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The serial interval of an infectious disease is the time between illness onset in an infector-infectee pair. This repository contains routines to estimate features of the serial interval based on transmission pair data. The approach is entirely data-driven and relies on a resampling technique (bootstrap).

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Nonparametric serial interval estimation with uniform mixtures

Oswaldo Gressani

Reproducibility instructions

This repository contains all the routines required to reproduce the results of the article “Nonparametric serial interval estimation with uniform mixtures” by Oswaldo Gressani and Niel Hens. https://doi.org/10.1371/journal.pcbi.1013338.

This repository is organized in three main folders (01-Simulations, 02-RealData and 03-Figures).

  • 01-Simulations can be used to recover the results from the simulation study.

  • 02-RealData can be used to recover results related to real data applications.

  • 03-Figures can be used to recover the Figures in the article.

Readers and users are encouraged to reproduce the results contained in this folder. The EpiDelays package (version 0.0.1) will be needed and can be installed from the GitHub repository https://github.com/oswaldogressani/EpiDelays.

Repository version

This is version 0.0.3 (2025-09-01) - “SIEpiDelays-V3”.

License

GPL-3.0

Funding statement

OG and NH were supported by the VERDI project (101045989) and the ESCAPE project (101095619), funded by the European Union. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Health and Digital Executive Agency (HADEA). Neither the European Union nor the granting authority can be held responsible for them. OG and NH acknowledge the financial support of the Fondation Universitaire de Belgique (file nr. AS-0608). OG and NH were also supported by the BE-PIN project (contract nr. TD/231/BE-PIN) funded by BELSPO (Belgian Science Policy Office) as part of the POST-COVID programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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The serial interval of an infectious disease is the time between illness onset in an infector-infectee pair. This repository contains routines to estimate features of the serial interval based on transmission pair data. The approach is entirely data-driven and relies on a resampling technique (bootstrap).

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