vegan: CRAN release 2.4-0

A new major release of vegan was released and is available on CRAN. This release is directly lifted from the current master branch and closes the gap between development and release versions. The release will start the new 2.4 series, and the master branch will be 2.5-0 for the next major release. As this is a major release, there are numerous large changes. Most important user visible changes are listed in the NEWS with the package. Largest families of changes are: distance-based RDA and associated analyses were redesigned to directly compose dissimilarities. With semimetric indices (such as Bray-Curtis) this means that the components of inertia include negative eigenvalues. The release has a new function dbrda for distance-based RDA while it also keeps the old capscale but with redefined inertia. In addition, we have a new implementation of permutational anova as adonis2 along side the classic adonis. Variation partition can also be based on dissimilarities with similar tools. We also include tools for euclidifying dissimilarities in all cases where negative eigenvalues may appear. The changes touch functions capscale, adonis, betadisper and varpart and their support functions. null models are expanded. We have new "curveball" algorithm for binary matrices, and many other functions are streamlined. It is also possible to bind several null models together with new smbind functions. With this function, null models can be stratified by groups of species or sampling units, or it is possible to run models in pieces. The models can be expanded with new simulations, or null models can be simulated in parallel. several ordi* functions that add graphical items to ordination plots are now more flexible and easier to parametrize with colours, line types etc. This also concerns functions like plotting betadisper results. There is also a new function that can plot SD, SE or CI crosses instead of corresponding ellipses, and ordiellipse can draw ellipsoid hulls that enclose all points in each group. metaMDS strategies changed so that it is easier to avoid local optima and to see which stopping criterion should be changed to reach the solutions. The MDSrotate function can now rotate a multidimensional MDS solution to separate groups optimally in first dimensions. designdist knows now beta-diversity notation so that, e.g., Whittaker's index can be calculated as designdist(BCI, "gamma/alpha - 1", alphagamma = TRUE). permustats support functions were improved for analysing permutation test statistics from various vegan objects. Now several permutations can be combined with new c() function, and summary can be used to evaluate the P-values also for combined results. Adjusted R-squared can now be analysed for db-RDA and cca. Parallel to this 2.4-0 release, we also released a new version 1.0-1 of vegan3d with similar improvements and bug fixes