Files in epiforecasts/omicron-sgtf-forecast
Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy
.Rbuildignore
.devcontainer/Dockerfile
.devcontainer/devcontainer.json
.devcontainer/library-scripts/common-debian.sh
.gitattributes
.github/workflows/build-and-publish-documentation.yaml
.github/workflows/build-and-push-image.yaml
.gitignore
CITATION.cff
DESCRIPTION
LICENSE
LICENSE.md
NEWS.md
R/README.Rmd
R/README.md
R/build-models-by-region-and-age.R
R/build-models-by-region.R
R/build-models.R
R/estimate-generation-time.R
R/load-data.R
R/load-local-data.R
R/load-parameters.R
R/load-private-data.R
R/load-public-data.R
R/munge-data.R
R/plot-cumulative-percent.R
R/plot-daily-cases.R
R/plot-omicron-95.R
R/plot-summary.R
R/postprocess.R
README.md
bin/update-and-publish.sh
bin/update-git-remote.sh
bin/update-regional-estimates.sh
data/README.md
data/estimates/bias/2021-12-20/data.rds
data/estimates/bias/2021-12-20/diagnostics.rds
data/estimates/bias/2021-12-20/posterior.rds
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data/public/2021-12-15-cases-by-sgtf.csv
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data/public/2022-01-18-cases-by-sgtf.csv
data/retrospective/posterior_predictions.csv
data/retrospective/posterior_summary.csv
omicron-sgtf-forecast.Rproj
scripts/estimate-observed-transmission-parameters.R
scripts/update-age-and-region-estimates.R
scripts/update-regional-data.R
scripts/update-regional-estimates.R
scripts/update-sgtf-by-age.R
stan/functions/R_gamma_approx.stan
stan/functions/convolve.stan
stan/generation-time.stan
stan/omicron-delay.stan
writeup/day-of-week-effect.Rmd
writeup/footer.html
writeup/generation-time.Rmd
writeup/header.html
writeup/library.bib
writeup/paper.Rmd
writeup/summary.Rmd
