Forum: vegan 1.13-1 in CRAN

Posted by: Jari Oksanen
Date: 2008-06-12 08:20
Summary: vegan 1.13-1 in CRAN
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 version 1.13-1 was released on June 11, 2008, and is now available in CRAN. This is a bug fix release, and the major fixes concern handling ranks in constrained ordination and handling weights of ordination objects without weights.

Vegan had used only one kind of ranks for constrained ordination: that defined by the ordination, which in effect is the same as the number of constrained axes. This works nicely with "usual" ordination problems, where constraints reduce the number of axes. However, it is possible to have a larger number of constraints than there are species (the number of rows is crucial, and that must be higher than the nubmer of constraints). Now vegan correctly handles these cases. Ordination plots and summaries show now all constraints. The change has wide ranging side effects and may break some functions that escaped attention in testing. Please report problems to the vegan developers so that the bugs can be fixed for the next release. See vegan NEWS for more details.

Another major change was handling weights when there are no weights in ordination objects. Vegan uses always weighted fitting for ordination objects in its graphical functions so that correspondence analysis can be handled correctly. Therefore vegan queries weights of ordination objects. In R 2.7.0 this gave an error with some results that do not have weights (it still worked in R 2.6.2), but now there is a workaround for this R feature, and plotting should again work like in previously.

Function mso was upgraded to the latest version in vegan development branch. Function mso was added just before the release 1.13-0, and its user interface soon changed. Most importantly, plot() gives now a standard ordination scatter diagram, and for mso output you must use msoplot function.

There are small changes in several other functions: see NEWS in the package for details.

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