Previous steps

If you would like to return to information from the previous section, please click here.

Context

Along with the utility of version control and remotely synchronising with collaborators and project partners, Github provides a wiki that can be used to document a coral reef monitoring project. This includes providing documentation of How to?s, posting of monitoring results, and outlining of reports, manuscripts or student theses.

Depending on the project aims, the wiki can serve as a versatile tool for project documentation and support. For example, wikis can be designed to point directly to visualisation outputs located in the data repository figures folder, which will automatically update with the latest results when running integrate.R. As with this training course, we are using the wiki to provide an overview of individual modules, example code, links to reference materials and instructions for Homework.

In order to provide course participants with a basic understanding of how to set up a project wiki, this wiki page provides the basic steps for setting up and controlling a Github wiki.

Basic set up

Github wiki pages use the same general markdown syntax, with double ** to provide emphasis, reference to figures using ![](location/to/figure.png), *.html links (e.g. ICUNs [Redlist](https://www.iucnredlist.org)), code chunks and more:

Without going into too much detail on the markdown syntax, course participants that are seeking additional detail on documenting projects in the Github wiki should have a look here.

Controlling Sidebar

Chances are you have arrived at this page via the Sidebar of the Github wiki!

The sidebar can be set up with a *.md file named _Sidebar.md. The headings for sections of the wiki can be set up using the markdown notation for emphasis (i.e. **Context and Approach**) and individual pages are included in double square brackets (i.e. Why be excited about this training course).

For example:

Pages are then named with individual *.md files corresponding to the double square bracket label in the sidebar (e.g. Why-be-excited-about-this-training-course.md). As special characters (e.g. ?) can have a meaning in coding, so these are avoided in the file names.

If a page does not exist or if there is a discrepancy in the *.md file name and the notation in the _Sidebar.md, the link will appear red. This is a good way to check that names match and/or indicate future development of the wiki.

Next steps

After going over the use of markdown for routine reporting, presentations and maintaining a Github wiki, we will have a look at the homework for the Project Documentation & Reporting module.