AAGI Shared Code Database

Our motivation

This project was motivated by our team’s desire to:

Reduce duplication in our coding practices
Offer shared resources to support growing AAGI community, especially new comers
Improve statistical rigour and coding practices
Create opportunites to connect and collaborate
Identify greatest code duplication/overlap for creating software

What is desk drawer code?

Desk drawer code refers to functions that have been created and reused for multiple projects. They may not be neccesarily packaged but have stood the test of successive projects. This type of code often resides in personal folders or your one’s “desk drawers” making it less accessible to others who might benefit from its use. This project is about bringing that code to one place for the benefit of the wider AAGI community.

🧑‍🍳 Attributes of desk-drawer code based on usage

Code that is:

in regularly use (implies is up-to-date) in your analytical workflow
often duplicated across projects for their usefulness
shared with others because it also solves a common problem
reused and improved over successive projects

🥚 Attributes of desk-drawer code based on the problems it solves

Code that:

Wrangles data that is always consistent format e.g. machine outputs, marker data into genomic related matrix
Checks or visualises data that has a predictable layout e.g. field/glasshouse design
Extracts useful components from model outputs for checking/reporting/visualising
Computes summary statistics from regularly used model outputs
Formats results nicely e.g. tables in QMD/RMD