Research Data Leeds Repository

Data set of the manuscript: Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance

Citation

Hernández-Navarro, Lluís and Asker, Matthew and Mobilia, Mauro (2023) Data set of the manuscript: Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance. University of Leeds. [Dataset] https://doi.org/10.5518/1360¹

Dataset description

Dataset for 'Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance'. A full description of the data, methods, and interpretation may be found in the related publication. Computational data: raw results from stochastic simulations of our full model and of the effective Moran model at fixed total population. Scripts: codes to run the simulations (in Python), as well as codes to generate each of the 4+1 main and supplementary figures (in Matlab) from the computational data.

Additional information:	Data made available under CC-BY; scripts under an MIT licence
Keywords:	Eco-evolutionary dynamics, Fluctuations, Coexistence, Antimicrobial resistance, Cooperation, Environmental variability
Subjects:	G000 - Mathematical sciences > G100 - Mathematics > G120 - Applied mathematics2 C000 - Biological sciences > C700 - Molecular biology, biophysics & biochemistry > C770 - Biophysical science3
Divisions:	Faculty of Engineering and Physical Sciences > School of Mathematics > Department of Applied Mathematics4
Related resources:	Location Type https://doi.org/10.1101/2023.07.06.5479295 Publication https://doi.org/10.1098/rsif.2023.03936 Publication https://eprints.whiterose.ac.uk/204859/7 Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	06 Jul 2023 14:36
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/11288
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Hernández-Navarro, Lluís https://orcid.org/0000-0002-7272-75979 University of Leeds https://ror.org/024mrxd33 ror Asker, Matthew https://orcid.org/0009-0003-5548-553510 University of Leeds https://ror.org/024mrxd33 ror Mobilia, Mauro https://orcid.org/0000-0002-1424-567X11 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: EPSRC Grant numbers: EP/V014439/1, EP/T517860/1 Publication date: 2023 Resource language: English Metadata language: English Research project title: DMS-EPSRC Eco-Evolutionary Dynamics of Fluctuating Populations, PhD scholarship Publisher: University of Leeds Contact email: L.Hernandez-Navarro@leeds.ac.uk12 Last Modified: 28 Nov 2024 12:26

Files

Documentation

README_Hernandez-Navarro-etal_2023.txt [4kB] 13 README_Hernandez-Navarro-etal_2023.txt [4kB] 14 README_Hernandez-Navarro-etal_2023.txt [4kB] 15 Security: Anyone File name: README_Hernandez-Navarro-etal_2023.txt16 Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 4kB

MIT_licence.txt [1kB] 17 MIT_licence.txt [1kB] 18 MIT_licence.txt [1kB] 19 Security: Anyone File name: MIT_licence.txt20 Content type: Documentation Mime-Type: text/plain License: MIT License File size: 1kB

Data

SimulationData.zip [520MB] 21 SimulationData.zip [520MB] 22 SimulationData.zip [520MB] 23 Security: Anyone File name: SimulationData.zip24 Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 520MB

Fig1Data.mat [1MB] 25 Fig1Data.mat [1MB] 26 Fig1Data.mat [1MB] 27 Security: Anyone File name: Fig1Data.mat28 Content type: Data License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1MB

Program

distribution.py [955B] 29 distribution.py [955B] 30 distribution.py [955B] 31 Security: Anyone File name: distribution.py32 Content type: Program License: MIT License File size: 955B

FinalFigure1.m [5kB] 33 FinalFigure1.m [5kB] 34 FinalFigure1.m [5kB] 35 Security: Anyone File name: FinalFigure1.m36 Content type: Program Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 5kB

FinalFigure2.m [12kB] 37 FinalFigure2.m [12kB] 38 FinalFigure2.m [12kB] 39 Security: Anyone File name: FinalFigure2.m40 Content type: Program Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 12kB

FinalFigure3.m [7kB] 41 FinalFigure3.m [7kB] 42 FinalFigure3.m [7kB] 43 Security: Anyone File name: FinalFigure3.m44 Content type: Program Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 7kB

FinalFigure4.m [16kB] 45 FinalFigure4.m [16kB] 46 FinalFigure4.m [16kB] 47 Security: Anyone File name: FinalFigure4.m48 Content type: Program Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 16kB

FinalFigureS1.m [8kB] 49 FinalFigureS1.m [8kB] 50 FinalFigureS1.m [8kB] 51 Security: Anyone File name: FinalFigureS1.m52 Content type: Program Mime-Type: application/vnd.wolfram.mathematica.package License: MIT License File size: 8kB

fixation_properties.py [1kB] 53 fixation_properties.py [1kB] 54 fixation_properties.py [1kB] 55 Security: Anyone File name: fixation_properties.py56 Content type: Program License: MIT License File size: 1kB

heatmap.py [1kB] 57 heatmap.py [1kB] 58 heatmap.py [1kB] 59 Security: Anyone File name: heatmap.py60 Content type: Program License: MIT License File size: 1kB

next_reaction_method.py [22kB] 61 next_reaction_method.py [22kB] 62 next_reaction_method.py [22kB] 63 Security: Anyone File name: next_reaction_method.py64 Content type: Program License: MIT License File size: 22kB

trajectories.py [898B] 65 trajectories.py [898B] 66 trajectories.py [898B] 67 Security: Anyone File name: trajectories.py68 Content type: Program License: MIT License File size: 898B

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• 2. https://archive.researchdata.leeds.ac.uk/view/subjects/G120.html
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• 45. https://archive.researchdata.leeds.ac.uk/1128/8/FinalFigure4.m
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