Trends in the use of commonly used antibiotics associated with antimicrobial resistance

Overview

• Study title: Trends in the use of commonly used antibiotics associated with antimicrobial resistance
• Study leads:
• ShinyApp:
• Publications:

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Prerequisites

• R and RStudio are required to run the code.
• Ensure that you have access to the database and necessary credentials to connect.

Setup Instructions

1. Download the Repository
   Download this repository:

   • Either download as a ZIP file using Code -> Download ZIP, then unzip.
   • Or, use GitHub Desktop to clone the repository.

2. Open the R Project

   • Navigate to the Study folder and open the project file Study.Rproj in RStudio.
   • You should see the project name in the top-right corner of your RStudio session.

3. Run the Analysis Code

   • Open the CodeToRun.R file. This is the main script you’ll use.
   • Follow the instructions within the file to add your database-specific information.
   • Run the code as directed. This will generate a Results folder containing the outputs, including a ZIP file with the results for sharing. The name of the zip file will be of the format DED_Results_database_name.zip.

4. OPTIONAL: Visualize Results in Shiny

   • Navigate to the Report folder, then the DED_shiny folder, and open the project file DrugExposureDiagnosticsShiny.Rproj in RStudio.
   • You should see the project name in the top-right corner of your RStudio session.
   • Copy the generated result file (in .zip format) into the data folder located within the DED_shiny folder.
   • Open the global.R script in the DED_shiny folder.
   • Click the Run App button in RStudio to launch the local Shiny app for interactive exploration of the results.

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This repo is organized as follows:

• Study: please find there the relevant code to obtain the study results.
• Report: please find there the code to visualise the results with the shiny app and generate the report with the plots and tables.