Overview
1
File Structure
1.1
Folder Naming
1.2
Google Shared Drive
1.2.1
General Structure
1.2.2
Project Folder Structure
1.3
GRIT data storage space
1.3.1
General Structure
1.3.2
Project Folder Structure
1.3.3
Data Directories
1.4
GitHub Structure
1.4.1
Project Repository Structure
1.4.2
A repo inside a repo
2
Data
2.1
Data File Naming
2.2
Metadata
2.2.1
Metadata Standards
2.2.2
emLab common data directory
2.2.3
Project-specific data directories
2.3
Accessing emLab data in R
2.4
Tidy Data
2.4.1
Recommended Resources
2.5
Data Formats
2.6
Data Use Agreements and Confidential Data
2.6.1
The process for establishing a Data Use Agreement or Non-Disclosure Agreement
2.6.2
Data storage options
2.6.3
Other best practices
3
Code
3.1
Scripts and Version Control
3.2
Style Guide
3.3
Reproducibility
3.3.1
Package management
3.3.2
Coding pipelines
3.4
Internal code review
3.5
Exploratory Data Analysis
4
High Performance Computing
4.1
Available resources
4.2
Available software
4.3
Installing packages
4.4
Setting up a GRIT account
4.5
Logging in
4.6
Accessing data
4.7
Accessing code
4.8
Using htop to monitor shared resources
4.9
Best practices for sharing our computational resources
5
Reports and Publications
5.1
emLab Affiliation
5.2
Reports
5.3
Author Contribution
5.4
Making Your Data Publicly Available
5.5
Preparing a Public GitHub Repository
5.5.1
Documentation
5.5.2
Sanitizing the repository
5.6
Sharing public data, Shiny apps, and tools on our website
emLab Standard Operating Procedures
5
Reports and Publications
This section describes best practices related to emLab reports and publications.