Update manuscript with minor changes for publication

[zkamvar]

There were some minor changes requested by PeerJ and caught by us before publication:

The initial changes requested by PeerJ were documented in #20, which mainly involved:

• removal of funding statements and COI
• add A-D labels on Figure 6
• cut out supplementary information into a different file (this is done via move-supplementary.sh, but still involves manually dividing the PDFs)

Upon receiving the proof, we made the following changes:

• Fix citations including the URL for the OSF repo and adding volume/page numbers to some citations
• add details on methods for calculating quantities such as e^H and h in the methods section
• Citing knitr and ezknitr (#21)

I will merge this into the master branch once we have confirmation that the publication will go through.