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In the face of an infectious disease, a key epidemiological measure is the basic reproduction number, which quantifies the average secondary infections caused by a single case in a susceptible population. In practice, the effective…
During an infectious disease outbreak, public health decision-makers require real-time monitoring of disease transmission to respond quickly and intelligently. In these settings, a key measure of transmission is the instantaneous…
We consider the problem of estimating the reproduction number $R_t$ of an epidemic for populations where the probability of detection of cases depends on a known covariate. We argue that in such cases the normal empirical estimator can fail…
The effective reproduction number, R(t), is a central point in the study of infectious diseases. It establishes in an explicit way the extent of an epidemic spread process in a population. The current estimation methods for the time…
The time varying effective reproduction number is an important parameter for communication and policy decisions during an epidemic. In this paper, we present new statistical methods for estimating the reproduction number based on the…
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…
The effective reproduction number is an important descriptor of an infectious disease epidemic. In small populations, ideally we would estimate the effective reproduction number using a Markov Jump Process (MJP) model of the spread of…
In this paper, we use a Bayesian method to estimate the effective reproduction number (R(t)), in the context of monitoring the time evolution of the COVID-19 pandemic in Brazil at different geographic levels. The focus of this study is to…
When an infectious disease strikes a population, the number of newly reported cases is often the only available information that one can obtain during early stages of the outbreak. An important goal of early outbreak analysis is to obtain a…
The correct evaluation of the reproductive number $R$ for COVID-19 -- which characterizes the average number of secondary cases generated by each typical primary case -- is central in the quantification of the potential scope of the…
Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective…
This paper deals with the problem of estimating variables in nonlinear models for the spread of disease and its application to the COVID-19 epidemic. First unconstrained methods are revisited and they are shown to correspond to the…
Branching process inspired models are widely used to estimate the effective reproduction number -- a useful summary statistic describing an infectious disease outbreak -- using counts of new cases. Case data is a real-time indicator of…
At the onset of the Covid-19 pandemic, a number of non-pharmaceutical interventions have been implemented in order to reduce transmission, thus leading to multiple phases of transmission. The disease reproduction number $R_t$, a way of…
During an epidemic outbreak, decision makers crucially need accurate and robust tools to monitor the pathogen propagation. The effective reproduction number, defined as the expected number of secondary infections stemming from one…
Nowcasting and forecasting of epidemic spreading rely on incidence series of reported cases to derive the fundamental epidemiological parameters for a given pathogen. Two relevant drawbacks for predictions are the unknown fractions of…
A major difficulty to estimate $R$ (the effective reproducing number) of COVID-19 is that most cases of COVID-19 infection are mild or asymptomatic, therefore true number of infection is difficult to determine. This paper estimates the…
The time-dependent reproduction number Rt can be used to track pathogen transmission and to assess the efficacy of interventions. This quantity can be estimated by fitting renewal equation models to time series of infectious disease case…
The expected number of secondary infections arising from each index case, referred to as the reproduction or $R$ number, is a vital summary statistic for understanding and managing epidemic diseases. There are many methods for estimating…
The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely…