Files in seabbs/inc2prev
Estimate incidence from Prevalence Estimates
.Rbuildignore
.devcontainer/Dockerfile
.devcontainer/devcontainer.json
.devcontainer/library-scripts/common-debian.sh
.github/workflows/_pkgdown.yml
.github/workflows/build-and-push-image.yaml
.gitignore
.lintr
.pre-commit-config.yaml
DESCRIPTION
LICENSE
NAMESPACE
R/archive-output.R
R/inc2prev-package.R
R/incidence.R
R/model.R
R/plot.R
R/plot_wrapper.R
R/postprocess.R
R/prob_detectable.R
R/simulate.R
R/tune_inv_gamma.R
R/utils.R
README.md
_pkgdown.yml
data-processed/ab.csv
data-processed/ab_age.csv
data-processed/cis.csv
data-processed/cis_age.csv
data-processed/cis_areas.csv
data-processed/cis_variants.csv
data-processed/early-seroprevalence.csv
data-processed/ons-prev.csv
data-processed/populations.csv
data-processed/populations_ab.csv
data-processed/prob_detectable.csv
data-processed/vacc.csv
data-raw/clean-prev.R
data-raw/extract_publication_dates.r
data-raw/gen-prob-positive.R
data-raw/uk_pop.xls
data-raw/update_ab.R
data-raw/update_cis.R
data-raw/update_vacc.R
docs/paper.Rmd
docs/references.bib
docs/report.Rmd
inst/WORDLIST
man/combine_incidence_fits.Rd
man/expose_stan_fns.Rd
man/i2p_model.Rd
man/i2p_sample.Rd
man/inc2prev-package.Rd
man/incidence.Rd
man/incidence_lapply.Rd
man/inv_logit.Rd
man/logit.Rd
man/tune_inv_gamma.Rd
outputs/cumulative_age.csv
outputs/cumulative_local.csv
outputs/cumulative_national.csv
outputs/cumulative_regional.csv
outputs/cumulative_regional_ab.csv
outputs/cumulative_regional_ab_higher.csv
outputs/cumulative_variants.csv
outputs/estimates_age.csv
outputs/estimates_age_ab.csv
outputs/estimates_local.csv
outputs/estimates_national.csv
outputs/estimates_regional.csv
outputs/estimates_regional_ab.csv
outputs/estimates_regional_ab_higher.csv
outputs/estimates_variants.csv
outputs/example-parameters.csv
outputs/inf_ab_local.csv
outputs/inf_ab_local_higher.csv
pkgdown/assets/figures/example/Rt.png
pkgdown/assets/figures/example/ab.png
pkgdown/assets/figures/example/example-estimates.png
pkgdown/assets/figures/example/growth.png
pkgdown/assets/figures/example/infections.png
pkgdown/assets/figures/example/pairs.png
pkgdown/assets/figures/example/prev.png
pkgdown/assets/figures/national_Rt_3months.svg
pkgdown/assets/figures/national_infections_all.svg
pkgdown/assets/figures/national_r_3months.svg
pkgdown/assets/paper.html
pkgdown/assets/paper.pdf
pkgdown/assets/report.html
scripts/analyse.R
scripts/estimate.R
scripts/generate_local_ab.r
scripts/local.sh
scripts/local_snapshots.sh
scripts/plot_data.r
scripts/plot_estimates.r
scripts/publish.sh
scripts/read.R
scripts/simple-example.R
scripts/update.sh
stan/functions/ab.stan
stan/functions/convolve.stan
stan/functions/gaussian_process.stan
stan/functions/generated_quantities.stan
stan/functions/observed_in_window.stan
stan/functions/rng.stan
stan/functions/rt.stan
stan/inc2prev.stan
stan/inc2prev_simple.stan
stan/tune_inv_gamma.stan
