Setup for all episodes.

Setup for all episodes.

Introduction to the Data for this Lesson

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. This is a real dataset that has been used in over 100 publications. It is published at Ecological Archives and can be found on Portal Project Database. This data is open and free to use for research purposes.

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

Download Data for Spreadsheets Lesson

For the purposes of training, this data has been simplified a bit (you can still download the full dataset and work with it using exactly the same tools we will learn here). This simplified version of data is available from the Portal Project Teaching Dataset. In this lesson, you will need to download the following five files from the Portal Project Teaching Dataset:

To interact with spreadsheets, you can use various software - for example Microsoft Excel, LibreOffice, Gnumeric, OpenOffice.org, Google Spreadsheets. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same.

For this lesson, if you do not have a spreadsheet program already, you can use a free and open source tool LibreOffice as it can open Excel spreadsheets, which is the format of the data we will work with during the lesson (also all examples used refer to Excel).

Windows

Mac OS X

Linux

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.

Install OpenRefine

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.

Windows

Mac

Linux

A text editor is the piece of software you use to view and write code. If you have a preferred text editor, please use it. Suggestions for text editors are, Notepad++ (Windows), TextEdit (macOS), Gedit (GNU/Linux), GNU Nano, Vim. Alternatively, there are IDE’s (integrated developer environments) that have more features specifically for coding such as VS Code; there are also IDEs specific to languages will be listed in the appropriate section(s) below.

Project Demo Repository

We’ll be showing you how to manage an example academic software project. If you’ve completed our Version Control with git workshop (linked here) , you’ll have an example project. If not, please create a copy of our demo repository from this template (linked here), and name it climate-analysis. You don’t need to run this code as part of the course! It’s purely for demonstration purposes.

Install Visual Studio Code

This workshop involves editing code files. Whilst you can use any text editor to do this, some code editors or Integrated Development Environments (IDEs) have features designed to make coding easier. If you’re already using a code editor or IDE (e.g. Atom, Sublime Text or Spyder), stick with what you’re comfortable with. If not, we’d recommend installing Visual Studio Code (link here).

Windows / MacOS

Go to the Visual Studio Code website, and download and run the installer.

Linux

If you’re on Ubuntu, Visual Studio Code should be available through the software centre! If not, follow the detailed instructions here to install it.

Open a Terminal

For this lesson, first you need to be able to open a terminal:

Git Setup

Windows

We’ll be using Git Bash for both git and a shell to run it in. If you’ve already installed Git Bash then go to the next section. Otherwise, go to git for windows and click Download, then install it. Most of the options can be left on default, but be sure you check these:

Mac OS

To use Git you must install the Apple Command Line Tools, this may take a few minutes.

You can obtain these from Apple (requires your Apple ID)

Alternatively, you can install the tools from the command line:

$ xcode-select --install

Linux

Git comes pre-installed on most Linux distributions. You can test if it’s installed by running git --version. If it’s not installed, you can install it by running sudo apt-get install git or sudo yum install git, depending on your distribution.

GitHub

Later on in the session, we’ll be demonstrating how to share work with collaborators using GitHub. You’ll need to create an account there. As your GitHub username will appear in the URLs of your projects there, it’s best to use a short, clear version of your name if you can.

In addition, we’ll need to set up SSH access to GitHub from your computer. This is how GitHub checks your identity when you try to access it - and is more secure than a password. To set up SSH access, we generate a pair of keys - one public, one private. We want to add the public key to GitHub, whilst the private one stays on our computer.

There are full guides in the GitHub documentation for how to Make an SSH Key and Add an SSH key. However today we have simplified it like so:

If you already have an ssh key you can use it for Github by coping the public key into the clipboard and pasting it into the GitHub settings page.

First we need to create a variable to store your GitHub email. Copy this command, substituting the email you signed up to GitHub with for your_github_email@example.com:

$ my_gh_email=your_github_email@example.com

Then we can run the following command to generate a key-pair and display the public half:

$ ssh-keygen -t ed25519 -C $my_gh_email; eval "$(ssh-agent -s)"; ssh-add ~/.ssh/id_ed25519; cat ~/.ssh/id_ed25519.pub

You will need to press enter a few times to select default options, and set the passphrase to empty.

Copy the last line of output that starts with ssh-ed25519 and ends with your email (it may have gone over multiple lines if your terminal isn’t wide enough).

SSH-Output

Finally, go to your Settings -> SSH keys page and add a new SSH key (you’ll need to be logged into GitHub with the account you have created). Give the key a memorable name (e.g. the name of the computer you are working on) and paste the key from your clipboard into the box labelled key. Then, click Add SSH key and you’re done!

Download Data for Shell Lesson

Type the following into the prompt that appears (pressing enter/return after each line):

$ cd
$ git clone https://github.com/Southampton-RSG-Training/shell-novice.git

cd will move to your home directory, and git clone will download a copy of the materials.

Alternatively, if you have SSH authentication with GitHub enabled (if you don’t know what this means don’t worry, it is covered in the Git SWC course if you want to know more!) you can use the following:

$ cd
$ git clone git@github.com:Southampton-RSG-Training/shell-novice.git

This should download all the content for the lesson to a new directory. Please let the instructors know if you run into any problems.

Download Data for Git Lesson

Now we are ready to download the code that we need for this lesson, using Git on the command line. Open a terminal on your machine, and enter:

$ cd
$ git clone https://github.com/Southampton-RSG-Training/git-novice

cd will move to your home directory, and git clone will download a copy of the materials.

Python Setup

IDEs: PyCharm, Spyder, VS Code

We use Python 3*. The “Anaconda3” package provides everything Python-related you will need for the workshop. To install Anaconda, follow the instructions below.

Some old research projects may be in Python 2 but Python 2 has been retired and new projects should be in Python 3.

Windows

Download the latest Anaconda Windows installer. Double-click the installer and follow the instructions. When asked “Add Anaconda to my PATH environment variable”, answer “yes”. It will warn you not to, but it’s required for it to be found by git bash After it’s finished, close and reopen any open terminals to reload the updated PATH and allow the installed Python to be found.

Once the Anaconda installation is finished you will be asked if you want the installer to initialize Anaconda3 by running conda init? You should select yes. Alternatively/additionally you will need to run the following command in GitBash

conda init bash

Then close and reopen GitBash.

Please test the python install open GitBash (or your favorite terminal) and run the following command to verify that the installation was successful.

cd ~
python

You can then type the following to exit:

quit()

In some cases GitBash will hang on this command and not launch the Python interpreter. 
In this case close and reopen git bash and issue the following commands:

cd ~
echo 'alias python="winpty python.exe"' >> .bashrc
source .bashrc
python

Mac OS X

Mac OS Intel

Download the latest Anaconda Mac OS X installer. Double-click the .pkg file and follow the instructions.

Mac OS M1

If you have a M1 Mac you need a specific version of Anaconda follow the link below.

M1 Compatible Anaconda

Once the Anaconda installation is finished you will be asked if you want the installer to initialize Anaconda3 by running conda init? You should select yes.

Linux

Download the latest Anaconda Linux Installer.

Install via the terminal like this (you will need to change the version number to the latest version):

First move to the folder where you downloaded the installer, this is likely to be the Downloads folder e.g.

$ cd ~/Downloads

$ bash Anaconda3-2021.11-Linux-x86_64.sh

Answer ‘yes’ to allow the installer to initialize Anaconda3 in your .bashrc.

Download Data for Python Lesson

Now we are ready to download the code that we need for this lesson. Open a terminal on your machine, and enter:

$ cd
$ git clone https://github.com/Southampton-RSG-Training/python-novice

cd will move to your home directory, and git clone will download a copy of the materials.

Install R and RStudio

R is a programming language and software environment for statistical computing and graphics. The RStudio Integrated Development Environment (IDE) is a set of tools designed to help you be more productive with R.

We need to install R and RStudio: The latest links can be found on the RStudio downloads page

R

R can be found at https://cran.rstudio.com/, from here pick your OS and download the latest release, see below for direct links to your OS.

Windows

Mac OS

Linux

RStudio

Your OS should be detected and a link provided under step 2 on this page RStudio downloads page. Else select your OS from the list under All Installers.

Windows

Download and run the .exe file and follow instructions given by your OS.

Mac OS

Download the .dmg file.

Linux

Download the appropriate install file (.rpm or .deb) for your distro.