Include all analyses scripts used to:
* clean data
* run analyses
* create figures/tables
* calculate power/make sample size decisions
If you have a lot of different scripts, think about using folders/subcomponents to organize. You also likely want to include a readme file (or in the wiki) to explain what the different files are an how to use them.
If you use github/github, make sure all the scripts are in one repo and then just connect that here as an addon.