Getting Started with sAMRat • sAMRat

Introduction

Welcome to sAMRat (Shiny Antimicrobial Resistance Analysis Tool)! This package provides an interactive Shiny application designed to facilitate antimicrobial resistance (AMR) data analysis and reporting.

The application builds on the powerful AMR package to provide an intuitive interface for:

Uploading and mapping microbiological datasets
Performing comprehensive AMR data analysis
Generating visualizations and statistical reports
Exporting results for further use

Installation

Currently, sAMRat is not available on CRAN, so you’ll need to install it from the GitHub repository.

Via cloning the repository

Clone the repository through your terminal/shell:

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

Then load it directly using devtools in your IDE (e.g., RStudio) console:

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

Installing dependencies

Make sure you have all required dependencies installed:

# Install required packages
install.packages(c("AMR", "dplyr", "ggplot2", "shiny"))

Quick Start

To run the application, simply invoke:

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

This will launch the Shiny application in your default web browser.

Using the Application

1. Data Upload

The first step is to upload your microbiological data. The application accepts various data formats and helps you map your columns to the AMR package structure.

2. Data Mapping

Once your data is uploaded, you’ll need to map your dataset columns to the expected AMR format. This includes:

Microorganism identification
Antimicrobial agent codes
Test results (MIC values, disk zones, or interpretations)
Patient/sample metadata

3. Analysis

After mapping your data, you can perform various analyses including:

Resistance patterns
Susceptibility trends over time
Comparison between different organisms or antibiotics
Statistical summaries

4. Visualization and Export

Generate publication-ready visualizations and export results in various formats for further analysis or reporting.

Core Functionality

Creating AMR Objects

The create_amr_obj() function is the core function for creating AMR-compatible data objects:

library(sAMRat)

# Example: Create an AMR object from your data
amr_data <- create_amr_obj(
  data = your_data,
  # Additional parameters as needed
)

Next Steps

Read the Architecture - not yet available article to understand how the package is structured
Check out the Contributing - not yet available guide if you’d like to contribute
Visit the AMR package website for more information about the underlying functionality

Getting Help

If you encounter any issues or have questions:

Check the GitHub Issues page
Open a new issue with a reproducible example