues/128}{#128} and
      \href{https://github.com/vegandevs/vegan/issues/166}{#166} in
      Github for details.

      \item \code{text} and \code{points} methods for
      \code{orditkplot} respect stored graphical parameters.

      \item Environmental data for the Barro Colorado Island forest
      plots gained new variables from Harms et al. (\emph{J. Ecol.} 89,
      947--959; 2001). Issue
      \href{https://github.com/vegandevs/vegan/issues/178}{#178} in
      Github.

    } %itemize
  } % features

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{

      \item Function \code{metaMDSrotate} was removed and replaced
      with \code{MDSrotate}.

      \item \code{density} and \code{densityplot} methods for
      various \pkg{vegan} objects were deprecated and replaced with
      \code{density} and \code{densityplot} for \code{permustats}.
      Function \code{permustats} can extract the permutation and
      simulation results of \pkg{vegan} result objects.

    } %itemize
  } % deprecated & defunct

} % v2.4-0

\section{Changes in version 2.3-5}{
  \subsection{BUG FIXES}{
    \itemize{

      \item \code{eigenvals} fails with \code{prcomp} results in
      \R-devel. The next version of \code{prcomp} will have an
      argument to limit the number of eigenvalues shown
      (\code{rank.}), and this breaks \code{eigenvals} in \pkg{vegan}.

      \item \code{calibrate} failed for \code{cca} and friends if
      \code{rank} was given.

    } % itemise
  } % bug fixes
} % v2.3-5

\section{Changes in version 2.3-4}{

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{betadiver} index \code{19} had wrong sign in one of
      its terms.

      \item \code{linestack} failed when the \code{labels} were given,
      but the input scores had no names. Reported by Jeff Wood (ANU,
      Canberra, ACT).

    } %itemize
  } % bug fixes

  \subsection{DEPRECATED}{
    \itemize{

      \item \code{vegandocs} is deprecated. Current \R{} provides better
      tools for seeing extra documentation (\code{news()} and
      \code{browseVignettes()}).

    } %itemize
  } %deprecated

  \subsection{VIGNETTES}{
    \itemize{

      \item All vignettes are built with standard \R{} tools and can be
      browsed with \code{browseVignettes}. \code{FAQ-vegan} and
      \code{partitioning} were only accessible with \code{vegandocs}
      function.
      
    } %itemize
  } %vignettes

  \subsection{BUILDING}{
    \itemize{

      \item Dependence on external software \code{texi2dvi} was
      removed. Version 6.1 of \code{texi2dvi} was incompatible with \R{}
      and prevented building \pkg{vegan}. The \code{FAQ-vegan} that was
      earlier built with \code{texi2dvi} uses now \pkg{knitr}. Because
      of this, \pkg{vegan} is now dependent on \R-3.0.0.  Fixes issue
      \href{https://github.com/vegandevs/vegan/issues/158}{#158} in
      Github.

    } %itemize
  } % building
    
  
} % v2.3-4

\section{Changes in version 2.3-3}{
  \subsection{BUG FIXES}{
     \itemize{

	\item \code{metaMDS} and \code{monoMDS} could fail if input
	dissimilarities were huge: in the reported case they were of
	magnitude 1E85. Fixes issue
	\href{https://github.com/vegandevs/vegan/issues/152}{#152} in
	Github.

       \item Permutations failed if they were defined as \pkg{permute}
       control structures in \code{estaccum}, \code{ordiareatest},
       \code{renyiaccum} and \code{tsallisaccum}. Reported by Dan
       Gafta (Cluj-Napoca) for \code{renyiaccum}.

       \item \code{rarefy} gave false warnings if input was a vector
       or a single sampling unit.

       \item Some extrapolated richness indices in \code{specpool}
       needed the number of doubletons (= number of species occurring
       in two sampling units), and these failed when only one sampling
       unit was supplied.  The extrapolated richness cannot be
       estimated from a single sampling unit, but now such cases are
       handled smoothly instead of failing: observed non-extrapolated
       richness with zero standard error will be reported. The issue
       was reported in
       \href{http://stackoverflow.com/questions/34027496/error-message-when-using-specpool-in-vegan-package}{StackOverflow}.

    } %itemize
  } % bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

       \item \code{treedist} and \code{treedive} refuse to handle
       trees with reversals, i.e, higher levels are more homogeneous
       than lower levels. Function \code{treeheight} will estimate
       their total height with absolute values of branch
       lengths. Function \code{treedive} refuses to handle trees with
       negative branch heights indicating negative
       dissimilarities. Function \code{treedive} is faster.

       \item \code{gdispweight} works when input data are in a matrix
       instead of a data frame.

       \item Input dissimilarities supplied in symmetric matrices or
       data frames are more robustly recognized by \code{anosim},
       \code{bioenv} and \code{mrpp}.

    } %itemize
  } %new features

} %v2.3-3

\section{Changes in version 2.3-2}{

  \subsection{BUG FIXES}{
    \itemize{

      \item Printing details of a gridded permutation design would fail
      when the grid was at the within-plot level.

      \item \code{ordicluster} joined the branches at wrong coordinates
      in some cases.

      \item \code{ordiellipse} ignored weights when calculating standard
      errors (\code{kind = "se"}). This influenced plots of \code{cca},
      and also influenced \code{ordiareatest}.

    } % itemize
  } % bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{adonis} and \code{capscale} functions recognize
      symmetric square matrices as dissimilarities. Formerly
      dissimilarities had to be given as \code{"dist"} objects such as
      produced by \code{dist} or \code{vegdist} functions, and data
      frames and matrices were regarded as observations x variables
      data which could confuse users (e.g., issue
      \href{https://github.com/vegandevs/vegan/issues/147}{#147}).

      \item \code{mso} accepts \code{"dist"} objects for the distances
      among locations as an alternative to coordinates of locations.

      \item \code{text}, \code{points} and \code{lines} functions for
      \code{procrustes} analysis gained new argument \code{truemean}
      which allows adding \code{procrustes} items to the plots of
      original analysis.

      \item \code{rrarefy} returns observed non-rarefied communities
      (with a warning) when users request subsamples that are larger
      than the observed community instead of failing. Function
      \code{drarefy} has been similar and returned sampling
      probabilities of 1, but now it also issues a warning. Fixes issue
      \href{https://github.com/vegandevs/vegan/issues/144}{#144} in
      Github.

    } % itemize
  } % new features
} %v2.3-2

\section{Changes in version 2.3-1}{

  \subsection{BUG FIXES}{
    \itemize{

      \item Permutation tests did not always correctly recognize ties
      with the observed statistic and this could result in too low
      \eqn{P}-values. This would happen in particular when all predictor
      variables were factors (classes). The changes concern functions
      \code{adonis}, \code{anosim}, \code{anova} and \code{permutest}
      functions for \code{cca}, \code{rda} and \code{capscale},
      \code{permutest} for \code{betadisper}, \code{envfit},
      \code{mantel} and \code{mantel.partial}, \code{mrpp}, \code{mso},
      \code{oecosimu}, \code{ordiareatest}, \code{protest} and
      \code{simper}. This also fixes issues
      \href{https://github.com/vegandevs/vegan/issues/120}{#120} and
      \href{https://github.com/vegandevs/vegan/issues/132}{#132} in
      GitHub.

      \item Automated model building in constrained ordination
      (\code{cca}, \code{rda}, \code{capscale}) with \code{step},
      \code{ordistep} and \code{ordiR2step} could fail if there were
      aliased candidate variables, or constraints that were completely
      explained by other variables already in the model. This was a
      regression introduced in \pkg{vegan} 2.2-0.

      \item Constrained ordination methods \code{cca}, \code{rda} and
      \code{capscale} treat character variables as factors in analysis,
      but did not return their centroids for plotting.

      \item Recovery of original data in \code{metaMDS} when computing
      WA scores for species would fail if the expression supplied to
      argument \code{comm} was long & got deparsed to multiple
      strings. \code{metaMDSdist} now returns the (possibly modified)
      data frame of community data \code{comm} as attribute
      \code{"comm"} of the returned \code{dist} object. \code{metaMDS}
      now uses this to compute the WA species scores for the NMDS. In
      addition, the deparsed expression for \code{comm} is now robust to
      long expressions.  Reported by Richard Telford.

      \item \code{metaMDS} and \code{monoMDS} rejected dissimilarities
      with missing values.

      \item Function \code{rarecurve} did not check its input and this
      could cause confusing error messages. Now function checks that
      input data are integers that can be interpreted as counts on
      individuals and all sampling units have some species. Unchecked
      bad inputs were the reason for problems reported in
      \href{http://stackoverflow.com/questions/30856909/error-while-using-rarecurve-in-r}{Stackoverflow}.

    }
  } % bug fixes

  \subsection{NEW FEATURES AND FUNCTIONS}{
    \itemize{
      
     \item Scaling of ordination axes in \code{cca}, \code{rda} and
     \code{capscale} can now be expressed with descriptive strings
     \code{"none"}, \code{"sites"}, \code{"species"} or
     \code{"symmetric"} to tell which kind of scores should be scaled by
     eigenvalues. These can be further modified with arguments
     \code{hill} in \code{cca} and \code{correlation} in \code{rda}. The
     old numeric scaling can still be used.

     \item The permutation data can be extracted from \code{anova}
     results of constrained ordination (\code{cca}, \code{rda},
     \code{capscale}) and further analysed with \code{permustats}
     function.

     \item New data set \code{BCI.env} of site information for the Barro
     Colorado Island tree community data. Most useful variables are the
     UTM coordinates of sample plots. Other variables are constant or
     nearly constant and of little use in normal analysis.
     
   }
  } % new features and functions

}

\section{Changes in version 2.3-0}{

  \subsection{BUG FIXES}{
    \itemize{

      \item Constrained ordination functions \code{cca}, \code{rda} and
      \code{capscale} are now more robust. Scoping of data set names and
      variable names is much improved. This should fix numerous
      long-standing problems, for instance those reported by Benedicte
      Bachelot (in email) and Richard Telford (in Twitter), as well as
      issues \href{https://github.com/vegandevs/vegan/issues/16}{#16}
      and \href{https://github.com/vegandevs/vegan/issues/100}{#100} in
      GitHub.

      \item Ordination functions \code{cca} and \code{rda} silently
      accepted dissimilarities as input although their analysis makes
      no sense with these methods. Dissimilarities should be analysed
      with distance-based redundancy analysis (\code{capscale}).

      \item The variance of the conditional component was over-estimated
      in \code{goodness} of \code{rda} results, and results were wrong
      for partial RDA. The problems were reported in an
      \href{https://stat.ethz.ch/pipermail/r-sig-ecology/2015-March/004936.html}{R-sig-ecology}
      message by Christoph von Redwitz.

    }
  } % bug fixes

  \subsection{WINDOWS}{
    \itemize{

      \item \code{orditkplot} did not add file type identifier to saved
      graphics in Windows although that is required. The problem only
      concerned Windows OS.

    }
  } % windows

  \subsection{NEW FEATURES AND FUNCTIONS}{
    \itemize{

      \item \code{goodness} function for constrained ordination
      (\code{cca}, \code{rda}, \code{capscale}) was redesigned. Function
      gained argument \code{addprevious} to add the variation explained
      by previous ordination components to axes when \code{statistic =
      "explained"}. With this option, \code{model = "CCA"} will include
      the variation explained by partialled-out conditions, and
      \code{model = "CA"} will include the accumulated variation
      explained by conditions and constraints. The former behaviour was
      \code{addprevious = TRUE} for \code{model = "CCA"}, and
      \code{addprevious = FALSE} for \code{model = "CA"}. The argument
      will have no effect when \code{statistic = "distance"}, but this
      will always show the residual distance after all previous
      components. Formerly it displayed the residual distance only for
      the currently analysed model.

      \item Functions \code{ordiArrowMul} and \code{ordiArrowTextXY} are
      exported and can be used in normal interactive sessions. These
      functions are used to scale a bunch arrows to fit ordination
      graphics, and formerly they were internal functions used within
      other \pkg{vegan} functions.

      \item \code{orditkplot} can export graphics in SVG format. SVG is
      a vector graphics format which can be edited with several external
      programs, such as Illustrator and Inkscape.

      \item Rarefaction curve (\code{rarecurve}) and species
      accumulation models (\code{specaccum}, \code{fitspecaccum})
      gained new functions to estimate the slope of curve at given
      location. Originally this was based on a response to an
      \href{https://stat.ethz.ch/pipermail/r-sig-ecology/2015-May/005038.html}{R-SIG-ecology}
      query. For rarefaction curves, the function is \code{rareslope},
      and for species accumulation models it is \code{specslope}.

      The functions are based on analytic equations, and can also be
      evaluated at interpolated non-integer values. In
      \code{specaccum} models the functions can be only evaluated for
      analytic models \code{"exact"}, \code{"rarefaction"} and
      \code{"coleman"}. With \code{"random"} and \code{"collector"}
      methods you can only use finite differences
      (\code{diff(fitted(<result.object>))}). Analytic functions for
      slope are used for all non-linear regression models known to
      \code{fitspecaccum}.

      \item Species accumulation models (\code{specaccum}) and
      non-liner regression models for species accumulation
      (\code{fitspecaccum}) work more consistently with weights. In
      all cases, the models are defined using the number of sites as
      independent variable, which with weights means that observations
      can be non-integer numbers of virtual sites. The \code{predict}
      models also use the number of sites with \code{newdata},
      and for analytic models they can estimate the expected values
      for non-integer number of sites, and for non-analytic randomized
      or collector models they can interpolate on non-integer values.

      \item \code{fitspecaccum} gained support functions \code{AIC}
      and \code{deviance}.

      \item The \code{varpart} plots of four-component models were
      redesigned following Legendre, Borcard & Roberts \emph{Ecology}
      93, 1234--1240 (2012), and they use now four ellipses instead of
      three circles and two rectangles. The components are now labelled
      in plots, and the circles and ellipses can be easily filled with
      transparent background colour.

    }
  } % new features
} % v2.2-2

\section{Changes in version 2.2-1}{

  \subsection{GENERAL}{
    \itemize{

      \item This is a maintenance release to avoid warning messages
      caused by changes in CRAN repository. The namespace usage is also
      more stringent to avoid warnings and notes in development versions
      of \R.

    }
  }% end general

  \subsection{INSTALLATION}{
    \itemize{

      \item \pkg{vegan} can be installed and loaded without \pkg{tcltk}
      package. The \pkg{tcltk} package is needed in \code{orditkplot}
      function for interactive editing of ordination graphics.

    }
  } % installation

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{ordisurf} failed if \pkg{gam} package was loaded due
      to namespace issues: some support functions of \pkg{gam} were used
      instead of \pkg{mgcv} functions.

      \item \code{tolerance} function failed for unconstrained
      correspondence analysis.

    }
  } % bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{estimateR} uses a more exact variance formula for
      bias-corrected Chao estimate of extrapolated number of
      species. The new formula may be unpublished, but it was derived
      following the guidelines of Chiu, Wang, Walther & Chao,
      \emph{Biometrics} 70, 671--682 (2014),
      \href{http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/suppinfo}{online
      supplementary material}.

      \item Diversity accumulation functions \code{specaccum},
      \code{renyiaccum}, \code{tsallisaccum}, \code{poolaccum} and
      \code{estaccumR} use now \pkg{permute} package for permutations
      of the order of sampling sites. Normally these functions only
      need simple random permutation of sites, but restricted
      permutation of the \pkg{permute} package and user-supplied
      permutation matrices can be used.

      \item \code{estaccumR} function can use parallel processing.

      \item \code{linestack} accepts now expressions as labels. This
      allows using mathematical symbols and formula given as
      mathematical expressions.

    }
  } % new features

} % v2.2-1

\section{Changes in version 2.2-0}{

  \subsection{GENERAL}{
    \itemize{
  
      \item Several \pkg{vegan} functions can now use parallel
      processing for slow and repeating calculations. All these
      functions have argument \code{parallel}. The argument can be an
      integer giving the number of parallel processes. In unix-alikes
      (Mac OS, Linux) this will launch \code{"multicore"} processing
      and in Windows it will set up \code{"snow"} clusters as desribed
      in the documentation of the \pkg{parallel} package. If \code{option}
      \code{"mc.cores"} is set to an integer > 1, this will be used to
      automatically start parallel processing. Finally, the argument
      can also be a previously set up \code{"snow"} cluster which will
      be used both in Windows and in unix-alikes. \pkg{Vegan} vignette
      on Design decision explains the implementation (use
      \code{vegandocs("decission")}, and \pkg{parallel} package has more
      extensive documentation on parallel processing in \R.

      The following function use parallel processing in analysing
      permutation statistics: \code{adonis}, \code{anosim},
      \code{anova.cca} (and \code{permutest.cca}), \code{mantel} (and
      \code{mantel.partial}), \code{mrpp}, \code{ordiareatest},
      \code{permutest.betadisper} and \code{simper}. In addition,
      \code{bioenv} can compare several candidate sets of models in
      paralle, \code{metaMDS} can launch several random starts in
      parallel, and \code{oecosimu} can evaluate test statistics for
      several null models in parallel.

      \item All permutation tests are based on the \pkg{permute} package
      which offers strong tools for restricted permutation. All these
      functions have argument \code{permutations}. The default usage of
      simple non-restricted permutations is achieved by giving a single
      integer number. Restricted permutations can be defined using the
      \code{how} function of the \pkg{permute} package. Finally, the
      argument can be a permutation matrix where rows define
      permutations. It is possible to use external or user constructed
      permutations.

      See \code{help(permutations)} for a brief introduction on
      permutations in \pkg{vegan}, and \pkg{permute} package for the
      full documention. The vignette of the \pkg{permute} package can
      be read from \pkg{vegan} with command
      \code{vegandocs("permutations")}.

      The following functions use the \pkg{permute} package:
      \code{CCorA}, \code{adonis}, \code{anosim}, \code{anova.cca} (plus
      associated \code{permutest.cca}, \code{add1.cca},
      \code{drop1.cca}, \code{ordistep}, \code{ordiR2step}),
      \code{envfit} (plus associated \code{factorfit} and
      \code{vectorfit}), \code{mantel} (and \code{mantel.partial}),
      \code{mrpp}, \code{mso}, \code{ordiareatest},
      \code{permutest.betadisper}, \code{protest} and \code{simper}.

      \item Community null model generation has been completely
      redesigned and rewritten. The communities are constructed with
      new \code{nullmodel} function and defined in a low level
      \code{commsim} function. The actual null models are generated
      with a \code{simulate} function that builds an array of null
      models. The new null models include a wide array of quantitative
      models in addition to the old binary models, and users can plug
      in their own generating functions. The basic tool invoking and
      analysing null models is \code{oecosimu}. The null models are
      often used only for the analysis of nestedness, but the
      implementation in \code{oecosimu} allows analysing any
      statistic, and null models are better seen as an alternative to
      permutation tests.
  
    } %end itemize
  } % end general

  \subsection{INSTALLATION}{
    \itemize{

      \item \pkg{vegan} package dependencies and namespace imports
      were adapted to changes in \R, and no more trigger warnings and
      notes in package tests.

      \item Three-dimensional ordination graphics using
      \pkg{scatterplot3d} for static plots and \pkg{rgl} for dynamic
      plots were removed from \pkg{vegan} and moved to a companion
      package \pkg{vegan3d}. The package is available in CRAN.

     } %end itemize
   } % end installation

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Function \code{dispweight} implements dispersion weighting
      of Clarke et al. (\emph{Marine Ecology Progress Series}, 320,
      11--27).  In addition, we implemented a new method for
      generalized dispersion weighting \code{gdispweight}. Both
      methods downweight species that are significantly
      over-dispersed.

      \item New \code{hclust} support functions \code{reorder},
      \code{rev} and \code{scores}. Functions \code{reorder} and
      \code{rev} are similar as these functions for \code{dendrogram}
      objects in base \R. However, \code{reorder} can use (and defaults
      to) weighted mean. In weighted mean the node average is always the
      mean of member leaves, whereas the \code{dendrogram} uses always
      unweighted means of joined branches.

      \item Function \code{ordiareatest} supplements \code{ordihull} and
      \code{ordiellipse} and provides a randomization test for the
      one-sided alternative hypothesis that convex hulls or ellipses in
      two-dimensional ordination space have smaller areas than with
      randomized groups.

      \item Function \code{permustats} extracts and inspects permutation
      results with support functions \code{summary}, \code{density},
      \code{densityplot}, \code{qqnorm} and \code{qqmath}. The
      \code{density} and \code{qqnorm} are standard \R{} tools that only
      work with one statistic, and \code{densityplot} and \code{qqmath}
      are \pkg{lattice} graphics that work with univariate and
      multivariate statistics. The results of following functions can be
      extracted: \code{anosim}, \code{adonis}, \code{mantel} (and
      \code{mantel.partial}), \code{mrpp}, \code{oecosimu},
      \code{permustest.cca} (but not the corresponding \code{anova}
      methods), \code{permutest.betadisper}, and \code{protest}.

      \item \code{stressplot} functions display the ordination distances
      at given number of dimensions against original distances.  The
      method functins are similar to \code{stressplot} for
      \code{metaMDS}, and always use the inherent distances of each
      ordination method. The functions are available for the results
      \code{capscale}, \code{cca}, \code{princomp}, \code{prcomp},
      \code{rda}, and \code{wcmdscale}.

    } % end itemize
  } % end new functions

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{cascadeKM} of only one group will be \code{NA} instead
      of a random value. 

      \item \code{ordiellipse} can handle points exactly on a line,
      including only two points (with a warning).

      \item plotting \code{radfit} results for several species failed if
      any of the communities had no species or had only one species.

      \item \code{RsquareAdj} for \code{capscale} with negative
      eigenvalues will now report \code{NA} instead of using biased
      method of \code{rda} results.

      \item \code{simper} failed when a group had only a single member.

      }% end itemize
  } % end bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{anova.cca} functions were re-written to use the
      \pkg{permute} package. Old results may not be exactly
      reproduced, and models with missing data may fail in several
      cases. There is a new option of analysing a sequence of models
      against each other.

      \item \code{simulate} functions for \code{cca} and \code{rda}
      can return several simulations in a \code{nullmodel} compatible
      object. The functions can produce simulations with correlated
      errors (also for \code{capscale}) in parametric simulation with
      Gaussian error.

      \item \code{bioenv} can use Manhattan, Gower and Mahalanobis
      distances in addition to the default Euclidean. New helper
      function \code{bioenvdist} can extract the dissimilarities
      applied in best model or any other model.

      \item \code{metaMDS(..., trace = 2)} will show convergence
      information with the default \code{monoMDS} engine.

      \item Function \code{MDSrotate} can rotate a \eqn{k}-dimensional
      ordination to \eqn{k-1} variables. When these variables are
      correlated (like usually is the case), the vectors can also be
      correlated to previously rotated dimensions, but will be
      uncorrelated to all later ones.

      \item \pkg{vegan} 2.0-10 changed the weighted \code{nestednodf}
      so that weighted analysis of binary data was equivalent to
      binary analysis. However, this broke the equivalence to the
      original method. Now the function has an argument \code{wbinary}
      to select the method of analysis. The problem was reported and a
      fix submitted by Vanderlei Debastiani (Universidade Federal do
      Rio Grande do Sul, Brasil).

      \item \code{ordiellipse}, \code{ordihull} and \code{ordiellipse}
      can handle missing values in \code{groups}.

      \item \code{ordispider} can now use spatial medians instead of
      means. 

      \item \code{rankindex} can use Manhattan, Gower and Mahalanobis
      distance in addition to the default Euclidean.

      \item User can set colours and line types in function
      \code{rarecurve} for plotting rarefaction curves.

      \item \code{spantree} gained a support function \code{as.hclust}
      to change the minimum spanning tree into an \code{hclust} tree.

      \item \code{fitspecaccum} can do weighted analysis. Gained
      \code{lines} method.

      \item Functions for extrapolated number of species or for the size
      of species pool using Chao method were modified following Chiu et
      al., \emph{Biometrics} 70, 671--682 (2014).

      Incidence based \code{specpool} can now use (and defaults to)
      small sample correction with number of sites as the sample
      size. Function uses basic Chao extrapolation based on the ratio of
      singletons and doubletons, but switches now to bias corrected Chao
      extrapolation if there are no doubletons (species found
      twice). The variance formula for bias corrected Chao was derived
      following the supporting
      \href{http://onlinelibrary.wiley.com/doi/10.1111/biom.12200/suppinfo}{online material}
      and differs slightly from Chiu et al. (2014).

      The \code{poolaccum} function was changed similarly, but the small
      sample correction is used always.

      The abundance based \code{estimateR} uses bias corrected Chao
      extrapolation, but earlier it estimated its variance with classic
      Chao model. Now we use the widespread
      \href{http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB}{approximate
	equation} for variance.

      With these changes these functions are more similar to
            \href{http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm#AppendixB}{EstimateS}.

      \item \code{tabasco} uses now \code{reorder.hclust} for
      \code{hclust} object for better ordering than previously when it
      cast trees to \code{dendrogram} objects.

      \item \code{treedive} and \code{treedist} default now to
       \code{match.force = TRUE} and can be silenced with
      \code{verbose = FALSE}.

      \item \code{vegdist} gained Mahalanobis distance.

      \item Nomenclature updated in plant community data with the help
      of \pkg{Taxonstand} and \pkg{taxize} packages. The taxonomy of
      the \code{dune} data was adapted to the same sources and APG
      III.  \code{varespec} and \code{dune} use 8-character names (4
      from genus + 4 from species epithet). New data set on
      phylogenetic distances for \code{dune} was extracted from Zanne
      et al. (\emph{Nature} 506, 89--92; 2014).

      \item User configurable plots for \code{rarecurve}.

    } %end itemize
  } % end new featuresq

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{

      \item \code{strata} are deprecated in permutations. It is still
      accepted but will be phased out in next releases. Use \code{how}
      of \pkg{permute} package.

      \item \code{cca}, \code{rda} and \code{capscale} do not return
      scores scaled by eigenvalues: use \code{scores} function to
      extract scaled results.

      \item \code{commsimulator} is deprecated. Replace
      \code{commsimulator(x, method)} with
      \code{simulate(nullmodel(x, method))}.

      \item \code{density} and \code{densityplot} for permutation
      results are deprecated: use \code{permustats} with its
      \code{density} and \code{densityplot} method.

    } %end itemize
  } % end deprecated
  

} % end version 2.2-0

\section{Changes in version 2.0-10}{

  \subsection{GENERAL}{
    \itemize{

      \item This version is adapted to the changes in \pkg{permute}
      package version 0.8-0 and no more triggers NOTEs in package
      checks.  This release may be the last of the 2.0 series, and the
      next \pkg{vegan} release is scheduled to be a major release with
      newly designed \code{oecosimu} and community pattern simulation,
      support for parallel processing, and full support of the
      \pkg{permute} package. If you are interested in these
      developments, you may try the development versions of
      \pkg{vegan} in
      \href{http://r-forge.r-project.org/projects/vegan/}{R-Forge} or
      \href{https://github.com/jarioksa/vegan}{GitHub} and report the
      problems and user experience to us.  }  } % end general

  \subsection{BUG FIXES}{

    \itemize{

      \item \code{envfit} function assumed that all external variables
      were either numeric or factors, and failed if they were, say,
      character strings. Now only numeric variables are taken as
      continuous vectors, and all other variables (character strings,
      logical) are coerced to factors if possible. The function also
      should work with degenerate data, like only one level of a
      factor or a constant value of a continuous environmental
      variable. The ties were wrongly in assessing permutation
      \eqn{P}-values in \code{vectorfit}.

      \item \code{nestednodf} with quantitative data was not
      consistent with binary models, and the fill was wrongly
      calculated with quantitative data.
      
      \item \code{oecosimu} now correctly adapts displayed quantiles
      of simulated values to the \code{alternative} test direction.

      \item \code{renyiaccum} plotting failed if only one level of
      diversity \code{scale} was used.
    
    }
  } % bug fixes

  \subsection{NEW FEATURES}{ 
    \itemize{ 

      \item The Kempton and Taylor algorithm was found unreliable in
      \code{fisherfit} and \code{fisher.alpha}, and now the estimation
      of Fisher \eqn{\alpha}{alpha} is only based on the number of
      species and the number of individuals.  The estimation of
      standard errors and profile confidence intervals also had to be
      scrapped.

      \item \code{renyiaccum}, \code{specaccum} and
      \code{tsallisaccum} functions gained \code{subset} argument.

      \item \code{renyiaccum} can now add a \code{collector} curve to
      to the analysis. The collector curve is the diversity
      accumulation in the order of the sampling units. With an
      interesting ordering or sampling units this allows comparing
      actual species accumulations with the expected randomized
      accumulation.
      
      \item \code{specaccum} can now perform weighted accumulation
      using the sampling effort as weights.

      }

  } % new features 


} % end 2.0-10

\section{Changes in version 2.0-9}{

\itemize{

   \item This version is released due to changes in programming
   interface and testing procedures in \R{} 3.0.2. If you are using an
   older version of \R, there is no need to upgrade \pkg{vegan}. There
   are no new features nor bug fixes. The only user-visible changes
   are in documentation and in output messages and formatting. Because
   of \R{} changes, this version is dependent on \R{} version 2.14.0
   or newer and on \pkg{lattice} package.

   }
}

\section{Changes in version 2.0-8}{

  \subsection{GENERAL}{
     \itemize{

       \item This is a maintenance release that fixes some issues
       raised by changed in \R{} toolset for processing vignettes.  In
       the same we also fix some typographic issues in the vignettes.

     }
  } % general

  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{ordisurf} gained new arguments for more flexible
      definition of fitted models to better utilize the
      \pkg{mgcv}\code{::gam} function. 

      The linewidth of contours can
      now be set with the argument \code{lwd}.

      \item Labels to arrows are positioned in a better way in
      \code{plot} functions for the results of \code{envfit},
      \code{cca}, \code{rda} and \code{capscale}. The labels should no
      longer overlap the arrow tips.

      \item The setting test direction is clearer in \code{oecosimu}.

      \item \code{ordipointlabel} gained a \code{plot} method that can
      be used to replot the saved result.

    }
  } % new features

}

\section{Changes in version 2.0-7}{

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item \code{tabasco()} is a new function for graphical display
      of community data matrix.  Technically it is an interface to \R
      \code{heatmap}, but its use is closer to \pkg{vegan} function
      \code{vegemite}. The function can reorder the community data
      matrix similarly as \code{vegemite}, for instance, by ordination
      results. Unlike \code{heatmap}, it only displays dendrograms if
      supplied by the user, and it defaults to re-order the
      dendrograms by correspondence analysis.  Species are ordered to
      match site ordering or like determined by the user.

    }
  } % new functions

  \subsection{BUG FIXES}{
    \itemize{

      \item Function \code{fitspecaccum(..., model = "asymp")} fitted
      logistic model instead of asymptotic model (or the same as 
      \code{model = "logis"}).

      \item \code{nestedtemp()} failed with very sparse data (fill
      \eqn{< 0.38}\%).

    }
  } % bug fixes 

  \subsection{NEW FEATURES}{
    \itemize{

      \item The \code{plot} function for constrained ordination
      results (\code{cca}, \code{rda}, \code{capscale}) gained
      argument \code{axis.bp} (defaults \code{TRUE}) which can be used
      to suppress axis scale for biplot arrays.

      \item Number of iterations in nonmetric multidimensional scaling
      (NMDS) can be set with keyword \code{maxit} (defaults
      \code{200}) in \code{metaMDS}.

    }
  } % new features

  \subsection{DEPRECATED}{

    \itemize{

      \item The result objects of \code{cca}, \code{rda} and
      \code{capscale} will no longer have scores \code{u.eig},
      \code{v.eig} and \code{wa.eig} in the future versions of
      \pkg{vegan}. This change does not influence normal usage,
      because \pkg{vegan} functions do not need these items.  However,
      external scripts and packages may need changes in the future
      versions of \pkg{vegan}.

    }   
  } % deprecated

} % vegan 2.0-7

\section{Changes in version 2.0-6}{

  \subsection{BUG FIXES}{

    \itemize{

      \item The species scores were scaled wrongly in
      \code{capscale()}. They were scaled correctly only when Euclidean
      distances were used, but usually \code{capscale()} is used with
      non-Euclidean distances.  Most graphics will change and should be
      redone.  The change of scaling mainly influences the spread of
      species scores with respect to the site scores.

      \item Function \code{clamtest()} failed to set the minimum
      abundance threshold in some cases. In addition, the output was
      wrong when some of the possible species groups were missing. Both
      problems were reported by Richard Telford (Bergen, Norway).

      \item Plotting an object fitted by \code{envfit()} would fail if
      \code{p.max} was used and there were unused levels for one or
      more factors. The unused levels could result from deletion of
      observations with missing values or simply as the result of
      supplying a subset of a larger data set to \code{envfit()}.

      \item \code{multipart()} printed wrong information about the
      analysis type (but did the analysis correctly). Reported by
      Valerie Coudrain.

      \item \code{oecosimu()} failed if its \code{nestedfun} returned a
      data frame. A more fundamental fix will be in \pkg{vegan} 2.2-0,
      where the structure of the \code{oecosimu()} result will change.

      \item The plot of two-dimensional \code{procrustes()} solutions
      often draw original axes in a wrong angle. The problem was
      reported by Elizabeth Ottesen (MIT).

      \item Function \code{treedive()} for functional or phylogenetic
      diversity did not correctly match the species names between the
      community data and species tree when the tree contained species
      that did not occur in the data.  Related function
      \code{treedist()} for phylogenetic distances did not try to match
      the names at all.

    }
 
  } % bug fixes

  \subsection{NEW FEATURES}{

    \itemize{

      \item The output of \code{capscale()} displays the value of the
      additive constant when argument \code{add = TRUE} was used.
      
      \item \code{fitted()} functions for \code{cca()}, \code{rda()} and
      \code{capscale()} can now return conditioned (partial) component
      of the response: Argument \code{model} gained a new alternative
      \code{model = "pCCA"}. 

      \item \code{dispindmorisita()} output gained a new column for
      Chi-squared based probabilities that the null hypothesis (random
      distribution) is true.

      \item \code{metaMDS()} and \code{monoMDS()} have new default
      convergence criteria. Most importantly, scale factor of the
      gradient (\code{sfgrmin}) is stricter. The former limit was too
      slack with large data sets and iterations stopped early without
      getting close to the solution. In addition, \code{scores()}
      ignore now requests to dimensions beyond those calculated
      instead of failing, and \code{scores()} for \code{metaMDS()}
      results do not drop dimensions.

      \item \code{msoplot()} gained \code{legend} argument for
      positioning the legend.

      \item Nestedness function \code{nestednodf()} gained a \code{plot}
      method.

      \item \code{ordiR2step()} gained new argument \code{R2scope}
      (defaults \code{TRUE}) which can be used to turn off the criterion
      of stopping when the adjusted \eqn{R^2}{R-squared} of the current
      model exceeds that of the scope.  This option allows model
      building when the \code{scope} would be overdetermined (number of
      predictors higher than number of observations).

      \code{ordiR2step()} now handles partial redundancy analysis
      (pRDA).

      \item \code{orditorp()} gained argument \code{select} to select
      the rows or columns of the results to display.

      \item \code{protest()} prints the standardized residual statistic
      \eqn{m_{12}^2}{squared m12} in addition to the squared Procrustes
      correlation \eqn{R^2}{R-squared}.  Both were calculated, but only
      the latter was displayed.

      Permutation tests are much faster in \code{protest()}. Instead
      of calling repeatedly \code{procrustes()}, the goodness of fit
      statistic is evaluated within the function. 

      \item \code{wcmdscale()} gained methods for \code{print},
      \code{plot} etc. of the results. These methods are only used if
      the full \code{wcmdscale} result is returned with, e.g., argument
      \code{eig = TRUE}. The default is still to return only a matrix of
      scores similarly as the standard \R function \code{cmdscale()},
      and in that case the new methods are not used.

    }

  } % new features
   

} % end 2.0-6

\section{Changes in version 2.0-5}{

  \subsection{BUG FIXES}{

    \itemize{

      \item \code{anova(<cca_object>, ...)} failed with
      \code{by = "axis"} and \code{by = "term"}. The bug was reported by
      Dr Sven Neulinger (Christian Albrecht University, Kiel, Germany).

      \item \code{radlattice} did not honour argument \code{BIC = TRUE},
      but always displayed AIC.

    }

  } % bug fixes

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Most \pkg{vegan} functions with permutation tests have now a
      \code{density} method that can be used to find empirical
      probability distributions of permutations. There is a new
      \code{plot} method for these functions that displays both the
      density and the observed statistic. The \code{density} function is
      available for \code{adonis}, \code{anosim}, \code{mantel},
      \code{mantel.partial}, \code{mrpp}, \code{permutest.cca} and
      \code{procrustes}.

      Function \code{adonis} can return several statistics, and it has
      now a \code{densityplot} method (based on \pkg{lattice}).

      Function \code{oecosimu} already had \code{density} and
      \code{densityplot}, but they are now similar to other \pkg{vegan}
      methods, and also work with \code{adipart}, \code{hiersimu} and
      \code{multipart}.

      \item \code{radfit} functions got a \code{predict} method that
      also accepts arguments \code{newdata} and \code{total} for new
      ranks and site totals for prediction.  The functions can also
      interpolate to non-integer \dQuote{ranks}, and in some models
      also extrapolate.

    }
  } % new functions

  \subsection{NEW FEATURES}{
    \itemize{

      \item Labels can now be set in the \code{plot} of \code{envfit}
      results. The labels must be given in the same order that the
      function uses internally, and new support function \code{labels}
      can be used to display the default labels in their correct order.

      \item Mantel tests (functions \code{mantel} and
      \code{mantel.partial}) gained argument \code{na.rm} which can be
      used to remove missing values. This options should be used with
      care: Permutation tests can be biased if the missing values were
      originally in matching or fixed positions.

      \item \code{radfit} results can be consistently accessed with
      the same methods whether they were a single model for a single
      site, all models for a single site or all models for all sites
      in the data.  All functions now have methods \code{AIC},
      \code{coef}, \code{deviance}, \code{logLik}, \code{fitted},
      \code{predict} and \code{residuals}.

    }

  } % new features
  
  \subsection{INSTALLATION AND BUILDING}{
    \itemize{

      \item Building of \pkg{vegan} vignettes failed with the latest
      version of LaTeX (TeXLive 2012).

      \item \R{} versions later than 2.15-1 (including development
      version) report warnings and errors when installing and checking
      \pkg{vegan}, and you must upgrade \pkg{vegan} to this version.
      The warnings concern functions \code{cIndexKM} and
      \code{betadisper}, and the error occurs in \code{betadisper}.
      These errors and warnings were triggered by internal changes in
      \R.
      
    }
  } % installation and building
  

} % version 2.0-5


\section{Changes in version 2.0-4}{

  \subsection{BUG FIXES}{
    \itemize{
    
      \item \code{adipart} assumed constant gamma diversity in
        simulations when assessing the \eqn{P}-value.  This could give
        biased results if the null model produces variable gamma
        diversities and option \code{weights = "prop"} is used.  The
        default null model (\code{"r2dtable"}) and the default option
        (\code{weights = "unif"}) were analysed correctly.

      \item \code{anova(<prc-object>, by = "axis")} and other
        \code{by} cases failed due to \file{NAMESPACE} issues.

      \item \code{clamtest} wrongly used frequencies instead of the
        counts when calculating sample coverage.  No detectable
        differences were produced when rerunning examples from Chazdon
        et al. 2011 and \pkg{vegan} help page.

      \item \code{envfit} failed with unused factor levels.

      \item \code{predict} for \code{cca} results with
        \code{type = "response"} or \code{type = "working"} failed with
        \code{newdata} if the number of rows did not match with the
        original data.  Now the \code{newdata} is ignored if it has a
        wrong number of rows.  The number of rows must match because
        the results in \code{cca} must be weighted by original row
        totals.  The problem did not concern \code{rda} or
        \code{capscale} results which do not need row weights.
        Reported by Glenn De'ath.
    
    }
  }% end bug fixes

  \subsection{NEW FEATURES}{
    \itemize{

      \item Functions for diversity partitioning (\code{adipart},
        \code{hiersimu} and \code{multipart}) have now \code{formula}
        and \code{default} methods.  The \code{formula} method is
        identical to the previous functions, but the \code{default}
        method can take two matrices as input. 

 	Functions \code{adipart} and \code{multipart} can be used for
 	fast and easy overall partitioning to alpha, beta and gamma
 	diversities by omitting the argument describing the hierarchy.

      \item The method in \code{betadisper} is biased with small
        sample sizes.  The effects of the bias are strongest with
        unequal sample sizes. A bias adjusted version was developed by
        Adrian Stier and Ben Bolker, and can be invoked with argument
        \code{bias.adjust} (defaults to \code{FALSE}).

      \item \code{bioenv} accepts dissimilarities (or square matrices
        that can be interpreted as dissimilarities) as an alternative to
        community data.  This allows using other dissimilarities than
        those available in \code{vegdist}.

      \item \code{plot} function for \code{envfit} results gained new
        argument \code{bg} that can be used to set background colour for
        plotted labels.

      \item \code{msoplot} is more configurable, and allows, for
        instance, setting y-axis limits.

      \item Hulls and ellipses are now filled using semitransparent
        colours in \code{ordihull} and \code{ordiellipse}, and the
        user can set the degree of transparency with a new argument
        \code{alpha}.  The filled shapes are used when these functions
        are called with argument \code{draw = "polygon"}.  Function
        \code{ordihull} puts labels (with argument \code{label = TRUE})
        now in the real polygon centre.

      \item \code{ordiplot3d} returns function \code{envfit.convert}
        and the projected location of the \code{origin}.  Together
        these can be used to add \code{envfit} results to existing
        \code{ordiplot3d} plots.

        Equal aspect ratio cannot be set exactly in \code{ordiplot3d}
        because underlying core routines do not allow this. Now
        \code{ordiplot3d} sets equal axis ranges, and the documents
        urge users to verify that the aspect ratio is reasonably equal
        and the graph looks like a cube.  If the problems cannot be
        solved in the future, \code{ordiplot3d} may be removed from
        next releases of \pkg{vegan}.

      \item Function \code{ordipointlabel} gained argument to
        \code{select} only some of the items for plotting. The
        argument can be used only with one set of points.

    }
  } % end new features 	 

}%end version 2.0-4

\section{Changes in version 2.0-3}{

  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Added new nestedness functions \code{nestedbetasor} and
      \code{nestedbetajac} that implement multiple-site dissimilarity
      indices and their decomposition into turnover and nestedness
      components following Baselga (\emph{Global Ecology and
      Biogeography} 19, 134--143; 2010).

      \item Added function \code{rarecurve} to draw rarefaction curves
      for each row (sampling unit) of the input data, optionally with
      lines showing rarefied species richness with given sample size
      for each curve.

      \item Added function \code{simper} that implements
      \dQuote{similarity percentages} of Clarke (\emph{Australian
      Journal of Ecology} 18, 117--143; 1993).  The method compares
      two or more groups and decomposes the average between-group
      Bray-Curtis dissimilarity index to contributions by individual
      species.  The code was developed in 
      \href{https://github.com/jarioksa/vegan}{GitHub}
      by Eduard Szöcs (Uni Landau, Germany).

    }
  } % end new functions

  \subsection{BUG FIXES}{
    \itemize{

      \item \code{betadisper()} failed when the \code{groups} was a
      factor with empty levels.

      \item Some constrained ordination methods and their support
      functions are more robust in border cases (completely aliased
      effects, saturated models, user requests for non-existng scores
      etc). Concerns \code{capscale}, \code{ordistep}, \code{varpart},
      \code{plot} function for constrained ordination, and
      \code{anova(<cca.object>, by = "margin")}.

      \item The \code{scores} function for \code{monoMDS} did not
      honour \code{choices} argument and hence dimensions could not be
      chosen in \code{plot}.

      \item The default \code{scores} method failed if the number of
      requested axes was higher than the ordination object had.  This
      was reported as an error in \code{ordiplot} in
      \href{https://stat.ethz.ch/pipermail/r-sig-ecology/2012-February/002768.html}{R-sig-ecology} mailing list.

    }
  } % end bug fixes	
		  
  \subsection{NEW FEATURES}{
     \itemize{

       \item \code{metaMDS} argument \code{noshare = 0} is now
       regarded as a numeric threshold that always triggers extended
       dissimilarities (\code{stepacross}), instead of being treated
       as synonymous with \code{noshare = FALSE} which always
       suppresses extended dissimilarities.

       \item Nestedness discrepancy index \code{nesteddisc} gained a
       new argument that allows user to set the number of iterations
       in optimizing the index.

       \item \code{oecosimu} displays the mean of simulations and
       describes alternative hypothesis more clearly in the printed
       output. 

       \item Implemented adjusted \eqn{R^2}{R-squared} for partial
       RDA. For partial model \code{rda(Y ~ X1 + Condition(X2))} this
       is the same as the component \code{[a] = X1|X2} in variance
       partition in \code{varpart} and describes the marginal (unique)
       effect of constraining term to adjusted \eqn{R^2}{R-squared}.

       \item Added Cao dissimilarity (CYd) as a new dissimilarity
       method in \code{vegdist} following Cao et al., \emph{Water
       Envir Res} 69, 95--106 (1997). The index should be good for
       data with high beta diversity and variable sampling
       intensity. Thanks to consultation to Yong Cao (Univ Illinois,
       USA).
     
     }
  } % end new features
} % end version 2.0-3

\section{Changes in version 2.0-2}{
  \subsection{BUG FIXES}{
   \itemize{

     \item Function \code{capscale} failed if constrained component
     had zero rank. This happened most likely in partial models when
     the conditions aliased constraints. The problem was observed in
     \code{anova(..., by ="margin")} which uses partial models to
     analyses the marginal effects, and was reported in an email
     message to
     \href{https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html}{R-News
     mailing list}.

     \item \code{stressplot} and \code{goodness} sometimes failed when
     \code{metaMDS} was based on \code{isoMDS} (\pkg{MASS} package)
     because \code{metaMDSdist} did not use the same defaults for
     step-across (extended) dissimilarities as
     \code{metaMDS(..., engine = "isoMDS")}. The change of defaults can
     also influence triggering of step-across in
     \code{capscale(..., metaMDSdist = TRUE)}.

     \item \code{adonis} contained a minor bug resulting from
     incomplete implementation of a speed-up that did not affect the
     results. In fixing this bug, a further bug was identified in
     transposing the hat matrices. This second bug was only active
     following fixing of the first bug. In fixing both bugs, a
     speed-up in the internal f.test() function is fully
     realised. Reported by Nicholas Lewin-Koh.
   
     }
 }  % end bug fixes 
 
 \subsection{NEW FEATURES}{
   \itemize{

     \item \code{ordiarrows} and \code{ordisegments} gained argument
     \code{order.by} that gives a variable to sort points within
     \code{groups}. Earlier the points were assumed to be in order.
      
     \item Function \code{ordispider} invisibly returns the
     coordinates to which the points were connected.  Typically these
     are class centroids of each point, but for constrained ordination
     with no \code{groups} they are the LC scores.

    }		 
  }  %end new features
		  
} %end version 2.0-2

\section{Changes in version 2.0-1}{
  \subsection{NEW FUNCTIONS}{
    \itemize{
  
      \item \code{clamtest}: new function to classify species as
      generalists and specialists in two distinct habitats (CLAM test of
      Chazdon et al., \emph{Ecology} 92, 1332--1343; 2011).  The test is
      based on multinomial distribution of individuals in two habitat
      types or sampling units, and it is applicable only to count data
      with no over-dispersion.

      \item \code{as.preston} gained \code{plot} and \code{lines}
      methods, and \code{as.fisher} gained \code{plot} method (which
      also can add items to existing plots). These are similar as
      \code{plot} and \code{lines} for \code{prestonfit} and
      \code{fisherfit}, but display only data without the fitted lines.

      \item \code{raupcrick}: new function to implement Raup-Crick
      dissimilarity as a probability of number of co-occurring species
      with occurrence probabilities proportional to species
      frequencies.  \pkg{Vegan} has Raup-Crick index as a choice in
      \code{vegdist}, but that uses equal sampling probabilities for
      species and analytic equations. The new \code{raupcrick}
      function uses simulation with \code{oecosimu}. The function
      follows Chase et al. (2011) \emph{Ecosphere} 2:art24
      [\href{http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1}{doi:10.1890/ES10-00117.1}],
      and was developed with the consultation of Brian Inouye.

    }
  } % end NEW FUNCTIONS

  \subsection{BUG FIXES}{
    \itemize{

      \item Function \code{meandist} could scramble items and give
      wrong results, especially when the \code{grouping} was
      numerical. The problem was reported by Dr Miguel Alvarez
      (Univ. Bonn).

      \item \code{metaMDS} did not reset \code{tries} when a new model
      was started with a \code{previous.best} solution from a different
      model. 

      \item Function \code{permatswap} for community null models using
      quantitative swap never swapped items in a \eqn{2 \times 2}{2 by 2}
      submatrix if all cells were filled.

      \item The result from \code{permutest.cca} could not be
      \code{update}d because of a \file{NAMESPACE} issue.

      \item \R 2.14.0 changed so that it does not accept using
      \code{sd()} function for matrices (which was the behaviour at
      least since \R 1.0-0), and several \pkg{vegan} functions were
      changed to adapt to this change (\code{rda}, \code{capscale},
      \code{simulate} methods for \code{rda}, \code{cca} and
      \code{capscale}). The change in \R 2.14.0 does not influence the
      results but you probably wish to upgrade \pkg{vegan} to avoid
      annoying warnings.

    }	
  } % end BUG FIXES

  \subsection{ANALYSES}{
    \itemize{

      \item \code{nesteddisc} is slacker and hence faster when trying
      to optimize the statistic for tied column frequencies. Tracing
      showed that in most cases an improved ordering was found rather
      early in tries, and the results are equally good in most cases.

    }
  } % end ANALYSES 

} % end version 2.0-1

\section{Changes in version 2.0-0}{
  \subsection{GENERAL}{
    \itemize{
      
      \item Peter Minchin joins the \pkg{vegan} team.
      
      \item \pkg{vegan} implements standard \R \file{NAMESPACE}. In
      general, \code{S3} methods are not exported which means that you
      cannot directly use or see contents of functions like
      \code{cca.default}, \code{plot.cca} or \code{anova.ccabyterm}. To
      use these functions you should rely on \R delegation and simply
      use \code{cca} and for its result objects use \code{plot} and
      \code{anova} without suffix \code{.cca}. To see the contents of
      the function you can use \code{:::}, such as
      \code{vegan:::cca.default}. This change may break packages,
      documents or scripts that rely on non-exported names.
      
      \item \pkg{vegan} depends on the \pkg{permute} package. This
      package provides powerful tools for restricted permutation
      schemes. All \pkg{vegan} permutation will gradually move to use
      \pkg{permute}, but currently only \code{betadisper} uses the new
      feature. 
      
    }
  } % end GENERAL
  
  \subsection{NEW FUNCTIONS}{
    \itemize{
      
      \item \code{monoMDS}: a new function for non-metric
      multidimensional scaling (NMDS). This function replaces
      \code{MASS::isoMDS} as the default method in
      \code{metaMDS}. Major advantages of \code{monoMDS} are that it
      has \sQuote{weak} (\sQuote{primary}) tie treatment which means
      that it can split tied observed dissimilarities.  \sQuote{Weak}
      tie treatment improves ordination of heterogeneous data sets,
      because maximum dissimilarities of \eqn{1} can be split. In
      addition to global NMDS, \code{monoMDS} can perform local and
      hybrid NMDS and metric MDS.  It can also handle missing and zero
      dissimilarities.  Moreover, \code{monoMDS} is faster than
      previous alternatives. The function uses \code{Fortran} code
      written by Peter Minchin.

      \item \code{MDSrotate} a new function to replace
      \code{metaMDSrotate}. This function can rotate both \code{metaMDS}
      and \code{monoMDS} results so that the first axis is parallel to
      an environmental vector.

      \item \code{eventstar} finds the minimum of the evenness profile
      on the Tsallis entropy, and uses this to find the corresponding
      values of diversity, evenness and numbers equivalent following
      Mendes et al. (\emph{Ecography} 31, 450-456; 2008). The code was
      contributed by Eduardo Ribeira Cunha and Heloisa Beatriz Antoniazi
      Evangelista and adapted to \pkg{vegan} by Peter Solymos.
      
      \item \code{fitspecaccum} fits non-linear regression models to
      the species accumulation results from \code{specaccum}. The
      function can use new self-starting species accumulation models
      in \pkg{vegan} or other self-starting non-linear regression
      models in \R. The function can fit Arrhenius, Gleason, Gitay,
      Lomolino (in \pkg{vegan}), asymptotic, Gompertz,
      Michaelis-Menten, logistic and Weibull (in base \R) models. The
      function has \code{plot} and \code{predict} methods.
      
      \item Self-starting non-linear species accumulation models
      \code{SSarrhenius}, \code{SSgleason}, \code{SSgitay} and
      \code{SSlomolino}. These can be used with \code{fitspecaccum} or
      directly in non-linear regression with \code{nls}. These functions
      were implemented because they were found good for species-area
      models by Dengler (\emph{J. Biogeogr.} 36, 728-744; 2009).
      
    }
  } % end NEW FUNCTIONS
  
  \subsection{NEW FEATURES}{
    \itemize{

      \item \code{adonis}, \code{anosim}, \code{meandist} and
      \code{mrpp} warn on negative dissimilarities, and
      \code{betadisper} refuses to analyse them. All these functions
      expect dissimilarities, and giving something else (like
      correlations) probably is a user error.
      
      \item \code{betadisper} uses restricted permutation of the
      \pkg{permute} package. 
      
      \item \code{metaMDS} uses \code{monoMDS} as its default ordination
      engine. Function gains new argument \code{engine} that can be used
      to alternatively select \code{MASS::isoMDS}.  The default is not
      to use \code{stepacross} with \code{monoMDS} because its
      \sQuote{weak} tie treatment can cope with tied maximum
      dissimilarities of one. However, \code{stepacross} is the default
      with \code{isoMDS} because it cannot handle adequately these tied
      maximum dissimilarities.
      
      \item \code{specaccum} gained \code{predict} method which uses
      either linear or spline interpolation for data between observed
      points. Extrapolation is possible with spline interpolation, but
      may make little sense.
      
      \item \code{specpool} can handle missing values or empty factor
      levels in the grouping factor \code{pool}.  Now also checks that
      the length of the \code{pool} matches the number of
      observations.

    }
  } % end NEW FEATURES

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{

      \item \code{metaMDSrotate} was replaced with \code{MDSrotate}
      that can also handle the results of \code{monoMDS}.

      \item \code{permuted.index2} and other \dQuote{new} permutation
      code was removed in favour of the \pkg{permute} package. This code
      was not intended for normal use, but packages depending on that
      code in \pkg{vegan} should instead depend on \pkg{permute}.

    }  
    
  } % end DEPRECATED
  
  \subsection{ANALYSES}{
    \itemize{
      
      \item \code{treeheight} uses much snappier code. The results
      should be unchanged.
      
    }
  } % end ANALYSES
}% end VERSION 2.0   
   	  
