As you can see, this file is nothing beyond a list of files and folders. The linear order decides what you get to see, and you can edit the layout.md file from the data folder to adjust the flow and logic of your paper. You can see there are mix of html and markdown files. You do not see individual images and tables but instead in the specific points where they are located, you get to see their "folder names" are organised. You can manipulate the configuration and the layout files to change the appearance of the documents and add templating to the Authorea document for your final data analysis results presentation. We will discuss these now.

Step 2: Link with github

Once you have set up the article (or say you use this as a template and this one contains a jupyter file as well), you can just set up the github links and you can work from github or git and jupyter to wwork with the Authorea article. You can adjust the main sections once your data analyses are complete but otherwise you can push your files from within your computer or from the web using the github web interface. In the rest of the article, I will guide you through it.

Step 3: Use a jupyter notebook to conduct your data analysis and link it here

Start a jupyter notebook in the parent directory and start working. Here are the principles:
  1. You can write in markdown and you can save the contents in markdown, upload and put it in the layout.md file
  2. Save your outputs as jpg files or csv files and push them to the figures folder
  3. Later edit the config.yml and layout md files
  4. Leave the ipynb text in the form of markdown
  5. git your changes
  6. Do the final editing in Authorea.