craig-shenton / rapR-package-template

An R/Quarto package template based on NHS Digital's python version that can be adapted for RAP projects.

rapR-package-template

An example {targets} analytics pipeline template that can be adapted for RAP projects.

About

This repository serves as a template for processing data from the NHSR-datasets package and NHS ODS codes using R, targets, and tarchetypes. The output of the data processing is a comprehensive report generated using Quarto. This repository also includes unit tests for the functions within the utilities folder to ensure robust data processing. Features

• Data Processing: Using the R programming language, targets, and tarchetypes to process data from the NHSR-datasets package and NHS ODS codes.
• Report Generation: The Quarto package is used to generate a report from the processed data.
• Unit Testing: This repository includes a set of unit tests for the functions in the utilities folder to help ensure data processing reliability and robustness.

Getting Started

Clone the repository: Start by cloning this repository to your local machine.

git clone https://github.com/<username>/nhs-data-processing.git

Install dependencies: Ensure you have R installed. You should also install the required packages. Run the following command in your R console to install the required packages.

install.packages(c("NHSRdatasets", "targets", "tarchetypes", "quarto", "testthat"))

Process the data: Use targets and tarchetypes to process the data. To run the pipeline, execute the following command in your R console:

targets::tar_make()

Generate report: To generate the report using Quarto, run the following command:

quarto::quarto_render()

Run unit tests: Unit tests for the utility functions can be run with the following command:

testthat::test_dir("utilities/tests")

Structure of the Repository

|-- README.md
|-- .gitignore
|-- quarto_report
|   |-- report.qmd
|-- R
|   |-- _targets.R
|-- utilities
|   |-- functions.R
|   |-- tests
|   |   |-- test-functions.R
|-- data
|   |-- nhsr_datasets
|   |-- ods_codes

Folder Descriptions:

• quarto_report: Contains Quarto markdown files for the report generation.
• R: Contains the R script defining the data processing targets pipeline.
• utilities: Contains utility functions used in data processing and their unit tests. data: Folder for the NHSR-datasets and NHS ODS codes data.

Folder structure

rap-package-template
│   README.md
|   _targets.R
│   create_report.R
│   params.R
|   report_template.qmd
|
├── pipeline
│   ├── interim
│   ├── processed
│   └── raw
│
├───utilities
|   |
│   ├───data_connections.R
│   ├───field_definitions.R
│   └───processing_steps.R
|
├───reports
│   │
│   ├───input_profile
│   └───output_profile
│
└───tests
    └───unittests
        └───testthat
            |
            ├───
            ├───test_data_connections.R
            ├─── test_field_definitions.R
            └───test_processing_steps.R