Forum: vegan 1.15-3 released

Posted by: Jari Oksanen
Date: 2009-06-17 08:36
Summary: vegan 1.15-3 released
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 versin 1.15-3 was submitted to CRAN on June 17, 2009. This contains some bugfixes and enhancements. The most important changes are:

-anosim, mantel, mrpp, protest & envfit now have the observed statistic among permutations. Functions adonis and permutest.cca already behaved so but now they format the results clearly so.
- capscale displays negative eigenvalues more prominently. There is a new component for "Imaginary" component of inertia for negative eigenvalues. The total inertia is now sum of all eigenvalues so that negative eigenvalues are subtracted from the total. The negative eigenvalues are listed after positive unconstrained ones. There is a new argument 'sqrt.dist' which avoids negative eigenvalues with Bray-Curtis and Jaccard indices and some others. The inertia and eigenvalues of indices with maximum = 1 are now smaller by a factor of sqrt(n-1).
- eigenvals: new function to extract eigenvalues if such can be found from the object. The summary function displays proportions and cumulative proportions. Function summary.cca uses now summary.eigenvals.
- meandist: a new sister function to 'mrpp'. Finds between and within group distances. The summary reports all three variants of the MRPP statitic plus classification strength. The plot method draws a dendrogam.
- ordisurf: fits linear or quadratic trend surfaces if knots is 0, 1, or 2.
- orditkplot: handels NA and NaN scores.
- ordixyplot: mixed x and y axes for biplot arrows and class centroids. Failed in constrained ordination.
- tsallis: new argument 'hill' to find results similar to Hill numbers of 'renyi'.
- wcmdscale: removes now zero eigenvalue instead of last eigenvalue (which may be large negative).

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