Day 4: End-of-day practice

Today you’re going to practice writing and using functions by continuing to encapsulate logic in your reef model. You’ll also learn a new GitHub feature: Issues.

Issues

Note

GitHub Issues are tools for tracking tasks, bugs, or questions related to a project. Like a shared to-do list or lab notebook for your code, each issue has a title, a description, and a conversation thread where you and your collaborators can discuss how to resolve it. Issues can be labeled, assigned to specific people, and closed once resolved, making them a simple way to organize and communicate about problems or planned improvements without cluttering the actual code.

How to make an Issue

1. Navigate to your repository on GitHub.com and click the Issues tab.
2. Click New issue, then add a descriptive title and a description of a task, bug, or question related to your reef model.
3. Click Submit new issue to create it.

Make two issues

1. Integrate initialization. The reef initialization step has been encapsulated in a function, but death_survival.R doesn’t have access to it yet. Create an Issue with the title “Integrate initialization”. The description should read “Source R/util.R at the top of death_survival.R and replace the existing reef initialization code with a call to the initialization function.”.
2. Encapsulate growth. The coral growth code in death_survival.R still needs to be turned into a function. The Issue should describe adding a growth function to R/util.R and replacing the coral growth code in the script with a call to that function.

Encapsulate your code

Integrate initialization

Earlier today, you encapsulated the reef initialization step in a function. But that function isn’t accessible to your reef model script yet - it’s in a separate file. Follow these steps to link the two together.

1. At the top of death_survival.R, add a line with the following code:

source("R/util.R")

The source() function runs the script found at the path you give it. In this case, R/util.R is the path to a script defining your reef initialization function. So sourcing that script defines the function and gives you access to it.

2. Replace the coral reef initialization code in your script with a call to your new function.

Link your changes and the issue

Including a closing keyword like fixes followed by an Issue number in a commit message will automatically close that Issue when the commit is pushed to GitHub.

1. Stage your changes to death_survival.R and util.R.
2. Commit your changes with a message that includes fixes #1.

Encapsulate growth

The activity this morning showed you how to encapsulate the code for coral growth into a function.

1. Add the growth function in util.R.
2. Replace the coral growth code in your script with a call to your new function.

Link your changes and the issue

1. Stage your changes to death_survival.R and util.R.
2. Commit your changes with a message that includes fixes #2.

Wrap up

When you’re done, push your changes to GitHub. Then check your Issues on GitHub - you should see that they’re closed now and linked to the specific code changes.

Tip

By default, the Issues tab only shows open issues, so your closed issues will disappear from the list. To see them, click the Closed tab (next to Open) above the issue list.