Forum: vegan 2.0-0 published

Posted by: Jari Oksanen
Date: 2011-09-09 13:13
Summary: vegan 2.0-0 published
Project: vegan - Community Ecology Package

Development Status : 5 - Production/Stable
Intended Audience : End Users/Desktop
License : GNU General Public License (GPL)
Natural Language : English
Operating System : OS Independent
Programming Language : C/C++ : Fortran : R
Topic : Environmetrics : Multivariate Statistics : Ecological Analysis

Content:

*Vegan* 2.0-0 was published in CRAN on September 8, 2011. This is a major release with changed dependencies, standard NAMESPACE and new functions and features. You can read more detailed news in

http://cran.r-project.org/web/packages/vegan/news.html

but here the main points:

1. *Vegan* depends on *permute* package. This package will provide new, strong schemes of restricted permutations. Currently only permutest() for betadisper() uses the new permutation infrastructure, but with time all vegan permutation will be transferred to use *permute*.

2. *Vegan* has a standard NAMESPACE which only exports the functions that are intended for users. In particular, S3 method functions are not exported, and you cannot any longer use commands line 'cca.default()', but you must only use 'cca()'. However, most *vegan* functions were intended to be visible for users, and are exported. This change may disrupt other packages, scripts etc that use *vegan*. If you think that some non-exported functions should be exported, please contact us.

3. There are several new functions and features. Most importantly, we have new non-metric multidimensional scaling (NMDS) function monoMDS which is the default engine in metaMDS. Function monoMDS can do local NMDS, hybrid MDS and metric MDS in addition to classical global NMDS, it handles tied dissimilarities adequately in heterogeneous data sets, it can handle zero and NA dissimilarities, and it is fast. The FORTRAN code for the function was written by Peter Minchin, who joined the *vegan* author team. For other new functions and features, see the vegan NEWS (link above).

Jari Oksanen

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