Revision bf777e95b555d62cf0b98a8279ff3ccb49e5f026 authored by drmsmith on 02 July 2021, 10:53:38 UTC, committed by GitHub on 02 July 2021, 10:53:38 UTC
1 parent 5b963af
README.md
# microbiomeR
Theoretical models for antibiotic resistance epidemiology. R code and a Mathematica notebook to support Smith et al., (2021). Microbiome-pathogen interactions drive epidemiological dynamics of antibiotic resistance: modelling insights for infection control
# about
We present a suite of ODE models describing bacterial colonization dynamics in the healthcare setting. Each model accounts for different within-host interactions:
* Model 1: bacterial colonization
* Model 2: exclusive colonization strain competition
* Model 3: microbiome-pathogen competition
* Model 4: strain-microbiome competition
* Model 5: strain-microbiome competition with interspecific horizontal gene transfer
Models are evaluated using the same parameter set corresponding to a generic pathogen (C^R). ODEs are integrated numerically. Epidemiological outcomes at population dynamic equilibrium are evaluated using univariate and bivariate analysis.
# repository files (R)
* microbiomeR.Rproj
* associated R project
* ODEs.R
* ODEs for each model
* parameters.R
* initial state variable vectors for each model
* parameter vector for generic C^R
* alternative parameter vectors for various analyses
* functions.R
* functions returning epidemiological outcomes at population dynamic equilibrium: prevalence, incidence, resistance rate
* solve.R
* execute analyses
* figures.R
* render figures
# repository files (Mathematica)
* microbiome_ecology.nb
* notebook containing model ODEs, R0 expressions, numerical solutions, figures
# contact
David Smith \
Institut Pasteur / Inserm / UVSQ \
david.smith@pasteur.fr \
davidrobertmundysmith@gmail.com
Computing file changes ...