covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

The estimateR package implements a modular pipeline to estimate the effective reproductive number from incidence data. The incidence data does not need to directly represent infections. Instead, the incidence data can represent indirect and temporally-delayed noisy observations of infection events. Typically, these could be: case confirmation via testing for the pathogen of interest, or hospital admissions of patients suffering from the disease of interest, ICU admissions of such patients, or deaths. In addition to incidence data, one needs an estimate of the delay distribution between infection events and their observations. Typically, the delay between an infection and its observation can be split into two independent delays: the incubation period and the delay between symptom onset and observation. If the incidence data represents dates of onset of symptoms, the latter delay is not needed. Once the original incidence data is transformed into incidence of infection events, the effective reproductive number is estimated using wrappers around the EpiEstim package (Cori et al. 2013).

install.packages("remotes")
remotes::install_github("covid-19-Re/estimateR")