edit and finish joss paper

[samueldmcdermott]

• [x] add citations
• [ ] include updated flowchart
• [x] expand discussion

tag @cavestruz for review when done

[samueldmcdermott]

waiting on #71 but for now @cavestruz would you take a glance and let me know if this is a good level of detail in the body?

[samueldmcdermott]

example paper here