References
Abbott, S.; Li, X.; Alahakoon, P. and others (2025). A Workflow for Infectious Disease Modelling,
https://github.com/seabbs/a-workflow-for-infectious-disease-modelling.Amuri-Aziza, A.; Adroba Tandele, P.; Luakanda-Ndelemo, G.; Kinganda-Lusamaki, E.; Lola-Loway, M.; Djemba-Fundji, B.; Ola-Mpumbe, R.; Cikaya-Kankolongo, F.; Paku-Tshambu, P.; Muswamba-Kayembe, P.-C.; Lumembe, R.; Kashali, N.; Makangara-Cigolo, J.-C.; Akil-Bandali, P.; Kimbonza, S.; Mabika-Bope, E.; Citenga, A.; Mukadi, P.; Mukadi-Bamuleka, D.; Pukuta, E.; Loman, N.; Wilkinson, S.; Quick, J.; Kent, C.; Hodcroft, E.; Ayouba, A.; Peeters, M.; Delaporte, E.; Nsio, J.; Ntumba-Tshitenge, O.; Otshudiema, J. O.; Keita, M.; Kuppalli, K.; Maes, P.; Ariën, K. K.; Liesenborghs, L.; Vercauteren, K.; O'Toole, Á.; Rambaut, A.; Kebede, Y.; Ahuka-Mundeke, S.; Ngandu, C.; Muyembe-Tamfum, J.-J.; Mwamba, D.; Wawina-Bokalanga, T.; Mbala-Kingebeni, P.; Nabadda, S.; Sewanyana, I.; Kyobe Bosa, H.; Wayengera, M.; Tessema, S. K.; Ssemwanga, D.; Balinandi, S.; Onywera, H.; Tanui, C. K.; Mwangi, S. W.; Andrew, T.; Nakintu, V.; Oundo, H. R.; Tenywa, W.; Wenka, G. T.; Murungi, M.; Kabahita, J. M.; Makoha, C.; Ssemaganda, A.; Mbambu, A.; Namakula, S.; Kanyerezi, S. and Ayitewala, A. (2026). Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event,
https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032. Virological.org post. Maximum-likelihood phylogeny of the initial BDBV genomes; the 2026-05-21 update adds a BEAST v10.5.0 temporal tree of the first ten genomes (HKY, strict clock fixed to literature EBOV rates, exponential coalescent) reporting the TMRCA.Charniga, K.; Park, S. W.; Akhmetzhanov, A. R.; Cori, A.; Dushoff, J.; Funk, S.; Gostic, K. M.; Linton, N. M.; Lison, A.; Overton, C. E.; Pulliam, J. R.; Ward, T.; Cauchemez, S. and Abbott, S. (2024). Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. PLOS Computational Biology 20, e1012520.
Danisch, S. and Krumbiegel, J. (2021). Makie.jl: Flexible high-performance data visualization for Julia. Journal of Open Source Software 6, 3349.
Ferguson, N. M. (2026). Genetic seeding-time estimate for the 2026 Bundibugyo virus disease outbreak. Personal communication. Source of the idea to combine the genetic TMRCA with the other data streams as a lower bound on the seeding time, originally via the root-to-tip distance of the first BDBV genomes (virological2026) and the holmes2016 clock rate.
Funk, S. and Abbott, S. (2026). Andes hantavirus joint Bayesian model — Epuyén 2018–19 line list,
https://github.com/epiforecasts/andv-linelist-analysis. Design template for code conventions: Mooncake AD, Integrals.jl integrand pattern, FlexiChains, PairPlots.Funk, S. and Abbott, S. (2026). Bundibugyo Ebola virus — Bayesian delay-distribution and stratified CFR estimation from the 2012 Isiro outbreak,
https://github.com/sbfnk/bdbv-linelist-analysis. Source of the informative onset-to-death gamma prior.Ge, H.; Xu, K. and Ghahramani, Z. (2018). Turing: A Language for Flexible Probabilistic Inference. In: Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics, Vol. 84; pp. 1682–1690.
Hancock, W.; Hawkins, W. and contributors (2024). Mooncake.jl — Source-to-source reverse-mode automatic differentiation for Julia,
https://github.com/chalk-lab/Mooncake.jl.Hoffman, M. D. and Gelman, A. (2014). The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research 15, 1593–1623.
Holmes, E. C.; Dudas, G.; Rambaut, A. and Andersen, K. G. (2016). The evolution of Ebola virus: Insights from the 2013–2016 epidemic. Nature 538, 193–200.
Imai, N.; Dorigatti, I.; Cori, A.; Riley, S. and Ferguson, N. M. (Jan 2020). Estimating the potential total number of novel coronavirus cases in Wuhan City, China. Technical Report Report 1 (Imperial College London).
McCabe, R. and others (May 2026). Estimation of the size of the Ebola outbreak caused by Bundibugyo virus in the Democratic Republic of the Congo: May 20, 2026 update,
https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/Report-ebola-update-20-05-2026.pdf.McCabe, R. and others (May 2026). Estimation of the size of the outbreak of Ebola disease caused by Bundibugyo virus in the Democratic Republic of the Congo,
https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/research-themes/preparedness-and-response-to-emerging-threats/report-ebola-18-05-2026/.Rosello, A. and others (2015). Ebola virus disease in the Democratic Republic of the Congo, 1976-2014, eLife 4, e09015.
Thompson, W. (2024). PairPlots.jl — Beautiful and flexible pair plots for Julia,
https://github.com/sefffal/PairPlots.jl.SciML contributors (2024). Integrals.jl — A unified Julia interface to numerical integration,
https://github.com/SciML/Integrals.jl.Stan Development Team (2024). Prior Choice Recommendations,
https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations. Stan wiki.