repository_project_title

Licensing and Use

License

This reposiotry is licenced under CC BY-NC-SA 4.0, an Attribution-NonCommercial-ShareAlike 4.0 International license.

Contributors

• Jane Doe (primary/first)
• Eyal Kimchi (Principle Investigator)
• John Doe (as of 20XX/XX/XX)

Contact Information

For any questions concerning this repository please contact:
Eyal Y Kimchi, MD PHD
Email: [email protected] | Website

Project Description

Objective

Hypotheses

(Possible link to pre-registration)

Methods

(protocols, sampling, instruments, coverage, etc.)

Data

(Range of years over which data was collected, location, size, quality assurance metrics, missing data, etc)

Results Overview

(Basic results tables and key context to understand the figures)

File Structure Overview

(File layers, naming convections, etc.)

Evironment Configuration

Prerequisite Programs

• Git v2.46+
• Python3 v3.12.6+
• Anaconda Distribution v3.12.4 or Minicondav24.7.1
• R v3.6.0+ and R Studio v2024.04.2+

Repository Cloning

To clone the repository to your local machine, paste the following in the command line:

git clone https://github.com/kimchilab/<example>.git

Environment Install

Both Python and R environment files are stored as .yaml files at the top level of the repository. To configure both environments, make sure that you have a conda package installed and run the corresponding lines from the top directory

To create the environment:

Python:

    conda env create -f <env_name_py>.yml

R:

    conda env create -f <env_name_py>.yml

To activate and use the environment:

Python:

    conda activate <env_name_py>

R:

    conda activate <env_name_py>

R Project Evironment

To populate the correct file paths and dependencies, please open <example>.Rproj before running any of the scripts for analysis in RStudio

Detailed File Structure

/Data

All relevant data is stored in the /Data folder off of the repository path.

Filename	Description	Functions Called By
VideoMetaData.csv	Detail all column meanings and units of measurement	What analyses are dependent on this file?
features_data.csv	---	---

/Scripts

Filename	Description	Prerequisite Files	Outputs
LMEM_Delirium_Analysis.R	---	---	---

/Results

Insert Description Here

Filename	Description	Analysis of Origin
Behavioral_bootstrapping_results.csv	Include description of tabular columns	---
LmemResults-Comprehensive-StratifiedDeliriumStatus.txt	---	---

/Figures

Define figure descriptions/captions