Forum: vegan: 1.17-12 released, 2.0 coming soon

Posted by: Jari Oksanen
Date: 2011-08-18 10:20
Summary: vegan: 1.17-12 released, 2.0 coming soon
Project: vegan - Community Ecology Package


A minor maintenance release vegan_1.17-12 was released on August 17. Changes are many but most of them improve the stability in exceptional cases. The only new function is tolerance() which finds the species "tolerances" and sample heterogeneities from a CA or CCA result. There is a small bug fix in metaMDSrotate(), and new arguments were added to make.cepnames(), ordilabel() and swan(), and adonis() is faster.

The maintenance release was made to clean the table for a new major release (vegan 2.0) which is expected in September. This includes several new features:

- Future versions of R require packages to have NAMESPACE, and vegan 2.0 introduces a standard R NAMESPACE. A major source of disruption may be that S3 methods are not exported, and commands like anova.cca(mod) will fail because anova.cca was not exported: you should use anova(mod) instead, and let R decide which function to use. Packages or scripts using vegan may fail because of this change. The current release (1.17-12) also has a NAMESPACE, but that exports every function so that the user experience should be similar as earlier.

- Vegan will start to use new more powerful permutation routines on the 'permute' package released soon. This package will have several alternatives of restricted permutation, and will replace vegan permuted.index2 routines. The shift to 'permute' package will be gradual, and first touch only betadisper(), but all vegan permutation will move to use new routines in next gradual releases. This also means that vegan will be dependent on 'permute' package.

- Peter Minchin joins the vegan team, and he has written for us new NMDS function called monoMDS(). This will replace MASS::isoMDS() as the default ordination engine in metaMDS(). The major advantage of monoMDS() is that it can use 'weak ties' or split tied dissimilarities (particularly dissimilarity = 1 for nothing shared) which hugely improves ordination of heterogeneous data sets. In addition, monoMDS can perform local and hybrid NMDS. It is even faster than the old engine. Some more capabilities will be taken into use in gradual releases, such as adding new points to existing ordinations.

- Another new set of functions will be fitspecaccum() that can fit some non-linear regression models to species accumulation results from specaccum(). In addition, vegan will have several new self-starting non-linear regression models that are used in fitspecaccum(), but can also be used separately. These include Arrhenius, Gleason, Gitay and Lomolino models.

Most of these features are already available in the R-Forge version of vegan (1.90-0 and above). Please test the new features and report the problems to us.

Latest News

vegan moves to GitHub and new release 2.2-0

Jari Oksanen - 2014-09-18 15:58 -

vegan moves to GitHub and new release 2.2-0

Jari Oksanen - 2014-09-18 15:57 -

vegan 2.0-6 in CRAN

Jari Oksanen - 2013-02-11 13:39 -

Trying GitHub

Jari Oksanen - 2012-02-26 16:27 -

Trying GitHub

Jari Oksanen - 2012-02-26 16:26 -


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