\name{NEWS} \title{vegan News} \encoding{UTF-8} \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(, ...)} 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(, 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(, 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