Introduction to community data analysis using the vegan package in R
Welcome to the GitHub repository for workshop on community ecology analyses using the vegan package at ESA 2016.
Location and time:
Saturday, August 6, 2016
12:00 PM - 5:00 PM
Location: Room 304, Ft. Lauderdale Convention Center
Organizers
Naupaka Zimmerman and Gavin Simpson.
Instructors and helpers
Naupaka Zimmerman and Andrew Tredennick.
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 the use of NMDS as an ordination method and on how to visualize the results using related plotting tools. We will also cover between-group tests such as PERMANOVA.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. Participants that do not have this basic level of familiarity with R may want to take the Introduction to R workshop offered earlier by the same organizers. 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.
Pre-workshop instructions
Installing R and RStudio
If you don't already have R set up with a suitable code editor, we recommend downloading and installing the most recent versions of R and RStudio Desktop for your platform. Once installed, open RStudio and install the following packages. Simply paste these commands into your prompt.
Installing packages
install.packages("vegan", dependencies = TRUE)
install.packages("plyr")
install.packages("reshape2")Extra check for MacOS X users
In order to use the orditkplot() function you need a working Tcl/Tk installation. This may not be installed on Macs; to check run the following code
library("vegan")
data(varespec)
orditkplot(rda(varespec))If you get errors and not a new window in which you can edit the biplot, then you probably don't have the correct setup on your system to use Tcl/Tk. Refer to the Tcl/Tk Issues section of the R Mac OS X FAQ. We may not have a chance to cover the use of the function in the workshop, but it can't hurt to get it properly configured since you may want to use it at some point on your own.
Downloading code/data from this repository
The slides, data, and code in this repository may change up until the start of the workshop, so please wait until as late as possible to download these files from GitHub to ensure that you have the most recent copy.
If you're already familiar with Git, then simply clone this repo. If you're not familiar with Git, simply click the green Clone or Download button on the top right side of this page and select Download ZIP. If you're not sure where to save it, just download and unzip to your Desktop.
If you're having any trouble with these steps please drop us an email. We'll also plan to have local copies if you forget to install any of these tools or have trouble downloading the files in this repository.
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
