README.md

About

This repo stores documents related to the Sleep Health In Perinatal Care (SHINE) Project, funded by National Health and Medical Research Council (NHMRC) Clinical Trials & Cohort Studies Grant. SHINE is a collaborative project amongst Monash University Sleep and Mental Health Laboratory (Lead), Stanford University (USA), Monash Health, and the Royal Women's Hospital. It studies changes in sleep and wellbeing across pregnancy and the postpartum years, and evaluates interventions for improving sleep during this important period for Australian families.

To make the research process transparent, documents in working progress are made publicly available via Creative Commons Attribution-ShareAlike 4.0 International CC BY-SA 4.0 . Briefly, it is free to share or adapt content in this repo as long as you credit the source and make the resulting content open access.

Questions or comment: bei.bei@monash.edu

Read-me-first for staff

Checks and training

• Required Working with Children Check
• Required Good Clinical Practice training: Monash Partners, SBM Online
• Consumer and Community Involvement training
• safeTALK and ASSIST
• Guidelines on creating accessible content for individuals with auditory, cognitive, physical, speech, and visual impairments.
• TBC

Systems to access

• Github, we require all staff to enable multi-factor authentification. Please also request a free Pro account via Github Education students or teachers programs.
• Github Desktop, or GitKracken can make using GitHub easier
• Microsoft Teams.
• REDCap, if new user, admin to request access.
• S Drive: setup information for users. You will need to be on the Monash VPN; admin's user management portal.
• Zoom phone.
• Ethics (Monash Health).
• Sleep and Circadian Rhythm mailing list, seminar program.
• M-Pass: Monash Staff/Student card Apply for M-pass
• With valid M-Pass apply for Building Access

Git

• Learn basics from Github Skills.
• Basics for GitHub Desktop.
• Student resources from GitKraken have a nice collection of videos explaining git concepts, and how to use GitKraken with GitHub.
• For a point and click git client, check out Github Desktop or GitKraken

Markdown

• Learn Markdown.
• Use a good plain text editor that supports syntax highlighting (e.g., Obsidian).

Files, formats, and naming conventions

• IMPORTANT: This repo is open to the public. Do not commit personally identifiable information to this repo.
• Use plain text (e.g., *.md, *.txt, *.R, *.Rmd) as much as possible to allow detailed version control. Only use other formats (e.g., *.docx, *.pdf) when necessary.
• Stick to strict folder/file naming convention. Problems with folder/file naming could lead to data loss. Read this link here. Do not use special characters, period, or spaces. You can use - (dash) or _ (underscore) instead. Try to use lowercase only, especially folders.
• R object naming conventions are different from folder and file naming. See this R code convention. In naming R objects, such as a data.table or variable, period . (not _) as a separator is the convention. Please also check out the File Names and Identifies sections of the link above.

How to work with a repo?

• Before you start, please learn basic git, and git workflow.
• The main branch is usually a stable version.
• When you work on a specific issue, make a branch from the main, and send pull request to merge your commits into the main.
• Branches can come and go. You can create as many branches as you need for working on specific sections, and once the changes you made are merged back to the main, you can delete them. Make a new branch when you work on the next issue.
• Please squash your commits into a single one before sending pull request. This helps the reviewer view only one set of differences.
• IMPORTANT: each time BEFORE you start working on your branch, make sure you fetch and merge any changes that occurred.

What is .gitignore?

• It is a (usually) hidden file that can be opened using any text editor.
• It is helpful to turn on "always show hidden files" to see all files being committed to a repo. Google how to do this and turn this on.
• .gitignore contains files and directories that are ignored by git. This is very helpful for items like private notes, messy temporary hidden files, or sensitive data. Adding these items to the .gitignore file will tell git to automatically skip them, so they will not be committed to Github server online, or to collaborators.
• A frequent use case is /data line being part of .gitignore. This way, we can store data locally in our repo without committing them to be shared with others.