CommEcol - Community Ecology analyses

CommEcol includes functions to perform recently proposed analyses in community ecology as well as analyses not easily available in other R packages. It is intended to be a complement to major R packages, particularly vegan.

The first release of CommEcol was early May 2013 and it is still in a development stage. That means that functions were not tested extensively and may produce errors. You can download CommEcol or install it using: install.packages("CommEcol", repos=c("", ""), dep=TRUE). See also the summary page at r-forge.

The current version of CommEcol includes the functions:

==> autosimi - AutoSimilarity curves.

==> compas - Simulated communities obtained from species response curves (Minchin 1987. Vegetatio 71:145-156).

==> dis.chao - Dissimilarity indices proposed by Chao et al. (2005) that takes into account (rare) unseen shared species.

==> dis.goodall - A probability-based Dissimilarity index in which rare species (or descriptors) are overweighted.

==> dis.nness - Dissimilarity indices that overweight rare species to a desired degree.

==> dis.nness.find.m - A procedure to find a m-value to be used in dis.nness() that is sensitive to both rare and abundant species.

==> part.m.tree, part.p.tree - Multiple and pair-wise of Sorensen, Jaccard as well as their turnover and richness-diference components of dissimilarity adapted to tree objects representing resemblance of descriptor variables

==> select.window - selection of a site-by-species dataframe representing cells around a focal cell in a gridded dataframe.

==> standExtent - Standardization of spatial extent for two metacommunities by subsampling.

==> treeNodf, treeNodfTest
- Nestedness for phylogenetic, functional and other diversity metrics based on resemblance of descriptor variables (Melo, Cianciaruso and Almeida-Neto 2014. Methods in Ecology and Evolution 5: 563-572).

==> betaRegDisp
- Beta diversity metrics between sites in a moving window along environmental gradients (Dala-Corte et al. 2019. Environmental Monitoring and Assessment 191:288).

Maintainer: Adriano S. Melo
Last update of this page:
03 May 2019