Data Analysis and Visualization in R for Ecologists
Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The lessons below were designed for those interested in working with ecology data in R.
This is an introduction to R designed for participants with no programming experience. These lessons can be taught in a day (~ 6 hours). They start with some basic information about R syntax, the RStudio interface, and move through how to import CSV files, the structure of data frames, how to deal with factors, how to add/remove rows and columns, how to calculate summary statistics from a data frame, and a brief introduction to plotting. The last lesson demonstrates how to work with databases directly from R.
This lesson assumes no prior knowledge of R or RStudio and no programming experience.
Contributors
The list of contributors to this lesson is available in the citation page.
Preparations
Data Carpentry’s teaching is hands-on, and to follow this lesson learners must have R and RStudio installed on their computers. They also need to install a number of R packages, create directories, and download files.
To avoid troubleshooting during the lesson, learners should follow the instructions below to download and install everything beforehand.
Install R and RStudio
R and RStudio are two separate pieces of software:
- R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis
- RStudio is an integrated development environment (IDE) that makes using R easier. In this course we use RStudio to interact with R.
- Install R from Software Center (Windows) or Self Service (Mac).
- Once complete, install RStudio from Software Center (Windows) or Self Service (Mac).
Windows - Download R from the CRAN
website. - Run the .exe file that was just downloaded -
Go to the RStudio
download page - Under All Installers, download the RStudio
Installer for Windows. - Double click the file to install it - Once it’s
installed, open RStudio to make sure it works and you don’t get any
error messages.
Mac - Download R from the CRAN website. - Select
the .pkg file for the latest R version - Double click on
the downloaded file to install R - It is also a good idea to install XQuartz (needed by some packages) -
Go to the RStudio
download page - Under All Installers, download the RStudio
Installer for MacOS. - Double click the file to install RStudio - Once
it’s installed, open RStudio to make sure it works and you don’t get any
error messages.
- Follow the instructions for your distribution from CRAN, they provide
information to get the most recent version of R for common
distributions. For most distributions, you could use your package
manager (e.g., for Debian/Ubuntu run
sudo apt-get install r-base, and for Fedorasudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.3.1. - Go to the RStudio download page
- Under All Installers, select the version that matches your
distribution and install it with your preferred method (e.g., with
Debian/Ubuntu
sudo dpkg -i rstudio-YYYY.MM.X-ZZZ-amd64.debat the terminal). - Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.
Update R and RStudio
Once you have R and RStudio installed, it’s a good idea to keep both up to date:
- For University of Auckland machines: Check Software Center or Self Service to see if there is an update for R or RStudio.
- For personal machines: Get the latest version of R from CRAN and
install over the current version. To update RStudio to the latest
version, open RStudio and click on
Help > Check for Updates. If a new version is available follow the instruction on screen. By default, RStudio will also automatically notify you of new versions every once in a while. - After installing a new version of R, you will have to reinstall all
your packages with the new version. For Windows, there is a package
called
installrthat can help you with upgrading your R version and migrate your package library.
Install required R packages
During the course we will need a number of R packages. Packages
contain useful R code written by other people. We will use the
tidyverse package.
To install these packages, open RStudio and copy and paste the following command into the console window (look for a blinking cursor on the bottom left), then press Enter (Windows and Linux) or Return (MacOS) to execute the command.
R
install.packages("tidyverse")
Alternatively, you can install packages using RStudio’s graphical
user interface by going to Tools > Install Packages and
typing the names of the packages separated by a comma.
R tries to download and install the package on your machine. When the installation has finished, you can try to load the package by pasting the following code into the console:
R
library(tidyverse)
If you do not see an error like
there is no package called ‘...' you are good to go!
Updating R packages
To update the packages that you have installed, click
Update in the Packages tab in the bottom right
panel of RStudio, or go to
Tools > Check for Package Updates....
Sometimes, package updates introduce changes that break your old
code, which can be very frustrating. To avoid this problem, you can use
a package called renv. It locks the package versions you
have used for a given project and makes it straightforward to reinstall
those exact package version in a new environment, for example after
updating your R version or on another computer. However, the details are
outside of the scope of this lesson.
Download the data
We will download the data directly from R during the lessons. However, if you are expecting problems with the network, it may be better to download the data beforehand and store it on your machine.
The data files for the lesson can be downloaded manually here: https://doi.org/10.6084/m9.figshare.1314459