Sam Abbott

13 papers Journal 13
YearRankTypeTitle / Venue / Authors
2024 J jnl
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.
PLoS Comput. Biol.
Kelly Charniga, Sang Woo Park, Andrei R. Akhmetzhanov, Anne Cori, Jonathan Dushoff, Sebastian Funk, Katelyn M. Gostic, Natalie M. Linton, Adrian Lison, Christopher E. Overton, Juliet R. C. Pulliam, Thomas Ward, Simon Cauchemez, Sam Abbott
2024 J jnl
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.
PLoS Comput. Biol.
Ciara E. Judge, Timothy G. Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill
2024 J jnl
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates.
PLoS Comput. Biol.
Adrian Lison, Sam Abbott, Jana S. Huisman, Tanja Stadler
2023 J jnl
Collaborative nowcasting of COVID-19 hospitalization incidences in Germany.
PLoS Comput. Biol.
Daniel Wolffram, Sam Abbott, Matthias an der Heiden, Sebastian Funk, Felix Günther, Davide Hailer, Stefan Heyder, Thomas Hotz, Jan van de Kassteele, Helmut Küchenhoff, Sören Müller-Hansen, Diellë Syliqi, Alexander Ullrich, Maximilian Weigert, Melanie Schienle, Johannes Bracher
2023 J jnl
Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England.
PLoS Comput. Biol.
James D. Munday, Sam Abbott, Sophie Meakin, Sebastian Funk
2023 J jnl
Nowcasting the 2022 mpox outbreak in England.
PLoS Comput. Biol.
Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward
2023 J jnl
Scoring epidemiological forecasts on transformed scales.
PLoS Comput. Biol.
Nikos I. Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk
2023 J jnl
Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany.
PLoS Comput. Biol.
Elisabeth K. Brockhaus, Daniel Wolffram, Tanja Stadler, Michael Osthege, Tanmay Mitra, Jonas M. Littek, Ekaterina A. Krymova, Anna J. Klesen, Jana S. Huisman, Stefan Heyder, Laura Marie Helleckes, Matthias an der Heiden, Sebastian Funk, Sam Abbott, Johannes Bracher
2022 J jnl
Comparing human and model-based forecasts of COVID-19 in Germany and Poland.
PLoS Comput. Biol.
Nikos I. Bosse, Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J. Quilty, Mark Jit, Edwin van Leeuwen, Anne Cori, Sebastian Funk
2021 J jnl
Correction: Practical considerations for measuring the effective reproductive number, Rt.
PLoS Comput. Biol.
Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey
2021 J jnl
covidregionaldata: Subnational data for COVID-19 epidemiology.
J. Open Source Softw.
Joseph Palmer, Katharine Sherratt, Richard Martin-Nielson, Jonnie Bevan, Hamish Gibbs, LSHTM CMMID COVID-19 Working Group, Sebastian Funk, Sam Abbott
2020 J jnl
Practical considerations for measuring the effective reproductive number, Rt.
PLoS Comput. Biol.
Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey
2019 J jnl
getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data.
J. Open Source Softw.
Sam Abbott