The project contains files for Dubinkina, V., Fridman, Y., Pandey, P., & Maslov, S. (2018). Alternative stable states in a model of microbial community limited by multiple essential nutrients. bioRxiv, 439547.
Related to Dubinkina V et al., 2019, 'Multistability and regime shifts in microbial communities explained by competition for essential nutrients'. eLife. https://doi.org/10.7554/eLife.49720
Contents of the folder:
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Dynamic_Stability_L2/ - contains code which performs dynamic perturbation analysis for 2Cx2Nx4S model
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Marriage_Algorithm.ipynb - implementation of marriage algorithm for enumeration of allowed and uninvadable states for a given set of lambdas
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MonteCarlo_Feasibility.ipynb - implementation of Monte-Carlo spanning of a flux space to get feasibility regions of states for a given set of lambdas and yields
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Yield_Variation.ipynb - implementation of Monte-Carlo spanning of a flux space to get feasibility regions of states for a given set of lambdas and various yields drawn from a distribution
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Analyze_2Cx2N.R - code which performs analysis of Monte-Carlo spanning results for 2Cx2Nx4S model (for one set of yields and number of yields drawn from a distribution)
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Analyze_6Cx6N.R - code which performs analysis of Monte-Carlo spanning results for 6Cx6Nx36S model
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Functions.R - some customized functions for plotting
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C6_N6_notes.m - file with Matlab code used in the analysis of 6Cx6Nx36S example
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Plots/ - folder containing plots ...
Additional files with numerical simulation results used in the above scripts could be obtained from: [Named Link]LINK