epiforecasts / omicron-sgtf-forecast
In this work, we use S-gene target failure (SGTF) as a proxy of variant status combined with reported case counts to explore the evidence for changes in transmission advantage over time for the Omicron variant. If present this could indicate the impact of immune escape, bias in SGTF data or differences in the populations within which the variant…
☆15Updated 2 years ago
Related projects: ⓘ
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆16Updated 10 months ago
- Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional appr…☆22Updated 9 months ago
- Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model wit…☆56Updated this week
- Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on red…☆13Updated last year
- Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States☆27Updated last week
- This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (RE…☆15Updated 4 months ago
- R package for estimation and monitoring of the effective reproduction number in a pathogen outbreak/epidemic☆10Updated last week
- Infectious disease model library and utilities☆15Updated 2 years ago
- R package for estimating excess deaths from daily count data☆20Updated 2 months ago
- R package for Bayesian nonparametric adaptive smoothing with Stan☆8Updated 3 years ago
- Analysis of COVID-19 transmission using cluster size distribution☆11Updated 2 years ago
- modelling SARS-CoV-2 vaccine efficacy from antibody titres, and impact of waning and variants on transmission☆18Updated 9 months ago
- Implication of overdispersed transmission of COVID-19 on the effectiveness of contact tracing☆8Updated 3 years ago
- Network Models of HIV Transmission Dynamics among MSM and Heterosexuals☆24Updated 2 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…☆11Updated 2 years ago
- Repo for the course Statistical Methods in Infectious Disease Epidemiology at UZH☆17Updated 2 years ago
- Some code for monkeypox☆10Updated last year
- An R package and Bayesian generative model to estimate epidemiological parameters from wastewater concentration measurements over time.☆13Updated this week
- Curated datasets on reported cases of the SARS-CoV-2 Omicron (B.1.1.529) Variant of Concern☆10Updated 2 years ago
- A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.☆18Updated 6 months ago
- Analysis of excess mortality in Italy during the COVID-19 pandemic☆15Updated 3 months ago
- Estimate Realtime Case Counts and Time-varying Epidemiological Parameters☆33Updated last year
- An R package for Bayes Linear emulation and history matching.☆16Updated last week
- Inferring high-resolution human mixing patterns for disease modeling☆41Updated last year
- Covid-19 epidemiology - data and analysis☆11Updated 9 months ago
- Basic Epidemic, Activity, and Response COVID-19 model☆32Updated 4 years ago
- R package for deriving social mixing matrices from survey data.☆38Updated last week
- ☆26Updated 3 years ago
- ☆10Updated 7 months ago
- An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wh…☆37Updated last year