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SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

View ORCID ProfileJori Liesenborgs, View ORCID ProfileDiana M Hendrickx, View ORCID ProfileElise Kuylen, View ORCID ProfileDavid Niyukuri, View ORCID ProfileNiel Hens, View ORCID ProfileWim Delva
doi: https://doi.org/10.1101/440834
Jori Liesenborgs
Expertise Centre for Digital Media, Hasselt University – tUL, Diepenbeek, Belgium
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  • ORCID record for Jori Liesenborgs
Diana M Hendrickx
Center for Statistics, I-BioStat, Hasselt University, Diepenbeek, Belgium
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  • ORCID record for Diana M Hendrickx
Elise Kuylen
IDLab, University of Antwerp, Antwerp, BelgiumCentre for Health Economics Research and Modelling Infectious Diseases and Centre for the Evaluation of Vaccination, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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David Niyukuri
The South African Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South AfricaDepartment of Global Health, Faculty of Medicine and Health, Stellenbosch University, Stellenbosch, South Africa
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Niel Hens
Center for Statistics, I-BioStat, Hasselt University, Diepenbeek, BelgiumCentre for Health Economics Research and Modelling Infectious Diseases and Centre for the Evaluation of Vaccination, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Wim Delva
Center for Statistics, I-BioStat, Hasselt University, Diepenbeek, BelgiumThe South African Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South AfricaDepartment of Global Health, Faculty of Medicine and Health, Stellenbosch University, Stellenbosch, South AfricaInternational Centre for Reproductive Health, Ghent University, Ghent, BelgiumRega Institute for Medical Research, KU Leuven, Leuven, BelgiumSchool for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
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  • For correspondence: wimdelva@gmail.com
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ABSTRACT

SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework.

Footnotes

  • Typos corrected; Supplementary tables and supplementary figure now merged into a single pdf file.

  • https://github.com/wdelva/SimpactCyanExamples

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 06, 2019.
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SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces
Jori Liesenborgs, Diana M Hendrickx, Elise Kuylen, David Niyukuri, Niel Hens, Wim Delva
bioRxiv 440834; doi: https://doi.org/10.1101/440834
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SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces
Jori Liesenborgs, Diana M Hendrickx, Elise Kuylen, David Niyukuri, Niel Hens, Wim Delva
bioRxiv 440834; doi: https://doi.org/10.1101/440834

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