Files in epiforecasts/EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

.Rbuildignore

.devcontainer/Dockerfile

.devcontainer/devcontainer.json

.devcontainer/library-scripts/common-debian.sh

.github/.gitignore

.github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md

.github/ISSUE_TEMPLATE/config.yml

.github/ISSUE_TEMPLATE/documentation.md .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/other_issue.md .github/PULL_REQUEST_TEMPLATE.md

.github/dependabot.yml

.github/workflows/R-CMD-as-cran-check.yaml

.github/workflows/R-CMD-check.yaml

.github/workflows/build-and-push-image.yaml

.github/workflows/lint-only-changed-files.yaml

.github/workflows/pkgdown.yaml

.github/workflows/pr-commands.yaml

.github/workflows/render-readme.yaml

.github/workflows/stan-model-benchmark.yaml

.github/workflows/synthetic-validation.yaml

.github/workflows/test-coverage.yaml

.github/workflows/touchstone-comment.yaml

.github/workflows/touchstone-receive.yaml

.github/workflows/update-citation-cff.yaml

.gitignore

.lintr

.pre-commit-config.yaml

CITATION.cff

CODE_OF_CONDUCT.md

CRAN-SUBMISSION

DESCRIPTION

EpiNow2.Rproj

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/EpiNow2-package.R R/adjust.R R/checks.R R/create.R R/data.R R/deprecated.R R/dist_spec.R R/epinow-internal.R R/epinow.R R/estimate_delay.R R/estimate_infections.R R/estimate_secondary.R R/estimate_truncation.R R/extract.R R/get.R R/opts.R R/plot.R R/regional_epinow.R R/report.R R/setup.R R/simulate_infections.R R/simulate_secondary.R R/stan.R R/stanmodels.R R/summarise.R R/utilities.R README.Rmd README.md

_pkgdown.yml

codecov.yml

configure

configure.win

cran-comments.md data-raw/estimate-infections.R data-raw/generation-time.R

data-raw/gi.rds

data-raw/incubation-period.R data-raw/reporting-delay.R data-raw/truncated.R

data/example_confirmed.rda

data/example_generation_time.rda

data/example_incubation_period.rda

data/example_reporting_delay.rda

data/example_truncated.rda

data/generation_times.rda

data/incubation_periods.rda

inst/CITATION

inst/WORDLIST

inst/dev/benchmark-functions.R inst/dev/benchmark.R inst/dev/design_dist.md

inst/dev/figs/rt_backcalc_nuts.png

inst/dev/figs/rt_gp_nuts.png

inst/dev/figs/rt_gp_rw_nuts.png

inst/dev/figs/rt_weekly_rw_nuts.png

inst/dev/load-stan-functions.R inst/dev/recover-synthetic/eval_rt.R inst/dev/recover-synthetic/plot.R inst/dev/recover-synthetic/rt.R

inst/extdata/example_estimate_infections.rds

inst/extdata/example_regional_epinow.rds

inst/extdata/example_truncated.rds

inst/extdata/example_truncation_data.rds

inst/include/stan_meta_header.hpp

inst/stan/data/backcalc.stan

inst/stan/data/delays.stan

inst/stan/data/gaussian_process.stan

inst/stan/data/generation_time.stan

inst/stan/data/observation_model.stan

inst/stan/data/observations.stan

inst/stan/data/rt.stan

inst/stan/data/secondary.stan

inst/stan/data/simulation_delays.stan

inst/stan/data/simulation_observation_model.stan

inst/stan/data/simulation_rt.stan

inst/stan/dist_fit.stan

inst/stan/estimate_infections.stan

inst/stan/estimate_secondary.stan

inst/stan/estimate_truncation.stan

inst/stan/functions/convolve.stan

inst/stan/functions/delays.stan

inst/stan/functions/gaussian_process.stan

inst/stan/functions/generated_quantities.stan

inst/stan/functions/infections.stan

inst/stan/functions/observation_model.stan

inst/stan/functions/pmfs.stan

inst/stan/functions/rt.stan

inst/stan/functions/secondary.stan

inst/stan/include/license.stan

inst/stan/simulate_infections.stan

inst/stan/simulate_secondary.stan

man/Distributions.Rd man/EpiNow2-package.Rd man/R_to_growth.Rd man/add_day_of_week.Rd man/adjust_infection_to_report.Rd man/allocate_delays.Rd man/allocate_empty.Rd man/apply_tolerance.Rd man/backcalc_opts.Rd man/bootstrapped_dist_fit.Rd man/c.dist_spec.Rd man/calc_CrI.Rd man/calc_CrIs.Rd man/calc_summary_measures.Rd man/calc_summary_stats.Rd man/check_reports_valid.Rd man/check_stan_delay.Rd man/clean_nowcasts.Rd man/clean_regions.Rd man/collapse.Rd man/construct_output.Rd man/convert_to_logmean.Rd man/convert_to_logsd.Rd man/convert_to_natural.Rd man/convolve_and_scale.Rd man/copy_results_to_latest.Rd man/create_backcalc_data.Rd man/create_clean_reported_cases.Rd man/create_complete_cases.Rd man/create_delay_inits.Rd man/create_future_rt.Rd man/create_gp_data.Rd man/create_initial_conditions.Rd man/create_obs_model.Rd man/create_rt_data.Rd man/create_shifted_cases.Rd man/create_stan_args.Rd man/create_stan_data.Rd man/create_stan_delays.Rd man/delay_opts.Rd man/discretise.Rd man/dist_fit.Rd man/dist_skel.Rd man/dist_spec.Rd man/epinow.Rd man/epinow2_cmdstan_model.Rd man/epinow2_rstan_model.Rd man/epinow2_stan_model.Rd man/estimate_delay.Rd man/estimate_infections.Rd man/estimate_secondary.Rd man/estimate_truncation.Rd man/estimates_by_report_date.Rd man/example_confirmed.Rd man/example_generation_time.Rd man/example_incubation_period.Rd man/example_reporting_delay.Rd man/example_truncated.Rd man/expose_stan_fns.Rd man/extract_CrIs.Rd man/extract_inits.Rd man/extract_parameter.Rd man/extract_parameter_samples.Rd man/extract_params.Rd man/extract_samples.Rd man/extract_single_dist.Rd man/extract_stan_param.Rd man/extract_static_parameter.Rd

man/figures/lifecycle-archived.svg

man/figures/lifecycle-defunct.svg

man/figures/lifecycle-deprecated.svg

man/figures/lifecycle-experimental.svg

man/figures/lifecycle-maturing.svg

man/figures/lifecycle-questioning.svg

man/figures/lifecycle-soft-deprecated.svg

man/figures/lifecycle-stable.svg

man/figures/lifecycle-superseded.svg

man/filter_opts.Rd man/fit_model.Rd man/fit_model_approximate.Rd man/fit_model_with_nuts.Rd man/fix_dist.Rd man/forecast_infections.Rd man/forecast_secondary.Rd man/format_fit.Rd man/gamma_dist_def.Rd man/generation_time_opts.Rd man/generation_times.Rd man/get_dist.Rd man/get_generation_time.Rd man/get_incubation_period.Rd man/get_raw_result.Rd man/get_regional_results.Rd man/get_regions.Rd man/get_regions_with_most_reports.Rd man/get_seeding_time.Rd man/gp_opts.Rd man/growth_to_R.Rd man/incubation_periods.Rd man/init_cumulative_fit.Rd man/lognorm_dist_def.Rd man/lower_bounds.Rd man/make_conf.Rd man/map_prob_change.Rd man/match_output_arguments.Rd man/max.dist_spec.Rd man/mean.dist_spec.Rd man/natural_params.Rd man/new_dist_spec.Rd man/obs_opts.Rd man/opts_list.Rd man/plot.dist_spec.Rd man/plot.epinow.Rd man/plot.estimate_infections.Rd man/plot.estimate_secondary.Rd man/plot.estimate_truncation.Rd man/plot_CrIs.Rd man/plot_estimates.Rd man/plot_summary.Rd man/plus-.dist_spec.Rd man/print.dist_spec.Rd man/process_region.Rd man/process_regions.Rd man/regional_epinow.Rd man/regional_runtimes.Rd man/regional_summary.Rd man/report_cases.Rd man/report_plots.Rd man/report_summary.Rd man/rstan_opts.Rd man/rstan_sampling_opts.Rd man/rstan_vb_opts.Rd man/rt_opts.Rd man/run_region.Rd man/sample_approx_dist.Rd man/save_estimate_infections.Rd man/save_input.Rd man/sd_dist.Rd man/secondary_opts.Rd man/set_dt_single_thread.Rd man/setup_default_logging.Rd man/setup_dt.Rd man/setup_future.Rd man/setup_logging.Rd man/setup_target_folder.Rd man/simulate_infections.Rd man/simulate_secondary.Rd man/stan_laplace_opts.Rd man/stan_opts.Rd man/stan_pathfinder_opts.Rd man/stan_sampling_opts.Rd man/stan_vb_opts.Rd man/summarise_key_measures.Rd man/summarise_results.Rd man/summary.epinow.Rd man/summary.estimate_infections.Rd man/trunc_opts.Rd man/update_horizon.Rd man/update_list.Rd man/update_secondary_args.Rd tests/spelling.R tests/testthat.R tests/testthat/_snaps/calc_CrI.md tests/testthat/_snaps/calc_CrIs.md tests/testthat/_snaps/calc_summary_measures.md tests/testthat/_snaps/calc_summary_stats.md tests/testthat/_snaps/simulate-infections.md tests/testthat/_snaps/simulate-secondary.md tests/testthat/setup.R tests/testthat/test-adjust_infection_to_report.R tests/testthat/test-calc_CrI.R tests/testthat/test-calc_CrIs.R tests/testthat/test-calc_summary_measures.R tests/testthat/test-calc_summary_stats.R tests/testthat/test-checks.R tests/testthat/test-create_clean_reported_cases.R tests/testthat/test-create_future-rt.R tests/testthat/test-create_obs_model.R tests/testthat/test-create_stan_args.R

tests/testthat/test-create_stan_data.R

tests/testthat/test-delays.R tests/testthat/test-dist.R tests/testthat/test-dist_spec.R tests/testthat/test-epinow.R tests/testthat/test-estimate_infections.R tests/testthat/test-estimate_secondary.R tests/testthat/test-estimate_truncation.R tests/testthat/test-extract_CrIs.R tests/testthat/test-forecast-infections.R tests/testthat/test-get_dist.R tests/testthat/test-match_output_arguments.R tests/testthat/test-opts.R tests/testthat/test-plot_estimates.R tests/testthat/test-regional_epinow.R tests/testthat/test-regional_runtimes.R tests/testthat/test-regional_summary.R tests/testthat/test-report_cases.R tests/testthat/test-report_plots.R tests/testthat/test-seeding-time.R tests/testthat/test-set_dt_single_thread.R tests/testthat/test-setup_future.R tests/testthat/test-simulate-infections.R tests/testthat/test-simulate-secondary.R tests/testthat/test-stan-convole.R tests/testthat/test-stan-generated_quantities.R tests/testthat/test-stan-infections.R tests/testthat/test-stan-rt.R tests/testthat/test-stan-secondary.R

touchstone/.gitignore

touchstone/config.json

touchstone/footer.R touchstone/header.R touchstone/script.R touchstone/setup.R

vignettes/.gitignore

vignettes/EpiNow2.Rmd

vignettes/EpiNow2.Rmd.orig

vignettes/case-studies.Rmd vignettes/epinow.Rmd

vignettes/epinow.Rmd.orig

vignettes/estimate_infections.Rmd vignettes/estimate_infections_options.Rmd

vignettes/estimate_infections_options.Rmd.orig

vignettes/estimate_infections_workflow.Rmd

vignettes/estimate_infections_workflow.Rmd.orig

vignettes/estimate_secondary.Rmd vignettes/estimate_truncation.Rmd

vignettes/figure/bp-1.png

vignettes/figure/data-1.png

vignettes/figure/default-1.png

vignettes/figure/fixed-1.png

vignettes/figure/gp_projection-1.png

vignettes/figure/lower_accuracy-1.png

vignettes/figure/no_delays-1.png

vignettes/figure/nonparametric-1.png

vignettes/figure/regional_epinow-1.png

vignettes/figure/regional_epinow_multiple-1.png

vignettes/figure/results-1.png

vignettes/figure/susceptible_depletion-1.png

vignettes/figure/truncation-1.png

vignettes/figure/unnamed-chunk-10-1.png

vignettes/figure/unnamed-chunk-14-1.png

vignettes/figure/weekly_rw-1.png

vignettes/gaussian_process_implementation_details.Rmd

vignettes/library.bib

vignettes/precompile.R

epiforecasts/EpiNow2 documentation built on April 27, 2024, 9:15 p.m.