EcolUtils: Utilities for community ecology analysis

The R package EcolUtils provides tools and extensions for community ecology analysis not present in up-to-date available packages. Designed with molecular 16S-derived data in mind.

EcolUtils depends on vegan and spaa package which can be installed from CRAN.

Content

The current version contains the following functions:

• rrarefy.perm() Rarefaction of a community matrix with permutations
• adonis.pair() Pairwise comparisons for Permutational Multivariate Analysis of Variance Using Distance Matrices
• spec.gen() Specialist/Generalist classification of OTUs based on niche width and permutation algorithms
• seasonality.test() Seasonality test based on autocorrelation and null communities
• niche.val() Niche value computation for OTUs in a community through abundance-weighted mean and matrix randomization
• niche.range() Niche range computation for OTUs in a community through abundance-weighted mean and matrix randomization
• smwda() Split moving-window distance analysis

Authors

Guillem Salazar

Citation

To see the preferable citation of the package, type:

citation("EcolUtils")

Software Versions

R: version 3.2.1
RStudio: Version 0.99.467

Contact Info

Guillem Salazar (guillems@ethz.ch)

Installation of the package

• Install the latest version of vegan and spaa from Bioconductor:

  install.packages("vegan")
  install.packages("spaa")

• Install EcolUtils' current development version from Github:

  devtools::install_github("GuillemSalazar/EcolUtils")

• After attaching the package, you are ready to start:

  library(EcolUtils)