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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.

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: 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 veganand 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The following functions use the permute package: CCorAadonisanosim744 how can i get cran package binaries for outdated versions of r. Community null model generation has been completely redesigned and rewritten. The communities are constructed with new nullmodel function and 744 how can i get cran package binaries for outdated versions of r in a low level commsim function.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.

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. Function dispweight implements dispersion weighting of Clarke et al. Marine Ecology Progress Series, 11— 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 reorderrev 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 744 how can i get cran package binaries for outdated versions of r and inspects permutation results with support functions summarydensitydensityplotqqnorm and qqmath. The density and qqnorm are standard R 744 how can i get cran package binaries for outdated versions of r 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: The 744 how can i get cran package binaries for outdated versions of r functins are similar to stressplot for metaMDSand always use the inherent distances of each ordination method.

The functions are available for the results capscaleccaprincompprcomprdaand wcmdscale. RsquareAdj for capscale with negative eigenvalues will now report NA instead of using biased method of rda results. 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.

The 744 how can i get cran package binaries for outdated versions of r can produce simulations with correlated errors also for capscale in parametric simulation with Gaussian error. New helper function bioenvdist can extract the dissimilarities applied in best model or any other model. Function MDSrotate can rotate a k -dimensional ordination to k-1 variables.

When these variables are correlated like usually is the casethe vectors can also be correlated to previously rotated dimensions, but will be uncorrelated to all later ones. However, this broke the equivalence to the original method. Now the function has an argument wbinary to select the method of analysis.

User can set colours and line types in function rarecurve for plotting rarefaction curves. Functions for extrapolated number of species or for the size of species pool using Chao method were modified following Chiu et al. 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 online material and differs slightly from Chiu et al.

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 equation for variance. With these changes these functions are more similar to EstimateS. Nomenclature updated in plant community data with the help of Taxonstand and taxize packages.

New data set on phylogenetic distances for dune was extracted from Zanne et al. Nature89—92; It is still accepted but will be phased out in next releases. Use how of permute package. Replace commsimulator x, method with simulate nullmodel x, method.

This version is adapted to the changes in permute package version 0. This release may be the last of the 2. If you are interested in these developments, you may try the development versions of vegan in R-Forge or GitHub and report the problems and user experience to us. 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. The Kempton and Taylor algorithm was found unreliable in fisherfit and fisher. The estimation of standard errors and profile confidence intervals also had to be scrapped. 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. This version is released due to changes in programming interface and testing procedures in R 3.

If you are using an older version of Rthere 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. 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.

Labels to arrows are positioned in a better way in plot functions for the results of envfitccarda and capscale. The labels should no longer overlap the arrow tips. Technically it is an interface to R heatmapbut its use is closer to vegan function vegemite. The function can reorder the community data matrix similarly as vegemitefor instance, by ordination results. Unlike heatmapit 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. The plot function for constrained ordination results ccardacapscale gained argument axis. The result objects of ccarda and capscale will no longer have scores u. 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. 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.

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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.