Document details for 'microPop: Modelling microbial populations in R'

Authors Kettle, H., Holtrop, G., Louis, P. and Flint, H.J.
Publication details Methods in Ecology and Evolution 9(2), 399-409.
Keywords microbial modelling
Abstract Microbial communities perform highly dynamic and complex ecosystem functions that impact plants, animals and humans. Here we present an R-package, microPop, which is a dynamic model based on a functional representation of different microbiota. micropop simulates the deterministic dynamics and interactions of microbial populations by solving a system of ordinary differential equations which are constructed automatically based on a description of the system to be simulated. Data frames for a number of microbial functional groups and default functions for rates of microbial growth, resource uptake, metabolite production are provided but can be modified or replaced by the user. microPop can simulate growth in a single compartment (e.g. bio-reactor) or `compartments' in series (e.g. human colon) or in a simple 1-d application (e.g. phytoplankton in a water column). Furthermore, a microbial functional group may contain multiple strains in order to study adaptation and diversity or parameter uncertainty. Also simple interactions between viruses (bacteriophages) and bacteria can be included in microPop.
Last updated 2018-02-15
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