Reproducible Scientific Practices for Conservation Biologists

Pre-workshop instructions

1. Please bring your own device, preferably with RStudio installed. It is recommended that users update their R/RStudio to the most recent version to avoid any errors. Please click these links to update R on Windows and Mac.
2. Create a account on GitHub - it's free!. Please note that when you are creating a GitHub account for the first time, please do not click the 'Continue with Google' option and instead manually enter your email address, set a password and username. Else, if you used one of your gmail addresses automatically, please ensure that you set a password for your account.
3. Download and install Git. Before you start this step, please close R and RStudio. For Step 3 alone, the process can vary for Windows and Mac systems. Please see below.

Windows Users

When you click the download link for Git above, it will take you to the page below. Please click the link marked within the red box to download the program and follow associated instructions.

MacOS Users

It's a two-step process. First, you need to install Homebrew using your terminal (Type cmd + spacebar to access terminal on a mac) or by downloading the .pkg file (both options are available through the link above). Option 1 will require you to use your Terminal on Mac and Option 2 requires a manual download and installation. The second screenshot provides an image of the page you will encounter if you try Option 2. Once you are done with either Option 1 or Option 2, and Homebrew is installed, you need to type brew install git and paste it in your terminal for the installation of Git to be completed.

Option 1:

For Option 2, when you click Homebrew's latest GitHub release, it will take you to a page on GitHub. You should scroll down to the bottom of the page and click the red box highlighted to download Homebrew manually:

Now please remember that after you install Homebrew, you need to type brew install git in your terminal for the installation of Git to be completed.

Check if you installed Git correctly

1. Please go to RStudio and open the Terminal pane located right next to the Console in the left-bottom panel and type in the following: which git. Please note that some Windows machines might recognize the command where git instead of which git. If you are not able to see the Terminal pane, please click on Tools > Terminal > New Terminal.

2. Do you get an error that says: git: command not found. If yes, close RStudio and redownload and install Git. Once you are done installing it successfully, open RStudio and try the above command in the Terminal pane again: which git or where git (depending on your Windows machine, where might work rather than which). MacOS Users might encounter a different error. Please see Step 4 below.

3. If you don't see any error yet, please double-check to ensure that the paths shown on Terminal for where git is located is the same as where RStudio is finding it. To do this, please click on Tools > Global Options > Git/SVN. Please note that you only need to ensure that both paths have /bin/git or /git. You don't have to worry about other content in the paths. Sometimes the /bin may not appear depending on the computer but should atleast see a /git to learn that your installation has been successful.

4. MacOS users: might encounter other errors when you type which git or where git. If you get an immediate offer to install command line developer tools, please go ahead and do it. You should accept the license agreement and click Install. Once installation is completed, please close RStudio and restart RStudio and go to Terminal and type xcode-select -p. When you hit enter, you should see /Library/Developer/CommandLineTools. Now type which git and redo the above Step 3.

5. If you don't get an automatic message to install Command Line Tools, close RStudio. Then go to https://developer.apple.com/download/ and download Command Line tools for your OS version. Once installation is completed, please restart RStudio and go to Terminal and type xcode-select -p. When you hit enter, you should see /Library/Developer/CommandLineTools. Now type which git and redo the above Step 3.

If you encounter any other installation errors, please contact me.

Workshop details

The first part of the workshop will focus on the necessity for reproducible approaches in conservation biology, followed by an introduction to data management, organization, and file naming conventions.

The second half of the workshop will be focused on version control, GitHub and using it with RStudio.

Towards the end, we will go over useful resources and functionality from packages that are commonly used.

Workshop materials

Within the folder workshop-materials, I have uploaded a Powerpoint presentation covering all the workshop content.