EpiNow2
Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

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EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
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Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

configure
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NEWS.md README.md
NAMESPACE
DESCRIPTION
LICENSE
configure.win
R/estimate_truncation.R R/get.R R/stanmodels.R R/estimate_infections.R R/utilities.R R/dist.R R/summarise.R R/data.R R/epinow-internal.R R/report.R R/create.R R/plot.R R/epinow.R R/regional_epinow.R R/EpiNow2-package.R R/estimate_secondary.R R/setup.R R/extract.R R/simulate_infections.R R/opts.R R/adjust.R
src/stanExports_estimate_secondary.cc
src/stanExports_simulate_infections.cc
src/Makevars
src/stanExports_estimate_infections.h
src/RcppExports.cpp
src/stanExports_estimate_infections.cc
src/stanExports_dist_fit.cc
src/stanExports_dist_fit.h
src/stanExports_estimate_secondary.h
src/stanExports_simulate_secondary.h
src/stanExports_estimate_truncation.cc
src/stanExports_estimate_truncation.h
src/stanExports_simulate_infections.h
src/stanExports_simulate_secondary.cc
inst/CITATION
inst/WORDLIST
inst/include/stan_meta_header.hpp
inst/doc/estimate_truncation.R inst/doc/estimate_infections.R inst/doc/case-studies.R inst/doc/estimate_infections.Rmd
inst/doc/estimate_truncation.html
inst/doc/estimate_secondary.html
inst/doc/estimate_infections.html
inst/doc/estimate_truncation.Rmd inst/doc/gaussian_process_implementation_details.R inst/doc/gaussian_process_implementation_details.Rmd inst/doc/estimate_secondary.R
inst/doc/gaussian_process_implementation_details.html
inst/doc/case-studies.html
inst/doc/case-studies.Rmd inst/doc/estimate_secondary.Rmd
inst/stan/estimate_secondary.stan
inst/stan/simulate_secondary.stan
inst/stan/estimate_infections.stan
inst/stan/estimate_truncation.stan
inst/stan/dist_fit.stan
inst/stan/simulate_infections.stan
inst/stan/include/license.stan
inst/stan/data/secondary.stan
inst/stan/data/simulation_rt.stan
inst/stan/data/simulation_observation_model.stan
inst/stan/data/gaussian_process.stan
inst/stan/data/simulation_delays.stan
inst/stan/data/observation_model.stan
inst/stan/data/delays.stan
inst/stan/data/backcalc.stan
inst/stan/data/rt.stan
inst/stan/data/generation_time.stan
inst/stan/data/observations.stan
inst/stan/functions/convolve.stan
inst/stan/functions/infections.stan
inst/stan/functions/secondary.stan
inst/stan/functions/gaussian_process.stan
inst/stan/functions/observation_model.stan
inst/stan/functions/pmfs.stan
inst/stan/functions/delays.stan
inst/stan/functions/rt.stan
inst/stan/functions/generated_quantities.stan
inst/templates/_all-region-summary.Rmd inst/templates/_add-region-reports.Rmd inst/templates/_region-report.Rmd inst/templates/_regional-summary.Rmd
build/vignette.rds
build/partial.rdb
tests/testthat.R tests/spelling.R tests/testthat/test-regional_summary.R tests/testthat/test-plot_estimates.R tests/testthat/test-create_obs_model.R tests/testthat/test-regional_runtimes.R tests/testthat/test-estimate_secondary.R tests/testthat/test-calc_CrIs.R tests/testthat/test-get_dist.R tests/testthat/test-report_cases.R tests/testthat/test-dist_spec.R tests/testthat/test-estimate_truncation.R tests/testthat/test-seeding-time.R tests/testthat/test-stan-convole.R tests/testthat/test-simulate_infections.R tests/testthat/test-dist.R tests/testthat/test-estimate_infections.R tests/testthat/test-epinow.R tests/testthat/test-create_stan_args.R tests/testthat/test-report_plots.R tests/testthat/test-regional_epinow.R tests/testthat/test-delays.R tests/testthat/test-adjust_infection_to_report.R tests/testthat/test-setup_future.R tests/testthat/test-stan-rt.R tests/testthat/test-extract_CrIs.R tests/testthat/test-match_output_arguments.R tests/testthat/test-set_dt_single_thread.R tests/testthat/setup.R tests/testthat/test-stan-secondary.R tests/testthat/test-calc_summary_measures.R tests/testthat/test-stan-infections.R tests/testthat/test-calc_CrI.R tests/testthat/test-calc_summary_stats.R tests/testthat/test-create_future-rt.R tests/testthat/_snaps/calc_CrI.md tests/testthat/_snaps/calc_summary_measures.md tests/testthat/_snaps/calc_CrIs.md tests/testthat/_snaps/calc_summary_stats.md tests/testthat/test-models/estimate_infections.R tests/testthat/test-models/regional_epinow.R
tests/testthat/test-models/regional_epinow/cases.rds
tests/testthat/test-models/regional_epinow/static.rds
tests/testthat/test-models/estimate_infections/static.rds
vignettes/estimate_infections.Rmd
vignettes/library.bib
vignettes/estimate_truncation.Rmd vignettes/gaussian_process_implementation_details.Rmd vignettes/case-studies.Rmd vignettes/estimate_secondary.Rmd
data/incubation_periods.rda
data/generation_times.rda
data/example_confirmed.rda
man/create_backcalc_data.Rd man/estimate_delay.Rd man/fit_model_with_vb.Rd man/construct_output.Rd man/gamma_dist_def.Rd man/tune_inv_gamma.Rd man/plot.estimate_secondary.Rd man/obs_opts.Rd man/get_dist.Rd man/incubation_periods.Rd man/dist_fit.Rd man/rt_opts.Rd man/secondary_opts.Rd man/setup_target_folder.Rd man/opts_list.Rd man/summary.epinow.Rd man/plot_CrIs.Rd man/copy_results_to_latest.Rd man/convert_to_logmean.Rd man/bootstrapped_dist_fit.Rd man/dist_spec.Rd man/example_confirmed.Rd man/extract_parameter_samples.Rd man/summarise_key_measures.Rd man/dist_spec_plus.Rd man/create_rt_data.Rd man/report_summary.Rd man/get_regional_results.Rd man/lognorm_dist_def.Rd man/plot_summary.Rd man/simulate_secondary.Rd man/create_initial_conditions.Rd man/allocate_delays.Rd man/generation_time_opts.Rd man/extract_CrIs.Rd man/forecast_secondary.Rd man/format_fit.Rd man/get_incubation_period.Rd man/setup_dt.Rd man/create_stan_data.Rd man/filter_opts.Rd man/create_clean_reported_cases.Rd man/extract_parameter.Rd man/rstan_sampling_opts.Rd man/trunc_opts.Rd man/extract_stan_param.Rd man/regional_epinow.Rd man/update_secondary_args.Rd man/save_estimate_infections.Rd man/convert_to_logsd.Rd man/create_stan_args.Rd man/calc_summary_stats.Rd man/setup_default_logging.Rd man/R_to_growth.Rd man/stan_opts.Rd man/get_raw_result.Rd man/clean_nowcasts.Rd man/clean_regions.Rd man/plot.dist_spec.Rd man/allocate_empty.Rd man/process_regions.Rd man/report_plots.Rd man/regional_runtimes.Rd man/map_prob_change.Rd man/summarise_results.Rd man/adjust_infection_to_report.Rd man/mean.dist_spec.Rd man/plus-.dist_spec.Rd man/create_stan_delays.Rd man/estimate_truncation.Rd man/estimates_by_report_date.Rd man/update_horizon.Rd man/setup_logging.Rd man/extract_static_parameter.Rd man/match_output_arguments.Rd man/save_input.Rd man/process_region.Rd man/EpiNow2-package.Rd man/plot_estimates.Rd man/update_list.Rd man/summary.estimate_infections.Rd man/sample_approx_dist.Rd man/rstan_opts.Rd man/setup_future.Rd man/gp_opts.Rd man/report_cases.Rd man/create_gp_data.Rd man/fit_model_with_nuts.Rd man/estimate_secondary.Rd man/plot.estimate_truncation.Rd man/get_regions.Rd man/calc_CrI.Rd man/calc_CrIs.Rd man/get_regions_with_most_reports.Rd man/plot.epinow.Rd man/get_seeding_time.Rd man/expose_stan_fns.Rd man/run_region.Rd man/simulate_infections.Rd man/init_cumulative_fit.Rd man/rstan_vb_opts.Rd man/extract_inits.Rd man/create_obs_model.Rd man/regional_summary.Rd man/create_shifted_cases.Rd man/print.dist_spec.Rd man/delay_opts.Rd man/c.dist_spec.Rd man/backcalc_opts.Rd man/estimate_infections.Rd man/add_day_of_week.Rd man/plot.estimate_infections.Rd man/create_future_rt.Rd man/get_generation_time.Rd man/make_conf.Rd man/dist_skel.Rd man/epinow.Rd man/calc_summary_measures.Rd man/set_dt_single_thread.Rd man/generation_times.Rd man/growth_to_R.Rd
man/figures/lifecycle-stable.svg
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man/figures/unnamed-chunk-19-1.png
man/figures/lifecycle-superseded.svg
man/figures/lifecycle-soft-deprecated.svg
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man/figures/unnamed-chunk-18-1.png
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-maturing.svg
EpiNow2 documentation built on Sept. 26, 2023, 5:11 p.m.

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