Dynamic resource allocation for controlling pathogen spread on a large metapopulation network (Cristancho-Fajardo L., Ezanno P., Vergu E.) Journal of the Royal Society Interface.
Python Simulation Code for generating the data and the figures in the article Dynamic resource allocation for controlling pathogen spread on a large metapopulation network (Cristancho-Fajardo L., Ezanno P., Vergu E.). Journal of the Royal Society Interface:
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The fixed_parameters folder contains the fixed simulation setting, fixed network structure and fixed demographic parameters. As well as the notebook on their generation.
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The vaccination folder, contains:
- The dynamic folder, contains:
- The score_list folder: contains the text files with the names of the score functions to be tested. As well as the notebook on their generation.
- The vaccination_functions.py script gathers the main functions used in the generation of the simulated epidemic under vaccination allocation
- vacc_endemicdynamic.py is the script that generates the simulated dynamics under vaccination according to a given scoring function with b_fix = 25% of initial total population, in the endemic scenario.
- vacc_epidemicdynamic.py is the script that generates the simulated dynamics under vaccination according to a given scoring function with b_fix = 25% of initial total population, in the epidemic scenario.
- launcher_vacc_endemicdynamic.sh: script shell that launches 50 runs of vacc_endemicdynamic.py for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring function according to the score_list folder).
- launcher_vacc_epidemicdynamic.sh: script shell that launches 50 runs of vacc_epidemicdynamic.py for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring function according to the score_list folder).
- simulated_data_vaccend_dynamics: folder that will contain simulated data once the launcher_vacc_endemicdynamic.py is run.
- simulated_data_vaccepi_dynamics: folder that will contain simulated data once the launcher_vacc_epidemicdynamic.py is run.
- The percolation folder, contains:
- The score_budget_list folder: contains the text files with the combinations of the score functions and quantity of resource (b_fix) to be tested. As well as the notebook on their generation.
- The vaccination_functions.py script gathers the main functions used in the generation of the simulated epidemic under vaccination allocation
- percolation_vaccendemic.py is the script that generates the percolation experiments for vaccination according to a given combination of scoring function - b_fix, in the endemic scenario.
- launcher_percolation_vaccendemic.sh script shell that generates 50 runs of percolation_vaccendemic.py, for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring-b_fix combination according to the score_budget_list folder).
- percolation_vacc_endemic_data: folder that will contain simulated data once the launcher_percolation_vaccendemic.sh is run.
- The dynamic folder, contains:
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The treatment folder, contains:
- The dynamic folder, contains:
- The score_list folder: contains the text files with the names of the score functions to be tested. As well as the notebook on their generation.
- The treatment_functions.py script gathers the main functions used in the generation of the simulated epidemic under treatment allocation
- treatment_endemic_dynamic.py is the script that generates the simulated dynamics under treatment according to a given scoring function with b_fix = 25 herds, in the endemic scenario.
- treatment_epidemic_dynamic.py is the script that generates the simulated dynamics under treatment according to a given scoring function with b_fix = 25 herds, in the epidemic scenario.
- launcher_treatment_endemicdynamic.sh: script shell that launches 50 runs of treatment_endemicdynamic.py for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring function according to the score_list folder).
- launcher_treatment_epidemicdynamic.sh: script shell that launches 50 runs of treatment_epidemicdynamic.py for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring function according to the score_list folder).
- simulated_data_treatend_dynamics: folder that will contain simulated data once the launcher_treatment_endemicdynamic.sh is run.
- simulated_data_treatepi_dynamics: folder that will contain simulated data once the launcher_treatment_epidemicdynamic.sh is run.
- The percolation folder, contains:
- The score_budget_list folder: contains the text files with the combinations of the score functions and quantity of resource (b_fix) to be tested. As well as the notebook on their generation.
- The treatment_functions.py script gathers the main functions used in the generation of the simulated epidemic under treatment allocation
- percolation_treatment_endemic.py is the script that generates the percolation experiments for treatment according to a given combination of scoring function - b_fix, in the endemic scenario.
- launcher_percolation_treatment_endemic.py script shell that launches 50 runs of percolation_treatment_endemic.py, for a given $SLURM_ARRAY_TASK_ID (which indicates the scoring-b_fix combination according to the score_budget_list folder).
- percolation_treatment_endemic_data: folder that will contain simulated data once the launcher_percolation_treatment_endemic.sh is run.
- The dynamic folder, contains:
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The plots_article.ipynb is a jupyter-notebook that reads the simulated datasets (once the launcher shell scripts are run) and generates the figures presented in the main text of the article.
SLURM queries to run the launcher scripts for all scores, and for all score-budget combinations:
- sbatch --array 1-29 DRAAnimalMetapop/vaccination/dynamic/launcher_vacc_endemicdynamic.sh
- sbatch --array 1-29 DRAAnimalMetapop/vaccination/dynamic/launcher_vacc_epidemicdynamic.sh
- sbatch --array 1-29 DRAAnimalMetapop/treatment/dynamic/launcher_treatment_endemicdynamic.sh
- sbatch --array 1-29 DRAAnimalMetapop/treatment/dynamic/launcher_treatment_epidemicdynamic.sh
- sbatch --array 1-156 DRAAnimalMetapop/vaccination/percolation/launcher_percolation_treatment_endemic.sh
- sbatch --array 1-180 DRAAnimalMetapop/treatment/percolation/launcher_percolation_treatment_endemic.sh
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Copyright or © or Copr. [INRAE]
Contributor(s) : [Lina Cristancho-Fajardo] ([2021])
[lina.cristancho-fajardo@inrae.fr]
This software is a computer program whose purpose is to simulate the stochastic spread of a pathogen on an animal trade-network, by generating social planner's dynamic resource allocation decisions (on vaccination or a treatment) on the pathogen's spread according to a certain indicator or scoring function for determining herds priority.
This software is governed by the [CeCILL-B] license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the [CeCILL-B] license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".
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In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.
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