Update notebooks for preprint release

[adelavega]

• Simplified analyses as much as possible, and removed all analyses not in paper.
• We've created a legacy branch to keep transparency about all analyses that did not make the cut for the paper

[adelavega]

Almost finished cleaning these up. Need to re-run all meta-analyses and then we need to :+1:

• Add code for surface plots
• Add Jeff's code for methods figure
• Possibly add more visualizations