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estimateR: an R package to estimate and monitor the effective reproductive number.

Jérémie ScireJana S HuismanAna GrosuDaniel C AngstAdrian LisonJinzhou LiMarloes H MaathuisSebastian BonhoefferTanja Stadler
Published in: BMC bioinformatics (2023)
The estimateR R package is a modular and extendable tool designed for outbreak surveillance and retrospective outbreak investigation. It extends the method developed for COVID-19 by Huisman et al. and makes it available for a variety of pathogens, outbreak scenarios, and observation types. Estimates obtained with estimateR can be interpreted directly or used to inform more complex epidemic models (e.g. for forecasting) on the value of [Formula: see text].
Keyphrases
  • coronavirus disease
  • sars cov
  • public health
  • climate change
  • cross sectional
  • gram negative
  • antimicrobial resistance
  • multidrug resistant
  • respiratory syndrome coronavirus