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 log file, zip file with the DED results, and a csv with the study results. The name of the zip file will be of the format DED_Results_database_name.zip, and the name of the csv will be results.csv.

4. OPTIONAL: Visualize Results in Shiny

   • To visualise the DED results, navigate to the Report folder, then the DED_shiny folder, and open the project file DrugExposureDiagnosticsShiny.Rproj in RStudio. Copy the generated .zip file into the data folder. Open the global.R script and click the Run App button in RStudio to launch the local Shiny app.
   • To visualise the study results, navigate to the Report folder, then the shiny folder, and open the project file shiny.Rproj in RStudio. Copy the generated results.csv file into the data folder. Open the global.R script and click the Run App button in RStudio to launch the local Shiny app.

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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.