inst/NEWS.md
In vegan: Community Ecology Package

NEW FEATURES

Support of scores for ggplot2 graphics is improved and extended for ordination functions. Suitable scores can be requested with argument tidy = TRUE, and in general all available types of scores are returned in a data frame with variable score labelling the type. The option was implemented in default method of scores and for structured wcmdscale objects, and glitches were fixed for rda family and decorana. Previously tidy scores were implemented for cca, rda, dbrda family of methods, metaMDS, envfit and rarecurve.
adonis2 and anova for constrained ordination results can perform a sequential test of one-degree-of-freedom effects where multi-level factors are split to their contrasts. Previously the test was available only in permutest.
New summary function for varpart for a brief overview. The summary shows unique and overall contributed variation for each set of variables. The fractions shared by several sets of variables are divided equally with all contributing sets following Lai J, Zou Y, Zhang J, Peres-Neto P (2022) Methods in Ecology and Evolution, 13: 782–788.
decorana estimates orthogonalized eigenvalues and the total inertia (scaled Chi-square). Orthogonalized eigenvalues can add up to the total inertia. Together these enabled implementing eigenvals, bstick and screeplot methods for decorana.
Axis lengths are reported for all decorana methods.
Implemented tolerance method for decorana. This returns the criterion that was used in rescaling DCA, and can be used to inspect the success of rescaling: it should be constant 1 over the whole axis.
New toCoda function to transform sequential null model results from oecosimu to an object that can be analysed with coda for convergence and independence as an MCMC model. Function replaces as.mcmc.oecosimu and as.mcmc.permat.
metaMDS is more informative about finding similar repeated results with random starts and uses less confusing language when reporting the results.
Hellinger distance is directly available in vegdist.
vegdist, betadiver and raupcrick set attribute maxdist giving the numeric value of theoretical maximum of the dissimilarity index. For many dissimilarities this is 1, but √2 for Chord and Hellinger distances, for instance. The attribute is NA for open indices that do not have such a ceiling. betadiver has three similarity indices and these set maxdist 0.
metaMDS defaults to halfchange scaling when the dissimilarities have a numeric maxdist attribute, and adapt the threshold to the ceiling value. For open indices without ceiling, the threshold will be in the scale of dissimilarities. metaMDS used a simple test to detect index ceiling 1, but the test is now more robust and can also find other maximum values. If such inference is made, the function will broadcast a message of assumed value of the ceiling.
Mountford index in vegdist is now scaled to maximum value log(2). Earlier Mountford distances were scaled to maximum 1.
hatvalues of constrained ordination objects can sometimes be practically 1 or above 1, but now these cases will be exactly 1. In those cases rstandard, rstudent and cooks.distance will be NaN. The behaviour is similar as in stats::lm.influence functions.
as.rad can handle multi-row data frames or matrices and return a list of Rank-Abundance data for each row. Earlier only one site was handled.
decostand returns attribute parameters of settings and variables used in standardization. New function decobackstand can use parameters to reconstruct original non-standardized data. Back-transformation is not exact but has round-off errors, although there is an attempt to keep original zeros exact. Back-transformation is not possible for methods pa, rank and rrank and it is not implemented for alr. Back-transformation queried in https://stackoverflow.com/questions/73263526/
Rarefaction and rarefaction-based methods make sense only with original observed counts and give misleading results if data are multiplied or rare species are removed. Observed counts usually have singletons (species with count one), and these method issue a warning if minimum count is higher than one (which may be a false positive, but inspect your data). Concerns functions rarefy, drarefy, rrarefy, rarecurve, specaccum(..., method="rarefy"), rareslope and avgdist. See github discussion #537.
avgdist exposes as.dist arguments and can return "dist"ance objects that appear as lower triangles instead of appearing as symmetric matrices.
betadisper plots accept col argument (PR #300).

BUG FIXES

decorana returned wrong results when Hill's piecewise transformation (arguments before/after) were used, unless downweighting was also used.
scores failed when metaMDS result had no species scores. Bug was introduced in release 2.6-2. Issue raised in https://stackoverflow.com/questions/72483924/
tolerance.cca failed when only one axis (choice) was requested.
decostand(..., method="alr") did not accept name as a reference, and could fail in some cases.
CRAN package proxy interfered with simper and caused an obscure error (github issue #528).

DEPRECATED AND DEFUNCT

adonis is on way to deprecation. Use adonis2 instead.
as.mcmc.oecosimu and as.mcmc.permat were deprecated: these could not be used as S3 methods without depending on coda package. Use toCoda instead.

INSTALLATION

Compiled code is adapted to the changes in R 4.2.0. See issues #447, #507.
Cross-references to function in other packages were adapted to more stringent tests in CRAN

NEW FEATURES

Aitchison and robust Aitchison distances were added to vegdist. Similar data transformations were added to decostand.
Several functions can return “tidy” data structures that can be used in ggplot2 graphics: rarecurve, scores functions for constrained ordination (cca etc.), decorana, envfit, metaMDS.
scores.envfit gained argument arrow.mul. vegan plot functions used this automatically, but now it is easier to use envfit in non-vegan plotting.
Added function simpson.unb for unbiased Simpson diversity that is more robust to the variation in sample sizes.
diversity gained argument group to calculate indices for pooled data. Discussed in issue #393.
simper is much faster even though parallel processing is not implemented in the new code.
pairs function was added to plot permustats variables against each other.
varpart accepts dissimilarities given as a symmetric square matrix instead of "dist" object per wish of issue #497.
metaMDS adopted a more user-friendly policy, and trymax will always be the maximum number of tries. See dicussion in https://stackoverflow.com/questions/66748605/.
adonis2 accepts strata. adonis2 is the new main function that replaces old adonis. See issue #427.
Fisher alpha (fisherfit) is badly suited for extreme communities that do not follow Fisher's model. Now fisherfit returns NA to communities that have 0 or 1 species, and issues a warning with communities consisting of singletons and having extreme Fisher alpha.
adipart and multipart formulae will automatically add unique id and and constant. This will always sandwich the requested grouping between alpha and gamma diversities, but not change the results for requested groupings.

BUG FIXES

anova function failed in marginal tests when constrained partial ordination model (cca, rda etc.) had interaction terms. Issue #463.
Constrained ordination (cca etc.) gave misleading results when all external variables (constraints, condition) were constant and explained nothing.
decorana could fail when some axes had zero eigenvalues. Issue #401.
Species accumulation (specaccum) failed when there was only one species, but several “communities”. Issue #501.
Parallel processing failed in Windows or with socket clusters in permutest of betadisper. Issue #369.
orditorp failed if numeric labels were supplied. Reported in https://stackoverflow.com/questions/69272366/.
Argument summarize was accidentally dropped from goodness.cca in 2017.
taxa2dist failed if there was only one usable taxonomic level. See https://stackoverflow.com/questions/67231431/.

DEPRECATED AND DEFUNCT

Function adonis2 will replace adonis.
humpfit functions are defunct and removed. They are available in non-CRAN package natto at https://github.com/jarioksa/natto.
commisimulator is defunct. Use simulate for nullmodel objects.
permuted.index is finally defunct (it was deprecated in vegan 2.2-0).
as.mlm is defunct. Use functions documented with influence.cca, such as hatvalues.cca, rstandard.cca, rstudent.cca, cooks.distance.cca and others.

BUG FIXES

Several distance-based functions failed if all distances were zero (betadisper, capscale, isomap, monoMDS, pcnm, wcmdscale). Reported in github issue #372.
Non-linear self-starting regression models SSarrhenius, SSgitay, SSgleason and SSlomolino failed in future R. The failure was caused by internal changes in R-devel. Github issue #382.
Arrow labels were in wrong position in plot.envfit(..., add = FALSE).
rarecurve added unnecessary names to the results. Github issue #352.
permutest for betadisper failed in parallel processing in Windows and in other systems when socket clusters were used. Github issue #369.

NEW FEATURES

Chi-square and Chord distances were added to vegdist. Both of these distances can be calculated as Euclidean distances of transformed data, and actually were available earlier, but many users did not notice this.
monoMDS (and hence metaMDS) uses stricter convergence criteria. This improves possibilities to find stable solutions. However, users may still need to tweak convergence criteria with their data. See discussion in Github issue #354.
text functions for constrained ordination plots (cca, rda, dbrda, capscale) accept now expression labels. This allows using subscripts, superscripts and mathematical expressions. New support function labels.cca returns the current text labels so that authors can change the desired ones. See github issue #374.
vegemite returns invisibly the final formatted table allowing further processing.
ordiplot passes cex argument to linestack and decorana plots.

BUG FIXES

vegdist silently accepted missing values (NA) and removed them from the analysis also with option na.rm = FALSE. The behaviour was introduced in vegan version 2.5-1. See GitHub issue #319.
The labels were displaced when the bunch of arrows was not drawn at the origin of the ordination graph in envfit. See GitHub issue #315.
Hill scale in coverscale is open-ended and is not limited to percent data, unlike most traditional cover class scales which are undefined above 100% cover.

NEW FEATURES

The results of as.rad no longer print the index attribute: the attribute is still in the object, but printing made the output messy.

INSTALLATION

vegan depends on R 3.4.0 or higher. The next vegan release may increase the dependence to R 3.6.0.
R 3.6.0 improved the method to find random indices for permuting and sampling data. Vegan relies now on the R functions in its ecological null models (functions nullmodel, oecosimu, commsim, permatfull, permatswap and others). Technically this change is compatible with R 3.4.0 and later, but you can only gain the benefits of improved code with a current release of R. The null models may change due to this change, and most certainly they change in R 3.6.0. See NEWS for the R 3.6.0 release and discussion in github issue #312.

Most vegan permutation routines rely on permute, and there you gain similar benefits of improved randomness when you upgrade R.

Thanks to the new R dependence, sigma for constrained ordination results works without workarounds of vegan 2.5-2. This fixes completely the issue discussed in #274.
Vegan test results cannot be reproduced in older versions than R 3.6.0. If you are worried about this, you should upgrade R.

BUG FIXES

metaMDS failed in scaling results when other engine than monoMDS was used. However, we recommend you use monoMDS. See github issue #310.

NEW FEATURES

betadisper changed interpretation of negative squared distances which give complex-valued distances. Now they are regarded as zero-distances whereas earlier we used their modulus. This will change the results in cases where you had negative squared distances. For further discussion, see github issue #306.

INSTALLATION AND TESTING

The code for interpreting formula will change in R 3.6.0, and this makes constrained ordination methods (cca, rda, dbrda, capscale) to fail. See github issue #299.
R 3.6.0 introduces a new environment variable _R_CHECK_LENGTH_1_LOGIC2_, and several functions fail if this variable is set. Changes concern ordiplot, plot and summary for constrained ordination objects, and ordixyplot. See github issue #305.

BUG FIXES

decorana gave incorrect results when downweighting was used (argument iweigh = 1). The bug was introduced in vegan 2.5-1 and reported as github issue #303.
goodness for constrained ordination methods failed when the constraints had rank = 1 (only one constraining variable). Reported by Pierre Legendre.

NEW FEATURES

Adjusted R2 is enabled for partial RDA models (functions rda and dbrda) and partial CCA models (function cca) in function RsquareAdj. The feature was disabled in vegan 2.5-1 for both. For RDA, the calculation is similar as in vegan 2.4-6 and earlier. Partial CCA is now consistent with RDA and differs from the earlier implementation. For both methods, the partial models are consistent with varpart. See github issue #295.

INSTALLATION

Tests for numerical analysis were written more robustly so that they give more similar results with alternative platforms and versions of R and BLAS/Lapack libraries. See github issue #282.

BUG FIXES

Constrained ordination gave misleading results when some constraints or conditions had data with NULL variables. This rarely happens in normal usage, but could happen in marginal anova as reported in github issue #291.
Several functions for numerical analysis wrongly accepted non-numeric data (for instance, factors) and gave either meaningless results or confusing error messages. Fixed functions include beals, designdist, diversity, gdispweight, indpower, spantree, specpool, tsallis, tsallisaccum and vegdist. See github issue #292.
envfit with vectors could fail with missing data.
The original data were not scaled and centred similarly as simulations in simulate.rda when several simulations were returned as a simmat object (which is compatible with nullmodel simulations and can be used in oecosimu).

NEW FEATURES

anosim checks its input to avoid confusing error messages like that reported in StackOverflow question 52082743.
Broken-stick distribution (function bstick) is no longer calculated for distance-based Redundancy Analysis (dbrda) with negative eigenvalues, because it is not clear how this should be done. Now dbrda and capscale are similar with this respect.
print function for betadisper results gained new argument neigen to select the number of eigenvalues shown. The print is more robust when the number of eigenvalues is lower than the requested neigen.

DEPRECATED

Function humpfit was moved to the natto package and is still available from https://github.com/jarioksa/natto. It is scheduled for complete removal in vegan 2.6-0.

INSTALLATION AND COMPATIBILITY

Vegan declares dependence on R version 3.2.0. This dependence was not yet noticed in the previous vegan release. However, the generic sigma function was only defined in R-3.3.0, and therefore sigma.cca of vegan must be spelt out completely when using R-3.2.x. See discussion in issue #274.
CRAN package klaR has function rda, and when loaded together with vegan this clashes with vegan rda for Redundancy Analysis. Vegan tries to mitigate the problem. In most cases vegan functions will be used if vegan was loaded after klaR, and an error message is issued if klaR objects are handled with vegan functions. klaR is also tricked to print an informative message if it handles vegan objects. However, vegan namespace can be attached automatically at the start-up and then klaR functions will take precedence. This was reported as issue #277.
Bioconductor package phyloseq has a problem with vegdist function for dissimilarities. The problem can be fixed by re-installing phyloseq from its source package. If you cannot do this, you must either downgrade to vegan version 2.4-6 or wait till Bioconductor binary packages are upgraded. This was reported in Stackoverflow, and as vegan issue #272, and as phyloseq issues #918 and #921.

BUG FIXES

Plotting betadisper failed if any of the groups had only one member. Reported in Stackoverflow as “Error: Incorrect no.of dimensions” when plotting multivariate data in Vegan.
Permutation tests for constrained ordination (anova.cca, permutest.cca) could fail in parallel processing with socket clusters. Socket clusters are always used in Windows and they can also be used in other operating systems when created with makeCluster. See issue #276.

GENERAL

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 https://github.com/vegandevs/vegan/issues/.
Compiled code is used much more extensively, and most compiled functions use .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 (anova.cca) and binary null models (nullmodel).
Constrained ordination functions (cca, rda, dbrda, 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 cca.object and github issue #262). Some support and analysis functions may no longer work with result objects created in previous vegan versions. You should use update(old.result.object) to fix these old result objects. See github issues #218, #227.
vegan includes some tests that are run when checking the package installation. See github issues #181, #271.
The informative messages (warnings, notes and error messages) are cleaned and unified which also makes possible to provide translations.

NEW FUNCTIONS

avgdist: new function to find averaged dissimilarities from several random rarefactions of communities. Code by Geoffrey Hannigan. See github issues #242, #243, #246.
chaodist: new function that is similar to designdist, but uses Chao terms that are supposed to take into account the effects of unseen species (Chao et al., Ecology Letters 8, 148-159; 2005). Earlier we had Jaccard-type Chao dissimilarity in vegdist, but the new code allows defining any kind of Chao dissimilarity.
New functions to find influence statistics of constrained ordination objects: hatvalues, sigma, rstandard, rstudent, cooks.distance, SSD, vcov, df.residual. Some of these could be earlier found via as.mlm function which is deprecated. See github issue #234.
boxplot was added for permustats results to display the (standardized) effect sizes.
sppscores: new function to add or replace species scores in distance-based ordination such as dbrda, capscale and metaMDS. Earlier dbrda did not have species scores, and species scores in capscale and metaMDS were based on raw input data which may not be consistent with the used dissimilarity measure. See github issue #254.
cutreeord: new function that is similar to 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.
sipoo.map: a new data set of locations and sizes of the islands in the Sipoo archipelago bird data set sipoo.

NEW FEATURES IN CONSTRAINED ORDINATION

The inertia of Correspondence Analysis (cca) is called “scaled Chi-square” instead of using a name of a little known statistic.
If elements for Constraints and Conditions are data frames in non-formula call of rda or 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.
Regression scores for constraints can be extracted and plotted for constrained ordination methods. See github issue #226.
Full model (model = "full") is again enabled in permutations tests for constrained ordination results in anova.cca and permutest.cca.
permutest.cca gained a new option by = "onedf" to perform tests by sequential one degree-of-freedom contrasts of factors. This option is not (yet) enabled in anova.cca.
The permutation tests are more robust, and most scoping issues should have been fixed.
Permutation tests use compiled C code and they are much faster. See github issue #211.
permutest printed layout is similar to anova.cca.
eigenvals gained a new argument (model) to select either constrained or unconstrained scores. The old argument (constrained) is deprecated. See github issue #207.
summary.eigenvals returns a matrix instead of a list containing only that matrix.
Adjusted R2 is not calculated for partial ordination, because it is unclear how this should be done (function RsquareAdj).
ordiresids can display standardized and studentized residuals.
Function to construct model.frame and model.matrix for constrained ordination are more robust and fail in fewer cases.
goodness and inertcomp for constrained ordination result object no longer has an option to find distances: only explained variation is available.
inertcomp gained argument unity. This will give “local contributions to beta-diversity” (LCBD) and “species contribution to beta-diversity” (SCBD) of Legendre & De Cáceres (Ecology Letters 16, 951-963; 2012).
goodness is disabled for capscale.
prc gained argument const for general scaling of results similarly as in rda.
prc uses regression scores for Canoco-compatibility.

NEW FEATURES IN NULL MODEL COMMUNITIES

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 2 times 2 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 vegan versions, and old binary model results cannot be replicated exactly. See github issues #197, #255 for details and timing.
Ecological null models (nullmodel, simulate, make.commsim, oecosimu) gained new null model "greedyqswap" which can radically speed up quasi-swap models with minimal risk of introducing bias.
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.

NEW FEATURES IN OTHER FUNCTIONS

adonis2 gained a column of R2 similarly as old adonis.
Great part of R code for decorana is written in C which makes it faster and reduces the memory footprint.
metaMDS results gained new points and text methods.
ordiplot and other ordination plot functions can be chained with their points and text functions allowing the use of magrittr pipes. The points and text functions gained argument to draw arrows allowing their use in drawing biplots or adding vectors of environmental variables with ordiplot. Since many ordination plot methods return an invisible "ordiplot" object, these points and text methods also work with them. See github issue #257.
Lattice graphics (ordixyplot) for ordination can add polygons that enclose all points in the panel and complete data.
ordicluster gained option to suppress drawing in plots so that it can be more easily embedded in other functions for calculations.
as.rad returns the index of included taxa as an attribute.
Random rarefaction (function rrarefy) uses compiled C code and is much faster.
plot of specaccum can draw short horizontal bars to vertical error bars. See StackOverflow question 45378751.
decostand gained new standardization methods rank and rrank which replace abundance values by their ranks or relative ranks. See github issue #225.
Clark dissimilarity was added to vegdist (this cannot be calculated with designdist).
designdist evaluates minimum terms in compiled code, and the function is faster than vegdist also for dissimilarities using minimum terms. Although designdist is usually faster than vegdist, it is numerically less stable, in particular with large data sets.
swan passes type argument to beals.
tabasco can use traditional cover scale values from function coverscale. Function coverscale can return scaled values as integers for numerical analysis instead of returning characters for printing.
varpart can partition Chi-squared inertia of correspondence analysis with new argument chisquare. The adjusted R2 is based on permutation tests, and the replicate analysis will have random variation.
The explanatory tables can be data frames with factors or single factors in 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. Montréal.

BUG FIXES

Very long Condition() statements (> 500 characters) failed in partial constrained ordination models (cca, rda, dbrda, capscale). The problem was detected in StackOverflow question 49249816.
Labels were not adjusted when arrows were rescaled in envfit plots. See StackOverflow question 49259747.
ordiArrowMul failed if there was only one arrow to be plotted in envfit.

DEPRECATED AND DEFUNCT

as.mlm function for constrained correspondence analysis is deprecated in favour of new functions that directly give the influence statistics. See github issue #234.
commsimulator is now defunct: use simulate for nullmodel objects.
ade4 cca objects are no longer handled in vegan: ade4 has had no cca since version 1.7-8 (August 9, 2017).

INSTALLATION AND BUILDING

CRAN packages are no longer allowed to use FORTRAN input, but 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 read.cep is less powerful and more fragile, and can only read data in “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 cepreader. See github issue #263. The cepreader package is developed in https://github.com/vegandevs/cepreader.

BUG FIXES

Some functions for rarefaction (rrarefy), species abundance distribution (preston) and species pool (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, sqrt(3)^2 would pass the test as 3, but was interpreted strictly as integer 2. See github issue #259.

NEW FEATURES

ordiresids uses now weighted residuals for cca results.

BUG FIXES

Several “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.
Lattice graphics for ordination (ordixyplot and friends) colour the arrows by groups instead of randomly mixed colours.
Information on constant or mirrored permutations was omitted when reporting permutation tests (e.g., in anova for constrained ordination).

NEW FEATURES

ordistep has improved interpretation of 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 46985029.
fitspecaccum gained new support functions nobs and logLik which allow better co-operation with other packages and functions. See GitHub issue #250.
The “backtracking” null model for community simulation is faster. However, “backtracking” is a biased legacy model that should not be used except in comparative studies.

INSTALLATION AND BUILDING

orditkplot should no longer give warnings in CRAN tests.

BUG FIXES

anova(..., by = "axis") for constrained ordination (cca, rda, dbrda) ignored partial terms in Condition().
inertcomp and summary.cca failed if the constrained component was defined, but explained nothing and had zero rank. See StackOverflow: R - Error message in doing RDA analysis - vegan package.
Labels are no longer cropped in the meandist plots.

NEW FEATURES

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, Methods Ecol Evol 2, 269–277 (2011) who regarded marginal tests as unbiased.
Canberra distance in vegdist can now handle negative input entries similarly as latest versions of R.

INSTALLATION AND BUILDING

vegan registers native C and Fortran routines. This avoids warnings in model checking, and may also give a small gain in speed.
Future versions of vegan will deprecate and remove elements pCCA$Fit, CCA$Xbar, and CA$Xbar from cca result objects. This release provides a new function 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 ordiYbar for smooth transition.

BUG FIXES

as.mlm methods for constrained ordination include zero intercept to give the correct residual degrees of freedom for derived statistics.
biplot method for rda passes correlation argument to the scaling algorithm.
Biplot scores were wrongly centred in cca which caused a small error in their values.
Weighting and centring were corrected in intersetcor and spenvcor. The fix can make a small difference when analysing cca results.

Partial models were not correctly handled in intersetcor.

envfit and ordisurf functions failed when applied to species scores.
Non-standard variable names can be used within 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 ordiR2step when using a variable name that contained a hyphen (which was wrongly interpreted as a minus sign in partial ordination).
ordispider did not pass graphical arguments when used to show the difference of LC and WA scores in constrained ordination.
ordiR2step uses only forward selection to avoid several problems in model evaluation.
tolerance function could return NaN in some cases when it should have returned 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.

BUG FIXES

Permutation tests (permutests, anova) for the first axis failed in constrained distance-based ordination (dbrda, capscale). Now 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 #198 and pull request #199.
Some support functions for dbrda or capscale gave results or some of their components in wrong scale. Fixes in stressplot, simulate, predict and fitted functions.
intersetcor did not use correct weighting for cca and the results were slightly off.
anova and permutest failed when betadisper was fitted with argument bias.adjust = TRUE. Fixes Github issue #219 reported by Ross Cunning, O'ahu, Hawaii.
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).
The cca method of tolerance was returning incorrect values for all but the second axis for sample heterogeneities and species tolerances. See issue #216 for details.

NEW FEATURES

Biplot scores are scaled similarly as site scores in constrained ordination methods cca, rda, capscale and dbrda. Earlier they were unscaled (or more technically, had equal scaling on all axes).
tabasco adds argument to scale the colours by rows or columns in addition to the old equal scale over the whole plot. New arguments labRow and 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.
Sequential null models are somewhat faster (up to 10%). Non-sequential null models may be marginally faster. These null models are generated by function nullmodel and also used in oecosimu.
vegdist is much faster. It used to be clearly slower than stats::dist, but now it is nearly equally fast for the same dissimilarity measure.
Handling of data= in formula interface is more robust, and messages on user errors are improved. This fixes points raised in Github issue #200.
The families and orders in dune.taxon were updated to APG IV (Bot J Linnean Soc 181, 1–20; 2016) and a corresponding classification for higher levels (Chase & Reveal, Bot J Linnean Soc 161, 122-127; 2009).

INSTALLATION

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 vegan issues.

BUG FIXES

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 goodness for constrained ordination, inertcomp, fitted for capscale, stressplot for RDA, CCA (GitHub issue #189).
goodness for CCA & friends ignored choices argument (GitHub issue #190).
goodness function did not consider negative eigenvalues of db-RDA (function dbrda).
Function meandist failed in some cases when one of the groups had only one observation.
linestack could not handle expressions in labels. This regression is discussed in GitHub issue #195.
Nestedness measures nestedbetajac and nestedbetasor expecting binary data did not cope with quantitative input in evaluating Baselga's matrix-wide Jaccard or Sørensen dissimilarity indices.
Function as.mcmc to cast oecosimu result to an MCMC object (coda package) failed if there was only one chain.

NEW FEATURES

diversity function returns now NA if the observation had NA values instead of returning 0. The function also checks the input and refuses to handle data with negative values. GitHub issue #187.
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.
Several functions are more robust if their factor arguments contain missing values (NA): betadisper, adipart, multipart, hiersimu, envfit and constrained ordination methods cca, rda, capscale and dbrda. GitHub issues #192 and #193.

DISTANCE-BASED ANALYSIS

Distance-based methods were redesigned and made consistent for ordination (capscale, new dbrda), permutational ANOVA (adonis, new adonis2), multivariate dispersion (betadisper) and variation partitioning (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 (Ecology 82, 290–297; 2001).
dbrda is a new function for distance-based Redundancy Analysis following McArdle & Anderson (Ecology 82, 290–297; 2001). With metric dissimilarities, the function is equivalent to old capscale, but negative eigenvalues of semimetric indices are handled differently. In 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 capscale and other constrained ordination methods, but full compatibility cannot be achieved (see issue #140 in Github). The function is based on the code by Pierre Legendre.
The old capscale function for constrained ordination is still based only on real components, but the total inertia of the components is assessed similarly as in dbrda.

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

adonis2 is a new function for permutational ANOVA of dissimilarities. It is based on the same algorithm as the dbrda. The function can perform overall tests of all independent variables as well as sequential and marginal tests of each term. The old adonis is still available, but it can only perform sequential tests. With same settings, adonis and adonis2 give identical results (but see Github issue #156 for differences).
Function varpart can partition dissimilarities using the same algorithm as dbrda.
Argument sqrt.dist takes square roots of dissimilarities and these can change many popular semimetric indices to metric distances in capscale, dbrda, wcmdscale, adonis2, varpart and betadisper (issue #179 in Github).
Lingoes and Cailliez adjustments change any dissimilarity into metric distance in capscale, dbrda, adonis2, varpart, betadisper and wcmdscale. Earlier we had only Cailliez adjustment in capscale (issue #179 in Github).
RsquareAdj works with capscale and dbrda and this allows using ordiR2step in model building.

BUG FIXES

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

NEW FUNCTIONS

ordibar is a new function to draw crosses of standard deviations or standard errors in ordination diagrams instead of corresponding ellipses.
Several permustats results can be combined with a new c() function.
New function 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 as.mcmc). See issue #164 in Github.

NEW FEATURES

Null model analysis was upgraded:

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

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

"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.

designdist can now use beta diversity notation (gamma, alpha) for easier definition of beta diversity indices.
metaMDS has new iteration strategy: Argument try gives the minimum number of random starts, and trymax the maximum number. Earlier we only hand try which gave the maximum number, but now we run at least try times. This reduces the risk of being trapped in a local optimum (issue #154 in Github).

If there were no convergent solutions, metaMDS will now tabulate stopping criteria (if 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 monoMDS and metaMDS give more detailed information on convergence criteria.

The summary of permustats prints now P-values, and the test direction (alternative) can be changed.

The qqmath function of permustats can now plot standardized statistics. This is a partial solution to issue #172 in Github.

MDSrotate can rotate ordination to show maximum separation of factor levels (classes) using linear discriminant analysis (lda in MASS package).
adipart, hiersimu and multipart expose argument method to specify the null model.
RsquareAdj works with cca and this allows using ordiR2step in model building. The code was developed by Dan McGlinn (issue #161 in Github). However, cca still cannot be used in varpart.
ordiellipse and ordihull allow setting colours, line types and other graphical parameters.

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

ordiellipse can now draw ellipsoid hulls that enclose points in a group.
ordicluster, ordisegments, ordispider and lines and plot functions for isomap and spantree can use a mixture of colours of connected points. Their behaviour is similar as in analogous functions in the the vegan3d package.
plot of betadisper is more configurable. See issues #128 and #166 in Github for details.
text and points methods for orditkplot respect stored graphical parameters.
Environmental data for the Barro Colorado Island forest plots gained new variables from Harms et al. (J. Ecol. 89, 947–959; 2001). Issue #178 in Github.

DEPRECATED AND DEFUNCT

Function metaMDSrotate was removed and replaced with MDSrotate.
density and densityplot methods for various vegan objects were deprecated and replaced with density and densityplot for permustats. Function permustats can extract the permutation and simulation results of vegan result objects.

BUG FIXES

eigenvals fails with prcomp results in R-devel. The next version of prcomp will have an argument to limit the number of eigenvalues shown (rank.), and this breaks eigenvals in vegan.
calibrate failed for cca and friends if rank was given.

BUG FIXES

betadiver index 19 had wrong sign in one of its terms.
linestack failed when the labels were given, but the input scores had no names. Reported by Jeff Wood (ANU, Canberra, ACT).

DEPRECATED

vegandocs is deprecated. Current R provides better tools for seeing extra documentation (news() and browseVignettes()).

VIGNETTES

All vignettes are built with standard R tools and can be browsed with browseVignettes. FAQ-vegan and partitioning were only accessible with vegandocs function.

BUILDING

Dependence on external software texi2dvi was removed. Version 6.1 of texi2dvi was incompatible with R and prevented building vegan. The FAQ-vegan that was earlier built with texi2dvi uses now knitr. Because of this, vegan is now dependent on R-3.0.0. Fixes issue #158 in Github.

BUG FIXES

metaMDS and monoMDS could fail if input dissimilarities were huge: in the reported case they were of magnitude 1E85. Fixes issue #152 in Github.
Permutations failed if they were defined as permute control structures in estaccum, ordiareatest, renyiaccum and tsallisaccum. Reported by Dan Gafta (Cluj-Napoca) for renyiaccum.
rarefy gave false warnings if input was a vector or a single sampling unit.
Some extrapolated richness indices in 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 StackOverflow.

NEW FEATURES

treedist and treedive refuse to handle trees with reversals, i.e, higher levels are more homogeneous than lower levels. Function treeheight will estimate their total height with absolute values of branch lengths. Function treedive refuses to handle trees with negative branch heights indicating negative dissimilarities. Function treedive is faster.
gdispweight works when input data are in a matrix instead of a data frame.
Input dissimilarities supplied in symmetric matrices or data frames are more robustly recognized by anosim, bioenv and mrpp.

BUG FIXES

Printing details of a gridded permutation design would fail when the grid was at the within-plot level.
ordicluster joined the branches at wrong coordinates in some cases.
ordiellipse ignored weights when calculating standard errors (kind = "se"). This influenced plots of cca, and also influenced ordiareatest.

NEW FEATURES

adonis and capscale functions recognize symmetric square matrices as dissimilarities. Formerly dissimilarities had to be given as "dist" objects such as produced by dist or vegdist functions, and data frames and matrices were regarded as observations x variables data which could confuse users (e.g., issue #147).
mso accepts "dist" objects for the distances among locations as an alternative to coordinates of locations.
text, points and lines functions for procrustes analysis gained new argument truemean which allows adding procrustes items to the plots of original analysis.
rrarefy returns observed non-rarefied communities (with a warning) when users request subsamples that are larger than the observed community instead of failing. Function drarefy has been similar and returned sampling probabilities of 1, but now it also issues a warning. Fixes issue #144 in Github.

BUG FIXES

Permutation tests did not always correctly recognize ties with the observed statistic and this could result in too low P-values. This would happen in particular when all predictor variables were factors (classes). The changes concern functions adonis, anosim, anova and permutest functions for cca, rda and capscale, permutest for betadisper, envfit, mantel and mantel.partial, mrpp, mso, oecosimu, ordiareatest, protest and simper. This also fixes issues #120 and #132 in GitHub.
Automated model building in constrained ordination (cca, rda, capscale) with step, ordistep and 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 vegan 2.2-0.
Constrained ordination methods cca, rda and capscale treat character variables as factors in analysis, but did not return their centroids for plotting.
Recovery of original data in metaMDS when computing WA scores for species would fail if the expression supplied to argument comm was long & got deparsed to multiple strings. metaMDSdist now returns the (possibly modified) data frame of community data comm as attribute "comm" of the returned dist object. metaMDS now uses this to compute the WA species scores for the NMDS. In addition, the deparsed expression for comm is now robust to long expressions. Reported by Richard Telford.
metaMDS and monoMDS rejected dissimilarities with missing values.
Function 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 Stackoverflow.

NEW FEATURES AND FUNCTIONS

Scaling of ordination axes in cca, rda and capscale can now be expressed with descriptive strings "none", "sites", "species" or "symmetric" to tell which kind of scores should be scaled by eigenvalues. These can be further modified with arguments hill in cca and correlation in rda. The old numeric scaling can still be used.
The permutation data can be extracted from anova results of constrained ordination (cca, rda, capscale) and further analysed with permustats function.
New data set 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.

BUG FIXES

Constrained ordination functions cca, rda and 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 #16 and #100 in GitHub.
Ordination functions cca and rda silently accepted dissimilarities as input although their analysis makes no sense with these methods. Dissimilarities should be analysed with distance-based redundancy analysis (capscale).
The variance of the conditional component was over-estimated in goodness of rda results, and results were wrong for partial RDA. The problems were reported in an R-sig-ecology message by Christoph von Redwitz.

WINDOWS

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

NEW FEATURES AND FUNCTIONS

goodness function for constrained ordination (cca, rda, capscale) was redesigned. Function gained argument addprevious to add the variation explained by previous ordination components to axes when statistic = "explained". With this option, model = "CCA" will include the variation explained by partialled-out conditions, and model = "CA" will include the accumulated variation explained by conditions and constraints. The former behaviour was addprevious = TRUE for model = "CCA", and addprevious = FALSE for model = "CA". The argument will have no effect when 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.
Functions ordiArrowMul and 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 vegan functions.
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.
Rarefaction curve (rarecurve) and species accumulation models (specaccum, fitspecaccum) gained new functions to estimate the slope of curve at given location. Originally this was based on a response to an R-SIG-ecology query. For rarefaction curves, the function is rareslope, and for species accumulation models it is specslope.

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

Species accumulation models (specaccum) and non-liner regression models for species accumulation (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 predict models also use the number of sites with 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.
fitspecaccum gained support functions AIC and deviance.
The varpart plots of four-component models were redesigned following Legendre, Borcard & Roberts 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.

GENERAL

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.

INSTALLATION

vegan can be installed and loaded without tcltk package. The tcltk package is needed in orditkplot function for interactive editing of ordination graphics.

BUG FIXES

ordisurf failed if gam package was loaded due to namespace issues: some support functions of gam were used instead of mgcv functions.
tolerance function failed for unconstrained correspondence analysis.

NEW FEATURES

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, Biometrics 70, 671–682 (2014), doi:10.1111/biom.12200, online supplementary material.
Diversity accumulation functions specaccum, renyiaccum, tsallisaccum, poolaccum and estaccumR use now 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 permute package and user-supplied permutation matrices can be used.
estaccumR function can use parallel processing.
linestack accepts now expressions as labels. This allows using mathematical symbols and formula given as mathematical expressions.

GENERAL

Several vegan functions can now use parallel processing for slow and repeating calculations. All these functions have argument parallel. The argument can be an integer giving the number of parallel processes. In unix-alikes (Mac OS, Linux) this will launch "multicore" processing and in Windows it will set up "snow" clusters as desribed in the documentation of the parallel package. If option "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 "snow" cluster which will be used both in Windows and in unix-alikes. Vegan vignette on Design decision explains the implementation (use vegandocs("decission"), and parallel package has more extensive documentation on parallel processing in R.

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

All permutation tests are based on the permute package which offers strong tools for restricted permutation. All these functions have argument permutations. The default usage of simple non-restricted permutations is achieved by giving a single integer number. Restricted permutations can be defined using the how function of the 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 help(permutations) for a brief introduction on permutations in vegan, and permute package for the full documention. The vignette of the permute package can be read from vegan with command vegandocs("permutations").

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

Community null model generation has been completely redesigned and rewritten. The communities are constructed with new nullmodel function and defined in a low level commsim function. The actual null models are generated with a 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 oecosimu. The null models are often used only for the analysis of nestedness, but the implementation in oecosimu allows analysing any statistic, and null models are better seen as an alternative to permutation tests.

INSTALLATION

vegan package dependencies and namespace imports were adapted to changes in R, and no more trigger warnings and notes in package tests.
Three-dimensional ordination graphics using scatterplot3d for static plots and rgl for dynamic plots were removed from vegan and moved to a companion package vegan3d. The package is available in CRAN.

NEW FUNCTIONS

Function dispweight implements dispersion weighting of Clarke et al. (Marine Ecology Progress Series, 320, 11–27). In addition, we implemented a new method for generalized dispersion weighting gdispweight. Both methods downweight species that are significantly over-dispersed.
New hclust support functions reorder, rev and scores. Functions reorder and rev are similar as these functions for dendrogram objects in base R. However, reorder can use (and defaults to) weighted mean. In weighted mean the node average is always the mean of member leaves, whereas the dendrogram uses always unweighted means of joined branches.
Function ordiareatest supplements ordihull and 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.
Function permustats extracts and inspects permutation results with support functions summary, density, densityplot, qqnorm and qqmath. The density and qqnorm are standard R tools that only work with one statistic, and densityplot and qqmath are lattice graphics that work with univariate and multivariate statistics. The results of following functions can be extracted: anosim, adonis, mantel (and mantel.partial), mrpp, oecosimu, permustest.cca (but not the corresponding anova methods), permutest.betadisper, and protest.
stressplot functions display the ordination distances at given number of dimensions against original distances. The method functins are similar to stressplot for metaMDS, and always use the inherent distances of each ordination method. The functions are available for the results capscale, cca, princomp, prcomp, rda, and wcmdscale.

BUG FIXES

cascadeKM of only one group will be NA instead of a random value.
ordiellipse can handle points exactly on a line, including only two points (with a warning).
plotting radfit results for several species failed if any of the communities had no species or had only one species.
RsquareAdj for capscale with negative eigenvalues will now report NA instead of using biased method of rda results.
simper failed when a group had only a single member.

NEW FEATURES

anova.cca functions were re-written to use the 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.
simulate functions for cca and rda can return several simulations in a nullmodel compatible object. The functions can produce simulations with correlated errors (also for capscale) in parametric simulation with Gaussian error.
bioenv can use Manhattan, Gower and Mahalanobis distances in addition to the default Euclidean. New helper function bioenvdist can extract the dissimilarities applied in best model or any other model.
metaMDS(..., trace = 2) will show convergence information with the default monoMDS engine.
Function MDSrotate can rotate a k-dimensional ordination to 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.
vegan 2.0-10 changed the weighted 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 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).
ordiellipse, ordihull and ordiellipse can handle missing values in groups.
ordispider can now use spatial medians instead of means.
rankindex can use Manhattan, Gower and Mahalanobis distance in addition to the default Euclidean.
User can set colours and line types in function rarecurve for plotting rarefaction curves.
spantree gained a support function as.hclust to change the minimum spanning tree into an hclust tree.
fitspecaccum can do weighted analysis. Gained lines method.
Functions for extrapolated number of species or for the size of species pool using Chao method were modified following Chiu et al., Biometrics 70, 671–682 (2014).

Incidence based 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 on line material of doi:10.1111/biom.12200 and differs slightly from Chiu et al. (2014).

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

The abundance based estimateR uses bias corrected Chao extrapolation, but earlier it estimated its variance with classic Chao model. Now we use the widespread approximate estimate from EstimateS for variance.

With these changes these functions are more similar to EstimateS

tabasco uses now reorder.hclust for hclust object for better ordering than previously when it cast trees to dendrogram objects.
treedive and treedist default now to match.force = TRUE and can be silenced with verbose = FALSE.
vegdist gained Mahalanobis distance.
Nomenclature updated in plant community data with the help of Taxonstand and taxize packages. The taxonomy of the dune data was adapted to the same sources and APG III. varespec and dune use 8-character names (4 from genus + 4 from species epithet). New data set on phylogenetic distances for dune was extracted from Zanne et al. (Nature 506, 89–92; 2014).
User configurable plots for rarecurve.

DEPRECATED AND DEFUNCT

strata are deprecated in permutations. It is still accepted but will be phased out in next releases. Use how of permute package.
cca, rda and capscale do not return scores scaled by eigenvalues: use scores function to extract scaled results.
commsimulator is deprecated. Replace commsimulator(x, method) with simulate(nullmodel(x, method)).
density and densityplot for permutation results are deprecated: use permustats with its density and densityplot method.

GENERAL

This version is adapted to the changes in 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 vegan release is scheduled to be a major release with newly designed oecosimu and community pattern simulation, support for parallel processing, and full support of the permute package. If you are interested in these developments, you may try the development versions of vegan in GitHub and report the problems and user experience to us.

BUG FIXES

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 P-values in vectorfit.
nestednodf with quantitative data was not consistent with binary models, and the fill was wrongly calculated with quantitative data.
oecosimu now correctly adapts displayed quantiles of simulated values to the alternative test direction.
renyiaccum plotting failed if only one level of diversity scale was used.

NEW FEATURES

The Kempton and Taylor algorithm was found unreliable in fisherfit and fisher.alpha, and now the estimation of Fisher α 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.
renyiaccum, specaccum and tsallisaccum functions gained subset argument.
renyiaccum can now add a 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.
specaccum can now perform weighted accumulation using the sampling effort as weights.

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 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 lattice package.

GENERAL

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.

NEW FEATURES

ordisurf gained new arguments for more flexible definition of fitted models to better utilize the mgcv::gam function.

The linewidth of contours can now be set with the argument lwd.

Labels to arrows are positioned in a better way in plot functions for the results of envfit, cca, rda and capscale. The labels should no longer overlap the arrow tips.
The setting test direction is clearer in oecosimu.
ordipointlabel gained a plot method that can be used to replot the saved result.

NEW FUNCTIONS

tabasco() is a new function for graphical display of community data matrix. Technically it is an interface to R heatmap, but its use is closer to vegan function vegemite. The function can reorder the community data matrix similarly as vegemite, for instance, by ordination results. Unlike 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.

BUG FIXES

Function fitspecaccum(..., model = "asymp") fitted logistic model instead of asymptotic model (or the same as model = "logis").
nestedtemp() failed with very sparse data (fill < 0.38%).

NEW FEATURES

The plot function for constrained ordination results (cca, rda, capscale) gained argument axis.bp (defaults TRUE) which can be used to suppress axis scale for biplot arrays.
Number of iterations in nonmetric multidimensional scaling (NMDS) can be set with keyword maxit (defaults 200) in metaMDS.

DEPRECATED

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

BUG FIXES

The species scores were scaled wrongly in capscale(). They were scaled correctly only when Euclidean distances were used, but usually 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.
Function 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).
Plotting an object fitted by envfit() would fail if 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 envfit().
multipart() printed wrong information about the analysis type (but did the analysis correctly). Reported by Valerie Coudrain.
oecosimu() failed if its nestedfun returned a data frame. A more fundamental fix will be in vegan 2.2-0, where the structure of the oecosimu() result will change.
The plot of two-dimensional procrustes() solutions often draw original axes in a wrong angle. The problem was reported by Elizabeth Ottesen (MIT).
Function 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 treedist() for phylogenetic distances did not try to match the names at all.

NEW FEATURES

The output of capscale() displays the value of the additive constant when argument add = TRUE was used.
fitted() functions for cca(), rda() and capscale() can now return conditioned (partial) component of the response: Argument model gained a new alternative model = "pCCA".
dispindmorisita() output gained a new column for Chi-squared based probabilities that the null hypothesis (random distribution) is true.
metaMDS() and monoMDS() have new default convergence criteria. Most importantly, scale factor of the gradient (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, scores() ignore now requests to dimensions beyond those calculated instead of failing, and scores() for metaMDS() results do not drop dimensions.
msoplot() gained legend argument for positioning the legend.
Nestedness function nestednodf() gained a plot method.
ordiR2step() gained new argument R2scope (defaults TRUE) which can be used to turn off the criterion of stopping when the adjusted R2 of the current model exceeds that of the scope. This option allows model building when the scope would be overdetermined (number of predictors higher than number of observations).

ordiR2step() now handles partial redundancy analysis (pRDA).

orditorp() gained argument select to select the rows or columns of the results to display.
protest() prints the standardized residual statistic squared m12 in addition to the squared Procrustes correlation R2. Both were calculated, but only the latter was displayed.

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

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

BUG FIXES

anova(<cca_object>, ...) failed with by = "axis" and by = "term". The bug was reported by Dr Sven Neulinger (Christian Albrecht University, Kiel, Germany).
radlattice did not honour argument BIC = TRUE, but always displayed AIC.

NEW FUNCTIONS

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

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

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

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

NEW FEATURES

Labels can now be set in the plot of envfit results. The labels must be given in the same order that the function uses internally, and new support function labels can be used to display the default labels in their correct order.
Mantel tests (functions mantel and mantel.partial) gained argument 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.
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 AIC, coef, deviance, logLik, fitted, predict and residuals.

INSTALLATION AND BUILDING

Building of vegan vignettes failed with the latest version of LaTeX (TeXLive 2012).
R versions later than 2.15-1 (including development version) report warnings and errors when installing and checking vegan, and you must upgrade vegan to this version. The warnings concern functions cIndexKM and betadisper, and the error occurs in betadisper. These errors and warnings were triggered by internal changes in R.

BUG FIXES

adipart assumed constant gamma diversity in simulations when assessing the P-value. This could give biased results if the null model produces variable gamma diversities and option weights = "prop" is used. The default null model ("r2dtable") and the default option (weights = "unif") were analysed correctly.
anova(<prc-object>, by = "axis") and other by cases failed due to ‘NAMESPACE’ issues.
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 vegan help page.
envfit failed with unused factor levels.
predict for cca results with type = "response" or type = "working" failed with newdata if the number of rows did not match with the original data. Now the newdata is ignored if it has a wrong number of rows. The number of rows must match because the results in cca must be weighted by original row totals. The problem did not concern rda or capscale results which do not need row weights. Reported by Glenn De'ath.

NEW FEATURES

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

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

The method in 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 bias.adjust (defaults to FALSE).
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 vegdist.
plot function for envfit results gained new argument bg that can be used to set background colour for plotted labels.
msoplot is more configurable, and allows, for instance, setting y-axis limits.
Hulls and ellipses are now filled using semitransparent colours in ordihull and ordiellipse, and the user can set the degree of transparency with a new argument alpha. The filled shapes are used when these functions are called with argument draw = "polygon". Function ordihull puts labels (with argument label = TRUE) now in the real polygon centre.
ordiplot3d returns function envfit.convert and the projected location of the origin. Together these can be used to add envfit results to existing ordiplot3d plots.

Equal aspect ratio cannot be set exactly in ordiplot3d because underlying core routines do not allow this. Now 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, ordiplot3d may be removed from next releases of vegan.

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

NEW FUNCTIONS

Added new nestedness functions nestedbetasor and nestedbetajac that implement multiple-site dissimilarity indices and their decomposition into turnover and nestedness components following Baselga (Global Ecology and Biogeography 19, 134–143; 2010).
Added function 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.
Added function simper that implements “similarity percentages” of Clarke (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 GitHub by Eduard Szöcs (Uni Landau, Germany).

BUG FIXES

betadisper() failed when the groups was a factor with empty levels.
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 capscale, ordistep, varpart, plot function for constrained ordination, and anova(<cca.object>, by = "margin").
The scores function for monoMDS did not honour choices argument and hence dimensions could not be chosen in plot.
The default scores method failed if the number of requested axes was higher than the ordination object had. This was reported as an error in ordiplot in R-sig-ecology mailing list.

NEW FEATURES

metaMDS argument noshare = 0 is now regarded as a numeric threshold that always triggers extended dissimilarities (stepacross), instead of being treated as synonymous with noshare = FALSE which always suppresses extended dissimilarities.
Nestedness discrepancy index nesteddisc gained a new argument that allows user to set the number of iterations in optimizing the index.
oecosimu displays the mean of simulations and describes alternative hypothesis more clearly in the printed output.
Implemented adjusted R2 for partial RDA. For partial model rda(Y ~ X1 + Condition(X2)) this is the same as the component [a] = X1|X2 in variance partition in varpart and describes the marginal (unique) effect of constraining term to adjusted R2.
Added Cao dissimilarity (CYd) as a new dissimilarity method in vegdist following Cao et al., 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).

BUG FIXES

Function 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 anova(..., by ="margin") which uses partial models to analyses the marginal effects, and was reported in an email message to R-News mailing list.
stressplot and goodness sometimes failed when metaMDS was based on isoMDS (MASS package) because metaMDSdist did not use the same defaults for step-across (extended) dissimilarities as metaMDS(..., engine = "isoMDS"). The change of defaults can also influence triggering of step-across in capscale(..., metaMDSdist = TRUE).
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.

NEW FEATURES

ordiarrows and ordisegments gained argument order.by that gives a variable to sort points within groups. Earlier the points were assumed to be in order.
Function 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 groups they are the LC scores.

NEW FUNCTIONS

clamtest: new function to classify species as generalists and specialists in two distinct habitats (CLAM test of Chazdon et al., 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.
as.preston gained plot and lines methods, and as.fisher gained plot method (which also can add items to existing plots). These are similar as plot and lines for prestonfit and fisherfit, but display only data without the fitted lines.
raupcrick: new function to implement Raup-Crick dissimilarity as a probability of number of co-occurring species with occurrence probabilities proportional to species frequencies. Vegan has Raup-Crick index as a choice in vegdist, but that uses equal sampling probabilities for species and analytic equations. The new raupcrick function uses simulation with oecosimu. The function follows Chase et al. (2011) Ecosphere 2:art24 [doi:10.1890/ES10-00117.1], and was developed with the consultation of Brian Inouye.

BUG FIXES

Function meandist could scramble items and give wrong results, especially when the grouping was numerical. The problem was reported by Dr Miguel Alvarez (Univ. Bonn).
metaMDS did not reset tries when a new model was started with a previous.best solution from a different model.
Function permatswap for community null models using quantitative swap never swapped items in a 2x2 submatrix if all cells were filled.
The result from permutest.cca could not be updated because of a ‘NAMESPACE’ issue.
R 2.14.0 changed so that it does not accept using sd() function for matrices (which was the behaviour at least since R 1.0-0), and several vegan functions were changed to adapt to this change (rda, capscale, simulate methods for rda, cca and capscale). The change in R 2.14.0 does not influence the results but you probably wish to upgrade vegan to avoid annoying warnings.

ANALYSES

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.

GENERAL

Peter Minchin joins the vegan team.
vegan implements standard R ‘NAMESPACE’. In general, S3 methods are not exported which means that you cannot directly use or see contents of functions like cca.default, plot.cca or anova.ccabyterm. To use these functions you should rely on R delegation and simply use cca and for its result objects use plot and anova without suffix .cca. To see the contents of the function you can use :::, such as vegan:::cca.default. This change may break packages, documents or scripts that rely on non-exported names.
vegan depends on the permute package. This package provides powerful tools for restricted permutation schemes. All vegan permutation will gradually move to use permute, but currently only betadisper uses the new feature.

NEW FUNCTIONS

monoMDS: a new function for non-metric multidimensional scaling (NMDS). This function replaces MASS::isoMDS as the default method in metaMDS. Major advantages of monoMDS are that it has ‘weak’ (‘primary’) tie treatment which means that it can split tied observed dissimilarities. ‘Weak’ tie treatment improves ordination of heterogeneous data sets, because maximum dissimilarities of 1 can be split. In addition to global NMDS, monoMDS can perform local and hybrid NMDS and metric MDS. It can also handle missing and zero dissimilarities. Moreover, monoMDS is faster than previous alternatives. The function uses Fortran code written by Peter Minchin.
MDSrotate a new function to replace metaMDSrotate. This function can rotate both metaMDS and monoMDS results so that the first axis is parallel to an environmental vector.
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. (Ecography 31, 450-456; 2008). The code was contributed by Eduardo Ribeira Cunha and Heloisa Beatriz Antoniazi Evangelista and adapted to vegan by Peter Solymos.
fitspecaccum fits non-linear regression models to the species accumulation results from specaccum. The function can use new self-starting species accumulation models in vegan or other self-starting non-linear regression models in R. The function can fit Arrhenius, Gleason, Gitay, Lomolino (in vegan), asymptotic, Gompertz, Michaelis-Menten, logistic and Weibull (in base R) models. The function has plot and predict methods.
Self-starting non-linear species accumulation models SSarrhenius, SSgleason, SSgitay and SSlomolino. These can be used with fitspecaccum or directly in non-linear regression with nls. These functions were implemented because they were found good for species-area models by Dengler (J. Biogeogr. 36, 728-744; 2009).

NEW FEATURES

adonis, anosim, meandist and mrpp warn on negative dissimilarities, and betadisper refuses to analyse them. All these functions expect dissimilarities, and giving something else (like correlations) probably is a user error.
betadisper uses restricted permutation of the permute package.
metaMDS uses monoMDS as its default ordination engine. Function gains new argument engine that can be used to alternatively select MASS::isoMDS. The default is not to use stepacross with monoMDS because its ‘weak’ tie treatment can cope with tied maximum dissimilarities of one. However, stepacross is the default with isoMDS because it cannot handle adequately these tied maximum dissimilarities.
specaccum gained 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.
specpool can handle missing values or empty factor levels in the grouping factor pool. Now also checks that the length of the pool matches the number of observations.

DEPRECATED AND DEFUNCT

metaMDSrotate was replaced with MDSrotate that can also handle the results of monoMDS.
permuted.index2 and other “new” permutation code was removed in favour of the permute package. This code was not intended for normal use, but packages depending on that code in vegan should instead depend on permute.

ANALYSES

treeheight uses much snappier code. The results should be unchanged.

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vegan documentation built on Oct. 11, 2022, 5:06 p.m.

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vegan Community Ecology Package

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