qleclerc / gosh_mrsa

Data and code repository for analysis of AMR dynamics at GOSH

Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data.

Quentin J Leclerc, Alastair Clements, Helen Dunn, James Hatcher, Jodi A Lindsay, Louis Grandjean, Gwenan M Knight

This repository contains the cleaned data and analysis script for our work on antimicrobial resistance diversity at Great Ormond Street Hospital (GOSH), using routinely collected data.

For any questions please contact me by email ([email protected]) or on Twitter (@QuentinLclrc).

\Clean

Folder containing the cleaned versions of the datasets. These were generated from the raw datasets using the scripts in that folder. The raw datasets are the property of GOSH and are not publicly available.

The datasets labelled x_diversity.csv were generated by the corresponding scripts in the folder. These datasets describe within-host AMR diversity of S. aureus isolates from patients at GOSH.

\Analysis

This folder contains the scripts to generate all the figures in the manuscript. Each script is named according to the figure(s) it generates.

Some of these scripts also contain descriptive statistics mentioned in the manuscript.

\Figures

Contains all the figures and supplementary figures.