Kettle, H., Holtrop, G., Louis, P. and Flint, H.J.
Methods in Ecology and Evolution 9(2), 399-409.
||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
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.
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