The data used in this lesson comes from a project observing a small mammal community in southern Arizona, US. This is part of a project studying the effects of rodents and ants on the plant community that has been running for almost 40 years. The rodents are sampled on a series of 24 plots, with different experimental manipulations controlling which rodents are allowed to access which plots.
The Portal Project Teaching Dataset is a real dataset that has been used in over 100 publications. We have simplified it for the purposes of this lesson, but you can download the full dataset (see below for details) and work with it using exactly the same tools we will learn here.
For this lesson, you will need to download the following file (remember where you downloaded the file!):
Data in some of the columns of the above file (e.g. geolocation, locality, county, country, JSON) are contrived for the purpose of the lessons and are in no way related to the original dataset.
For Interest Only: Portal Project Teaching Dataset
The Portal Project Teaching Database is a simplified version of the Portal Project Database designed for teaching. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught. The database is currently available in csv, json, and sqlite formats.
The Portal Project Teaching Database’s GitHub repository can be found at: https://github.com/weecology/portal-teachingdb, where suggested changes or additions to this dataset can be requested or contributed. This database is not designed for research as it intentionally removes some of the real-world complexities. The Python code used for converting the original database to this teaching version can be found in create_portal_teach_dataset.py.
CITATION: Ernest, Morgan; Brown, James; Valone, Thomas; White, Ethan P. (2017): Portal Project Teaching Database. Figshare. https://doi.org/10.6084/m9.figshare.1314459.v6
For this lesson you will need OpenRefine (formerly GoogleRefine) and a web browser. Download the most recent version of OpenRefine for your operating system, then follow the instructions below.
OpenRefine is a Java program that runs locally on your machine (i.e. you are not accessing a remote service on the Internet). Most recent versions of OpenRefine for Windows and Mac come with embedded Java, in which case you do not need a separate Java installation.
Once it is running on your machine, you access it via your browser at the address http://localhost:3333. No Internet connection is needed for this as the programme is running locally.
Extract.... Name that directory something like OpenRefine.openrefine.exe in the extracted folder and launch OpenRefine by double-clicking on it. This will launch a command prompt window first..dmg file and Ctrl-click it. You may get the warning “macOS cannot verify the developer of “OpenRefine.app”. Are you sure you want to open it?” Click ‘Yes’/’Open’ to this.OpenRefine.app into your Applications folder, and Ctrl-click to open it. You may get the warning “macOS cannot verify the developer of “OpenRefine.app”. Are you sure you want to open it?” Click ‘Yes’/’Open’ to this.Once you’ve downloaded the file above, you can start the lesson.