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Supplementary Material of Bargués-Ribera & Gokhale, agriculture project
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EcoEvo_agriculture_1SEQ.ipynb code agriculture 1SEQ Jun 15, 2018
EcoEvo_agriculture_MULTISEQ.ipynb modification code agriculture MULTISEQ Jun 15, 2018
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README.md

agriculture

Supplementary Material of Bargués-Ribera & Gokhale, agriculture project

This folder contains the following Jupyter notebooks:

(1) EcoEvo_agriculture_1SEQ.ipynb

(2) EcoEvo_agriculture_MULTISEQ.ipynb

Notebook (1) contains the code for running the model for 1 rotation sequence. The sequence needs to be specified at the section "Sequence population", in the variable 'seq', as a combination of 'h1', 'h2' and 'h1_r'. The program will automatically ask for which conditions of infection do we want to run the model, as 'pathogen true' (1 for T, 0 for F) and 'infection time' (any discrete time number in the range of the length of the sequence). Plots for soil quality/cash yield and eco-evolutionary dynamics will be displayed for the defined sequence.

Notebook (2) contains the code for running the model for multiple rotation sequences of a certain length L. All possible combinations of length L (to be specified) will be created in the section "Sequence population". The program will automatically ask for which conditions of infection do we want to run the model, as 'pathogen true' (1 for T, 0 for F) and 'infection time' (any discrete time number in the range of the length of the sequence). The program will generate .csv outputs for each sequence, containing the sequence pattern in binaries for each crop type, the delta values, the soil quality and cash yield time series, and the fitness value.

With these files, one can replicate the results shown in the paper. If interested in the generation of any plot not included, contact bargues[at]evolbio.mpg.de.

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