Sam Abbott
YOU?
Author Swipe
View article: Baseline nowcasting methods for handling delays in epidemiological data
Baseline nowcasting methods for handling delays in epidemiological data Open
Background Up-to-date real-time disease surveillance data can provide critical public health insights, however reporting delays can create downward bias in the latest data. Nowcasting methods designed to correct for this bias remain under…
View article: Improving modelling for epidemic response: a progress update from a community of UK infectious disease modellers
Improving modelling for epidemic response: a progress update from a community of UK infectious disease modellers Open
We reflect on the sustainability of modelling infectious disease outbreaks from the perspective of modelling as a field of practice. We formed a community of practice among UK infectious disease modellers who had contributed to the UK COVI…
View article: Baseline nowcasting methods for handling delays in epidemiological data
Baseline nowcasting methods for handling delays in epidemiological data Open
Background Up-to-date real-time disease surveillance data can provide critical public health insights, however reporting delays can create downward bias in the latest data. Nowcasting methods designed to correct for this bias remain underu…
View article: The influence of model structure and geographic specificity on predictive accuracy among European COVID-19 forecasts
The influence of model structure and geographic specificity on predictive accuracy among European COVID-19 forecasts Open
Modellers take many approaches to predicting the course of infectious diseases, and achieve a wide range of accuracy in resulting forecasting performance. For example, forecasters vary in their use of different underlying model structures,…
View article: Correlation of As-read and As-run Dosimetry Data
Correlation of As-read and As-run Dosimetry Data Open
The Nuclear Science Users Facilities (NSUF) is responsible for the coordination of experiments conducted in Advanced Test Reactor (ATR) by Universities and other outside organizations. Completion of the experiment and data reporting proces…
View article: The Impact of Public Health and Social Measures (PHSMs) on SARS‐CoV‐2 Transmission in the WHO European Region (2020–2022)
The Impact of Public Health and Social Measures (PHSMs) on SARS‐CoV‐2 Transmission in the WHO European Region (2020–2022) Open
Background Between 2020 and 2022, countries used a range of different public health and social measures (PHSMs) to reduce the transmission of SARS‐CoV‐2. The impact of these PHSMs varied as the pandemic progressed, variants of concern (VOC…
View article: EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering Open
Accurately estimating the effective reproduction number (R t ) of a circulating pathogen is a fundamental challenge in the study of infectious disease. The fields of epidemiology and pathogen phylodynamics both share this goal, but to date…
View article: Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases Open
Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that ce…
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: Correction: The importance of investing in data, models, experiments, team science, and public trust to help policymakers prepare for the next pandemic
Correction: The importance of investing in data, models, experiments, team science, and public trust to help policymakers prepare for the next pandemic Open
[This corrects the article DOI: 10.1371/journal.pgph.0002601.].
View article: Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data Open
Epidemiological delays, such as incubation periods, serial intervals, and hospital lengths of stay, are among key quantities in infectious disease epidemiology that inform public health policy and clinical practice. This information is use…
View article: Assessing Human Judgment Forecasts in the Rapid Spread of the Mpox Outbreak: Insights and Challenges for Pandemic Preparedness
Assessing Human Judgment Forecasts in the Rapid Spread of the Mpox Outbreak: Insights and Challenges for Pandemic Preparedness Open
In May 2022, mpox (formerly monkeypox) spread to non-endemic countries rapidly. Human judgment is a forecasting approach that has been sparsely evaluated during the beginning of an outbreak. We collected -- between May 19, 2022 and July 31…
View article: Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates Open
The time-varying effective reproduction number R t is a widely used indicator of transmission dynamics during infectious disease outbreaks. Timely estimates of R t can be obtained from reported cases counted by their date of symptom onset,…
View article: Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates Open
The time-varying effective reproduction number $R_t$ is a widely used indicator of transmission dynamics during infectious disease outbreaks. Timely estimates of $R_t$ can be obtained from observations close to the original date of infecti…
View article: Human judgement forecasting of COVID-19 in the UK
Human judgement forecasting of COVID-19 in the UK Open
Background In the past, two studies found ensembles of human judgement forecasts of COVID-19 to show predictive performance comparable to ensembles of computational models, at least when predicting case incidences. We present a follow-up t…
View article: Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants
Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants Open
The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need…
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: Estimating epidemiological delay distributions for infectious diseases
Estimating epidemiological delay distributions for infectious diseases Open
Understanding and accurately estimating epidemiological delay distributions is important for public health policy. These estimates directly influence epidemic situational awareness, control strategies, and resource allocation. In this stud…
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic
Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic Open
Background The COVID-19 pandemic both relied and placed significant burdens on the experts involved from research and public health sectors. The sustained high pressure of a pandemic on responders, such as healthcare workers, can lead to l…
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering Open
Accurately estimating the effective reproduction number (Rt) of a circulating pathogen is a fundamental challenge in the study of infectious disease. The fields of epidemiology and pathogen phylodynamics both share this goal, but to date, …
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: European Covid-19 Forecast Hub
European Covid-19 Forecast Hub Open
European Covid-19 Forecast Hub.
View article: The importance of investing in data, models, experiments, team science, and public trust to help policymakers prepare for the next pandemic
The importance of investing in data, models, experiments, team science, and public trust to help policymakers prepare for the next pandemic Open
The COVID-19 pandemic has brought about valuable insights regarding models, data, and experiments. In this narrative review, we summarised the existing literature on these three themes, exploring the challenges of providing forecasts, the …