WK 3
Community Data Analysis Using the Vegan Package in R
Saturday, August 9, 2014: 12:00 PM-5:00 PM
105, Sacramento Convention Center
Organizer:
Naupaka Zimmerman, University of Arizona
Co-organizers:
Gavin L. Simpson, University of Regina; and
Nate Hough-Snee, Utah State University
Speakers:
Gavin L. Simpson, University of Regina; and
Naupaka Zimmerman, University of Arizona
The R statistical language has enjoyed wide and rapid adoption by many ecologists, and is used across many ecological subdisciplines for statistical analyses and the production of publication-quality figures. For community ecologists using R, one of the most-used, and most-useful, add-on packages is vegan, which provides a wide range of functionality covering
inter alia ordination, diversity analysis, and ecological simulation. This workshop will offer participants a practical introduction to some of the most useful functions available within vegan. We will focus in particular on multivariate methods including constrained (CCA, RDA) and unconstrained ordination (PCA, CA, and NMDS) and their related plotting tools, as well as between-group tests such as PERMANOVA. In addition, we will demonstrate how to use newly-developed restricted permutations to test a range of experimental designs. The workshop will assume that participants have a basic level of familiarity with working with data in R, including data import and basic indexing and subsetting. Some familiarity with distance measures is recommended but not required as we will briefly cover data transformation, standardization and multivariate distance measures. All participants must bring their own laptop with R and RStudio (available free online for all platforms at rstudio.com) pre-installed. All data files and code for this workshop will be made publicly available for self-teaching to the general public via github.com, ensuring workshop resources are available indefinitely. The organizers are expert users of vegan and include one of the maintainers of the package.
