covid-19-Re / estimateRView external linksLinks
R package for estimation and monitoring of the effective reproduction number in a pathogen outbreak/epidemic
☆11Sep 10, 2024Updated last year
Alternatives and similar repositories for estimateR
Users that are interested in estimateR are comparing it to the libraries listed below
Sorting:
- Covid-19 epidemiology - data and analysis☆11Dec 7, 2023Updated 2 years ago
- A Bayesian model for time-series count data with weekend effects and a lagged reporting process☆10Mar 7, 2022Updated 3 years ago
- Bayesian Modelling in Epidemiology Case Line Lists☆14Oct 7, 2025Updated 4 months ago
- An R package for Bayes Linear emulation and history matching.☆18Dec 1, 2025Updated 2 months ago
- Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on red…☆13Dec 18, 2022Updated 3 years ago
- Monte-Carlo State Space Models☆19Jul 1, 2024Updated last year
- This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (RE…☆17May 9, 2024Updated last year
- ☆19Apr 9, 2021Updated 4 years ago
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆17Nov 10, 2023Updated 2 years ago
- Code to replicate 'Quantifying impacts of the COVID-19 pandemic through life expectancy losses: a population-level study of 29 countries'☆17Nov 1, 2021Updated 4 years ago
- Workshop on hhh4 and the endemic-epidemic framework☆18Oct 13, 2022Updated 3 years ago
- A tool for detection of signals in infectious disease surveillance data.☆15Updated this week
- Repo for the course Statistical Methods in Infectious Disease Epidemiology at UZH☆20Dec 22, 2021Updated 4 years ago
- ☆10Sep 30, 2025Updated 4 months ago
- Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional appr…☆22Dec 9, 2023Updated 2 years ago
- modelling SARS-CoV-2 vaccine efficacy from antibody titres, and impact of waning and variants on transmission☆17Dec 7, 2023Updated 2 years ago
- Code associated with A population-level SEIR model for COVID-19 scenarios (updated) by James P. Gleeson, Thomas Brendan Murphy, Joseph D.…☆11May 4, 2021Updated 4 years ago
- Data and forecast submission repository for the 2023 CDC West Nile virus Forecasting Challenge☆11Oct 30, 2023Updated 2 years ago
- ☆10Apr 16, 2020Updated 5 years ago
- Analysis of COVID-19 transmission using cluster size distribution☆11Jun 14, 2022Updated 3 years ago
- Excess deaths due to COVID-19 pandemic in 2020☆11Jan 27, 2022Updated 4 years ago
- R code to replicate analyses in Clark et al 2025 (Beyond single-species models: leveraging multispecies forecasts to navigate the dynamic…☆14Feb 19, 2025Updated 11 months ago
- Applied category theory applied to epidemiological models☆12Aug 7, 2024Updated last year
- Shiny app to infer caes from new deaths of COVID-19☆11Mar 30, 2020Updated 5 years ago
- A tool to estimate time varying instantaneous reproduction number during epidemics☆102Updated this week
- ☆27Feb 25, 2021Updated 4 years ago
- Code of PriorVAE: encoding spatial priors with variational autoencoders☆12Jul 13, 2023Updated 2 years ago
- Population-wide Testing, Tracing and Isolation Models☆15Jan 14, 2021Updated 5 years ago
- Additional censored event tools for Distributions.jl☆14Feb 4, 2026Updated last week
- Code and data for the manuscript "Optimal, near-optimal, and robust epidemic control"☆11Jul 23, 2022Updated 3 years ago
- A repository of the data and code used for aggregating expert predictions of COVID19☆11Oct 25, 2021Updated 4 years ago
- Some code for monkeypox☆10Jan 24, 2023Updated 3 years ago
- Data and code to support Barnard et al., Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era, Nat…☆12Aug 31, 2022Updated 3 years ago
- Influpaint : Inpainting denoising diffusion probabilistic models for infectious disease (such as influenza) forecasting☆16Jan 29, 2026Updated 2 weeks ago
- An R package to help assess the sensitivity of a Bayesian model (fitted with Stan) to the specification of its likelihood and priors☆11Apr 8, 2025Updated 10 months ago
- Survival modelling via ODEs☆11Mar 17, 2025Updated 10 months ago
- Basic Tools for the Analysis of Disease Outbreaks☆12Oct 24, 2019Updated 6 years ago
- Supplementary code for paper "Bayesian workflow for disease transmission model".☆28Feb 3, 2021Updated 5 years ago
- Grouped dates in R☆20Dec 19, 2025Updated last month