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See github issue 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.
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. See Stackoverflow question See GitHub issue R - Error message in doing RDA analysis - vegan package.
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. Canberra distance in vegdist can now handle negative input entries similarly as latest versions of R.
This avoids warnings in model checking, and may also give a small gain in speed. 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. 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. 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. 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. 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 and pull request 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. The cca method of tolerance was returning incorrect values for all but the second axis for sample heterogeneities and species tolerances.
See issue for details. 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.
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: Non-sequential null models may be marginally faster. These null models are generated by function nullmodel and also used in oecosimu. It used to be clearly slower than stats:: This fixes points raised in Github issue The families and orders in dune.
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. 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.
Function meandist failed in some cases when one of the groups had only one observation. This regression is discussed in GitHub issue The function also checks the input and refuses to handle data with negative values. Several functions are more robust if their factor arguments contain missing values NA: GitHub issues and 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. 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 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. 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 for differences. Function varpart can partition dissimilarities using the same algorithm as dbrda.
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 in Github. RsquareAdj works with capscale and dbrda and this allows using ordiR2step in model building.
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.
See issue in Github. New "curveball" algorithm provides a fast null model with fixed row and column sums for binary matrices after Strona et al. The "quasiswap" algorithm gained argument thin which can reduce the bias of null models. 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 in Github. This can help in deciding if any of the criteria should be made more stringent or the number of iterations increased.
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 in Github. MDSrotate can rotate ordination to show maximum separation of factor levels classes using linear discriminant analysis lda in MASS package.
RsquareAdj works with cca and this allows using ordiR2step in model building. The code was developed by Dan McGlinn issue in Github. However, cca still cannot be used in varpart. The alpha channel can now be given also as a real number in Their behaviour is similar as in analogous functions in the the vegan3d package.
See issues and in Github for details. Environmental data for the Barro Colorado Island forest plots gained new variables from Harms et al. Issue in Github. Function permustats can extract the permutation and simulation results of vegan result objects. The next version of prcomp will have an argument to limit the number of eigenvalues shown rank.
Current R provides better tools for seeing extra documentation news and browseVignettes. All vignettes are built with standard R tools and can be browsed with browseVignettes. FAQ-vegan and partitioning were only accessible with vegandocs function.
Dependence on external software texi2dvi was removed. The FAQ-vegan that was earlier built with texi2dvi uses now knitr. Because of this, vegan is now dependent on R Fixes issue 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. The extrapolated richness cannot be estimated from a single sampling unit, but now such cases are handled smoothly instead of failing: The issue was reported in StackOverflow.