EpiLPS: a fast and flexible Bayesian tool for estimation of the time-varying reproduction number ================ Oswaldo Gressani (oswaldo.gressani@uhasselt.be)

EpiLPS (Gressani et al. 2022) is an Epidemiological modeling tool using Laplacian-P-Splines. It can be used to estimate the time-varying reproduction number (the average number of secondary cases generated by an infected individual) and to smooth the epidemic curve based on a time series of incidence data and a (discretized) serial interval distribution. The website associated to the project https://epilps.com/ provides a detailed documentation (or vignette) on how to use the routines.

Citation

For the paper explaining the methodology:

Gressani, O., Wallinga, J., Althaus, C. L., Hens, N. and Faes, C. (2022). EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. PLoS Comput Biol 18(10): e1010618. https://doi.org/10.1371/journal.pcbi.1010618

To cite the EpiLPS package in publications use:

  Gressani, O. (2021). EpiLPS: a fast and flexible Bayesian tool for estimation of the time-varying
  reproduction number. [Computer Software]. https://github.com/oswaldogressani/EpiLPS.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {EpiLPS: a fast and flexible Bayesian tool for estimation
    of the time-varying reproduction number. [Computer Software]},
    author = {Oswaldo Gressani},
    year = {2021},
    url = {https://github.com/oswaldogressani/EpiLPS},
  }

Package version

This is version 1.1.0 (2023-03-22) - “Reducing cyclomatic complexity”.

Acknowledgments

This project is funded by the European Union’s Research and Innovation Action under the H2020 work programme, EpiPose (grant number 101003688).

License

EpiLPS: a fast and flexible Bayesian tool for estimation of the time-varying reproduction number. Copyright (C) 2021-2023 Oswaldo Gressani.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.