ArticleBMC bioinformatics2023
estimateR: an R package to estimate and monitor the effective reproductive number.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed, 54 citations in OpenAlex.
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- Unjustified Poisson assumptions lead to overconfident estimates of the effective reproductive number.Epidemiology and infection · 2026Article
- The influence of age-dependent susceptibility on RSV transmission dynamics and immunisation population-level impact.BMC medicine · 2026Article
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- The construction of a prognostic nomogram model for colorectal cancer and the prediction of immune characteristics and immune treatment responses based on the bioinformatics analysis of soluble mediator-related genes.Human vaccines & immunotherapeutics · 2025Article
- Single-cell and bulk RNA analysis identifies EMT-associated CAF signatures and prognostic model in lung adenocarcinoma.Discover oncology · 2025Article
- Development and validation of a risk model for effective immune and stromal related signature predicting prognosis of patients with ovarian cancer.Scientific reports · 2025Article
- Multi‑omics analysis identifies different molecular subtypes with unique outcomes in early-stage poorly differentiated lung adenocarcinoma.Molecular cancer · 2025Article
- Comprehensive analysis of glycometabolism-related genes reveals PLOD2 as a prognostic biomarker and therapeutic target in gastric cancer.BMC gastroenterology · 2025Article
- Rapid geographic expansion of local dengue community transmission in Peru.PLoS neglected tropical diseases · 2025Article
- Synergistic potential of CDH3 in targeting CRC metastasis and enhancing immunotherapy.BMC cancer · 2025Article
- A flexible framework for local-level estimation of the effective reproductive number in geographic regions with sparse data.BMC medical research methodology · 2025Article
- Integrative single-cell and bulk RNA-seq analysis identifies lactylation-related signature in osteosarcoma.Functional & integrative genomics · 2025Article
- A Flexible Framework for Local-Level Estimation of the Effective Reproductive Number in Geographic Regions with Sparse Data.medRxiv : the preprint server for health sciences · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundAccurate estimation of the effective reproductive number ([Formula: see text]) of epidemic outbreaks is of central relevance to public health policy and decision making. We present estimateR, an R package for the estimation of the reproductive number through time from delayed observations of infection events. Such delayed observations include confirmed cases, hospitalizations or deaths. The package implements the methodology of Huisman et al. but modularizes the [Formula: see text] estimation procedure to allow easy implementation of new alternatives to the currently available methods. Users can tailor their analyses according to their particular use case by choosing among implemented options.
resultsThe estimateR R package allows users to estimate the effective reproductive number of an epidemic outbreak based on observed cases, hospitalization, death or any other type of event documenting past infections, in a fast and timely fashion. We validated the implementation with a simulation study: estimateR yielded estimates comparable to alternative publicly available methods while being around two orders of magnitude faster. We then applied estimateR to empirical case-confirmation incidence data for COVID-19 in nine countries and for dengue fever in Brazil; in parallel, estimateR is already being applied (i) to SARS-CoV-2 measurements in wastewater data and (ii) to study influenza transmission based on wastewater and clinical data in other studies. In summary, this R package provides a fast and flexible implementation to estimate the effective reproductive number for various diseases and datasets.
conclusionsThe 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].
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.