/esa_vegan

Content for a workshop that was held at ESA 2014 on using R's vegan package for community ecology analyses.

Primary LanguageJavaScript

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 2014.

Location and time:
Saturday, August 9, 2014
12:00 PM - 5:00 PM
Location: Room 105, Sacramento Convention Center

Organizers

Naupaka Zimmerman and Gavin Simpson.

Pre workshop instructions

Installing R

If you don't already have R set up with a suitable code editor, we recommend downloading and installing 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.

Downloading code/data from this repository

If you're already familiar with Git, then simply clone this repo. If you're not familiar with Git, simply hit the Download ZIP button on the right side of this page. 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 strive to have local copies if you forget to install any of these tools.

License

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.