R for Data Analysis in Ecology
2016-08-15
Chapter 1 Overview
Content Contributors: Sarah Supp, John Blischak, Gavin Simpson, Tracy Teal, Greg Wilson, Diego Barneche, Stephen Turner, Francois Michonneau
Lesson Maintainers: Francois Michonneau, Auriel Fournier**
Lesson status: Teaching
1.1 Lessons
1.2 Data
Data files for the lesson are available here: http://dx.doi.org/10.6084/m9.figshare.1314459
Please download the *.csv (Comma Separated Value) files: species.csv, plots.csv, surveys.csv, and combined.csv.
1.2.1 Requirements
Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to insure the proper setup of tools for an efficient workflow. These lessons assume no prior knowledge of the skills or tools, but working through this lesson requires working copies of the software described below. To most effectively use these materials, please make sure to install everything before working through this lesson.
1.2.2 R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio. Make sure you have a recent version of R ( or higher).
1.2.2.1 Windows
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.
1.2.2.2 Mac OS X
Install R by downloading and running this .pkg file from CRAN. If you have Snow Leopard, you might run into issues when trying to download the datasets directly from R using the download.file() function. If it’s the case, you will need to download the data files manually. Don’t hesitate to ask the instructor for help if you run into issues. Also, please install the RStudio IDE.
1.2.2.3 Linux
You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). This workshop requires a version of R no older than version 3.2.2; the default software repositories for some Linux distributions maybe out of date. It is recommended that you use a more recent version of R by adding the relevant entries to your package manager. See the instructions for your distribution on the CRAN website. Also, please install the RStudio IDE.