Files in annecori/EpiEstim
Estimate Time Varying Reproduction Numbers from Epidemic Curves
.Rbuildignore
.github/.gitignore
.github/pull_request_template.md
.github/workflows/R-CMD-check.yaml
.github/workflows/lint-changed-files.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.lintr
DESCRIPTION
EpiEstim.Rproj
NAMESPACE
NEWS.md
R/aggregate_inc.R
R/backimputation.R
R/check_cdt_samples_convergence.R
R/coarse2estim.R
R/compatibility.R
R/data.R
R/discr_si.R
R/estimate_R.R
R/estimate_R_agg.R
R/estimate_R_plots.R
R/gibbs_draws.R
R/init_mcmc_params.R
R/make_config.R
R/make_mcmc_control.R
R/overall_infectivity.R
R/plot.R
R/sample_posterior_R.R
R/utilities.R
R/wallinga_teunis.R
README.md
codecov.yml
data/Flu1918.rda
data/Flu2009.rda
data/Measles1861.rda
data/MockRotavirus.rda
data/SARS2003.rda
data/Smallpox1972.rda
data/covid_deaths_2020_uk.rda
data/flu_2009_NYC_school.rda
data/mers_2014_15.rda
man/DiscrSI.Rd
man/EstimateR.Rd
man/Flu1918.Rd
man/Flu2009.Rd
man/Measles1861.Rd
man/MockRotavirus.Rd
man/OverallInfectivity.Rd
man/SARS2003.Rd
man/Smallpox1972.Rd
man/WT.Rd
man/aggregate_inc.Rd
man/backimpute_I.Rd
man/check_cdt_samples_convergence.Rd
man/coarse2estim.Rd
man/compute_lambda.Rd
man/compute_si_cutoff.Rd
man/compute_t_min.Rd
man/covid_deaths_2020_uk.Rd
man/default_mcmc_controls.Rd
man/default_priors.Rd
man/discr_si.Rd
man/draw_R.Rd
man/draw_epsilon.Rd
man/estimate_R.Rd
man/estimate_R_agg.Rd
man/estimate_R_plots.Rd
man/estimate_advantage.Rd
man/first_nonzero_incid.Rd
man/flu_2009_NYC_school.Rd
man/get_shape_R_flat.Rd
man/get_shape_epsilon.Rd
man/init_mcmc_params.Rd
man/make_config.Rd
man/make_mcmc_control.Rd
man/mers_2014_15.Rd
man/overall_infectivity.Rd
man/plot.estimate_R.Rd
man/process_I_multivariant.Rd
man/sample_posterior_R.Rd
man/wallinga_teunis.Rd
tests/expected_output/Example1.rda
tests/expected_output/Example2.rda
tests/expected_output/Example3.rda
tests/expected_output/Example4.rda
tests/figs/deps.txt
tests/figs/flu2009-incidence-import.svg
tests/figs/flu2009-instantaneous-no-legend.svg
tests/figs/flu2009-rc.svg
tests/figs/flu2009-ri.svg
tests/figs/flu2009-si.svg
tests/incidence_files/incid.rds
tests/incidence_files/si_for_est.rds
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/test-backimpute.R
tests/testthat/test-estimate_R.R
tests/testthat/test-multivariant-input.R
tests/testthat/test-plot.R
tests/testthat/test-samplers.R
tests/testthat/test-stample_posterior_R.R
tests/testthat/test-weekly.R
vignettes/.gitignore
vignettes/EpiEstim_aggregated_data.Rmd
vignettes/EpiEstim_backimputation.Rmd
vignettes/MV_EpiEstim_vignette.Rmd
vignettes/aggregated_data/UK_covid_cases.rds
vignettes/alternative_software.Rmd
vignettes/data_full_vignette/evd_linelist.csv
vignettes/data_mv_vignette/incid.rds
vignettes/figs/Delays_in_reporting.png
vignettes/figs/Illustration_of_process.png
vignettes/figs/Infector_infected_exact.png
vignettes/figs/Infector_infected_intervals.png
vignettes/figs/Renewal_equation.png
vignettes/figs/Serial_interval_with_uncertainty.png
vignettes/figs/Time_varying_reporting.png
vignettes/figs/Weekly_sliding_windows.png
vignettes/figs/interval_censored_example.png
vignettes/full_EpiEstim_vignette.Rmd
vignettes/short_demo.Rmd
