schistop_model

Agent-based stochastic model for the transmission dynamics of Schistosoma mansoni in humans. The model incorporates specification of multiple assumptions for the mechanisms regulating transmission. An ODE-module is integrated into the agent-based framework to simulate explicit infection dynamics in the snail intermediate host.

https://github.com/veronicamalizia/schistop_model

Keywords

agent-based-modeling regulating-mechanisms schistosomiasis snails transmission-model

Last synced: 6 months ago · JSON representation ·

Repository

Agent-based stochastic model for the transmission dynamics of Schistosoma mansoni in humans. The model incorporates specification of multiple assumptions for the mechanisms regulating transmission. An ODE-module is integrated into the agent-based framework to simulate explicit infection dynamics in the snail intermediate host.

Basic Info

Host: GitHub
Owner: VeronicaMalizia
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://cordis.europa.eu/project/id/846873
Size: 178 MB

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Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Topics

agent-based-modeling regulating-mechanisms schistosomiasis snails transmission-model

Created about 4 years ago · Last pushed 11 months ago

Metadata Files

Readme License Citation

README.md

SchiSTOP model implementation

SchiSTOP (Beyond mass drug administration: understanding Schistosomiasis dynamics to STOP transmission),

a project funded by the European Marie Skłodowska-Curie fellowship.

Repository of code for SchiSTOP modelling framework: a stochastic agent-based (ABM) transmission model for the transmission dynamics of Schistosoma mansoni in human population. An ODE-based module for the infection dynamics within the snail intermidiate host is integrated into the ABM.

Detailed description of SchiSTOP has been published within the manuscript: "Revisiting the impact of Schistosoma mansoni regulating mechanisms on transmission dynamics using SchiSTOP , a novel modelling framework".

Mode of use

File 02.2_Setting_simulation_scenario.R: customize scenario-specific parameters. This will prepare the setting to run simulations.
File 05_Run_model.R : run the model and save results. The script allows to load input data, call previous scripts, customize the parameters for simulations, launch simulations with SchiSTOP from R source (04_Model_specification.R). Results are stored in two outputs:

-   population-level output, i.e. results aggregated at population level (e.g. prevalence)

-   individual-level output (optional), i.e. results tracked over time for each individuals

Author

Veronica Malizia¹

Supervision

Sake J. de Vlas², Federica Giardina^1*

¹ Radboud University Medical Center, Department IQ Health, Biostatistics Research Group, Nijmegen, The Netherlands

² Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands

^* Project leader

Owner

Name: Veronica Malizia
Login: VeronicaMalizia
Kind: user
Location: Nijmegen, The Netherlands
Company: Radboud UMC

Twitter: VeronicaMalizia
Repositories: 2
Profile: https://github.com/VeronicaMalizia

Infectious disease modeller

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: '"Schistosoma mansoni transmission model"'
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Veronica
    family-names: Malizia
    email: Veronica.Malizia@radboudumc.nl
    affiliation: 'Radboud UMC, Nijmegen, The Netherlands'
    orcid: 'https://orcid.org/0000-0002-8161-4092'
date-released: '2023-12-15'

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