Horizon Scanning, Demand Signalling (HSDS): MASH Pathway Analysis and Modelling Repository

This repository contains the codebase for undertaking all analysis and modelling of the MASH pathway.

Table of Contents

• Repository Structure
• Getting Started
• Contributors
• License

Repository Structure

The current structure of the repository is detailed below:

├───README.md
├───LICENSE
├───.gitignore
├───.Rproj
├───data
    ├───raw
    ├───reference
    └───theograph
├───documentation
    └───project_documentation
├───images
    └───theograph_example
└───src
    ├───config
    ├───outputs
    ├───requirements
    ├───results
      ├───charts
      └───tables
    └───scripts
      ├───analysis
      ├───etl
        └───udal_extracts
      ├───processing
      └───visualisation
    

• README.md: This file containing an overview and instructions for using the repository.
• LICENSE: License information for the repository.
• .gitignore: Specifies the files and folders that are ignored (not tracked) in the repository.
• .Rproj: The RStudio project file.
• data: Directory for data files used in the analysis
  • reference: Any reference files such as geospatial datasets or data dictionary files used in the analysis.
• documentation: Additional documentation that is helpful for understanding and replicating analysis and modelling.
• images: Directory containing any logos and other images used in creating outputs for the repository.
• src: All source code used for any analysis and modelling. This is comprised of the following:
  • config: Directory contains configuration files for outputs such as css and ggplot themes.
  • outputs: Contains the output files used to render the analysis or modelling such as .qmd or .rmd
  • requirements: Contains information on requirements for the repository. Scripts for required R packages and loading these into the environment.
  • results: Outputs of analysis or modelling such as specific charts and tables to be rendered in the outputs.
  • scripts: Directory containing the code used within the analysis and modelling. This is further broken down into:
    1. analysis: Scripts for analysing MASH datasets.
    2. etl: Scripts for loading datasets into environment.
    3. processing: Scripts for processing and cleaning loaded datasets.
    4. visualisation: Scripts for creating visualisations and functions for analysis.

Getting Started

This analysis has been undertaken in R and RStudio. You will need to have these installed to replicate the analysis or use an alternative IDE. The R packages that are required for replicating analysis and modelling are documented within the requirements directory.

The repository can be cloned locally using:

git clone https://github.com/NHS-Transformation-Unit/HSDS_MASH.git

Contributors

This repository has been created and developed by:

• Andy Wilson

License

This project is licensed under the GPL-3.0 license - see the LICENSE file for details.