sAMRat

An Open Source Shiny Application that uses the AMR package to facilitate Antimicrobial Resistance Data Analysis and Reporting.

Overview

sAMRat (Shiny Antimicrobial Resistance Analysis Tool) is an interactive web application built with R Shiny that simplifies antimicrobial resistance (AMR) data analysis. It leverages the powerful AMR package to provide:

• 🔬 Easy Data Upload: Import your microbiological data in various formats
• 🗺️ Intuitive Mapping: Map your dataset columns to AMR-compatible format
• 📊 Comprehensive Analysis: Generate resistance patterns, trends, and statistics
• 📈 Beautiful Visualizations: Create publication-ready plots and charts
• 💾 Flexible Export: Export results in multiple formats

Why sAMRat?

The AMR package is powerful but can be complex for users unfamiliar with R programming. sAMRat bridges this gap by providing:

• No Coding Required: Point-and-click interface for all operations
• Interactive Experience: Real-time feedback and previews
• Guided Workflow: Step-by-step process from data upload to reporting
• Professional Output: Generate reports ready for publication or presentation

Installation

Currently, sAMRat is not available on CRAN. Install from GitHub:

Via cloning the repository

git clone https://github.com/Gero1999/sAMRat

Then load it using devtools:

if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::load_all()

Quick Start

Launch the application with:

devtools::load_all()
shiny::runApp(system.file("shiny/app", package = "sAMRat"))

For detailed instructions, see the Getting Started guide.

Features

Current Features

• Data Upload & Preview: Support for common data formats
• Column Mapping: Interactive mapping interface for AMR data structure
• Analysis Tools: Basic resistance pattern analysis
• Visualization: Standard AMR visualizations
• Export Options: Download results and plots

Planned Features

• Database connectivity for large datasets
• Advanced statistical analyses
• Customizable report templates
• Batch processing capabilities
• Multi-language support

Documentation

• Getting Started: Learn the basics of using sAMRat
• Architecture: Understand how sAMRat is built
• Contributing: Join our community of contributors
• Function Reference: Detailed documentation of all functions

Contributing

We welcome contributions! sAMRat is in active development and we’d love your help to make it better. Whether you’re:

• 🐛 Reporting bugs
• 💡 Suggesting features
  
• 📝 Improving documentation
• 💻 Contributing code

Check out our Contributing Guide to get started!

Support

• Issues: Report bugs or request features on GitHub Issues
• Discussions: Ask questions on GitHub Discussions
• Email: Contact the maintainer at gerardo.jrac@gmail.com

Acknowledgments

This package builds on the excellent work of:

• AMR package: The foundation for all AMR analysis
• Shiny: The web application framework
• R Community: For the amazing ecosystem of packages

For the AMR package:

Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022).
"AMR: An R Package for Working with Antimicrobial Resistance Data."
Journal of Statistical Software, 104(3), 1-31. doi:10.18637/jss.v104.i03

Maintained by: Gerardo Jose Rodriguez (@Gero1999)