epiforecasts / omicron-sgtf-forecastLinks
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
Alternatives and similar repositories for omicron-sgtf-forecast
Users that are interested in omicron-sgtf-forecast are comparing it to the libraries listed below
Sorting:
- Estimate epidemiological quantities from repeated cross-sectional prevalence measurements☆17Updated last year
- Infectious disease model library and utilities☆14Updated 2 years ago
- Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on red…☆13Updated 2 years ago
- Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional appr…☆22Updated last year
- Epidemiological agent-based modelling packages in both python and C++. Published at: https://doi.org/10.5334/jors.449.☆18Updated this week
- An R package for the analysis of infectious disease transmission data☆10Updated 3 years ago
- R package for estimating excess deaths from daily count data☆20Updated 2 months ago
- Network Models of HIV Transmission Dynamics among MSM and Heterosexuals☆25Updated 3 months ago
- Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model wit…☆61Updated 3 weeks ago
- modelling SARS-CoV-2 vaccine efficacy from antibody titres, and impact of waning and variants on transmission☆17Updated last year
- A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.☆19Updated 8 months ago
- Estimate Realtime Case Counts and Time-varying Epidemiological Parameters☆33Updated 2 years ago
- Create Contact Matrices from Population Data☆20Updated last month
- An R package and Bayesian generative model to estimate epidemiological parameters from wastewater concentration measurements over time.☆22Updated this week
- Monte-Carlo State Space Models☆19Updated 11 months ago
- Some code for monkeypox☆10Updated 2 years ago
- R package for Bayesian nonparametric adaptive smoothing with Stan☆9Updated 4 years ago
- An R package for Bayes Linear emulation and history matching.☆16Updated 3 months 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…☆12Updated 2 years ago
- epidemia package☆48Updated 3 years 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 2 years ago
- R package for estimation and monitoring of the effective reproduction number in a pathogen outbreak/epidemic☆11Updated 9 months ago
- Analysis of COVID-19 transmission using cluster size distribution☆11Updated 3 years ago
- ☆30Updated 2 months ago
- Code for reconstructing influenza dynamics from surveillance data using evidence synthesis techniques☆21Updated 3 years ago
- Text project for theoretical primer on human evolutionary ecology☆34Updated 2 years ago
- ☆17Updated 4 years ago
- Repo for the LSHTM R Users Group (RUG)☆9Updated 3 years ago
- Course on nowcasting and forecasting of infectious disease dynamics☆19Updated this week
- This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (RE…☆17Updated last year