Forum: vegan 1.13-0 in CRAN

Posted by: Jari Oksanen
Date: 2008-05-23 20:37
Summary: vegan 1.13-0 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:

Version 1.13-0 of vegan is available in CRAN. This is a major version update that includes most features in R-Forge. Mitchell-Olds & Shaw test of R-Forge was excluded, however, since it was not yet quite mature for prime time.

The main NEWS for this version are:

NEW FUNCTIONS

- betadiver: beta diversity functions as reviewed by Patricia Koleff et al. (J. Anim. Ecol., 72, 367-382; 2003), with a plot function to produce triangular plots.

- mso: Helene Wagner's multiscale ordination or spatial partitioning of cca and rda. This is taken from the Ecological Archives with minimal edition with the permission of Helene Wagner.

- nestedtemp: matrix temperature method for oecosimu following Rodriguez-Girones & Santamaria (J. Biogeogr. 33, 924-935; 2006), but still without iterative optimization of row and column ordering.

- TukeyHSD.betadisper: pairwise comparisons for betadisper.

NEW FEATURES AND FIXES

- adonis: returns both species and site scores.
- betadisper: was not calculating distance to centroid correctly for observations where the imaginary distance to centroid was greater than the real distance. Now takes the absolute value of the combined distance before taking the square root. This is in-line with Marti Anderson's PERMDISP2.
- BCI: example has spatial coordinates of plots.
- biplot.rda: argument for arrow col.
- capscale: accepts other distance functions than vegdist, and can use metaMDSdist for extended dissimilarites & "metaPCoA".
- designdist: knows 2x2 contingency table notation with a, b, c, and d.
- metaMDS: transforms data like with distances for species WA.
- orditkplot: allows editing labels and zooming into plot.
- permDisper: renamed to permutest.betadisper.
- permutest: now a generic function, currently with methods 'cca' and 'permDisper'.
- rarefy: accepts vectors of sample sizes.
- rgl.isomap: dynamic rgl plots for isomap.
- screeplot.cca etc: return invisibly xycoords.
- specaccum: returns numbers of individuals with method = "rarefaction".
- summary.cca: returns more statistics on "variance explained by axes".
- zzz: vegan got startup message.