Files in epiforecasts/EpiNow
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
.Rbuildignore
.github/workflows/build-docker.yaml
.github/workflows/check-full.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
Dockerfile
EpiNow.Rproj
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/adjust.R
R/data.R
R/dist.R
R/epi_measures_pipeline.R
R/estimate_R0.R
R/estimate_littler.R
R/get.R
R/linelist_tools.R
R/map.R
R/nowcast_pipeline.R
R/plot.R
R/regional_rt_pipeline.R
R/report.R
R/rt_pipeline.R
R/simulate.R
R/stanmodels.R
R/summarise.R
R/utilities.R
README.Rmd
README.md
_pkgdown.yml
configure
configure.win
data-raw/ganyani-generation-time.R
data-raw/gi.rds
data-raw/incubation-period.R
data-raw/nishiura-lognormal-truncated.csv
data-raw/nishiura-serial-interval.R
data/covid_generation_times.rda
data/covid_generation_times_summary.rda
data/covid_incubation_period.rda
data/covid_serial_intervals.rda
inst/include/stan_meta_header.hpp
inst/pkg-structure/EpiNow_report.html
inst/pkg-structure/generate-pkgstructure-report.R
inst/stan/exp_fit.stan
inst/stan/gamma_fit.stan
inst/stan/include/license.stan
inst/templates/_add-region-reports.Rmd
inst/templates/_region-report.Rmd
inst/templates/_regional-summary.Rmd
man/R_to_growth.Rd
man/add_dates.Rd
man/adjust_for_truncation.Rd
man/adjust_infection_to_report.Rd
man/clean_nowcasts.Rd
man/country_map.Rd
man/covid_generation_times.Rd
man/covid_generation_times_summary.Rd
man/covid_incubation_period.Rd
man/covid_serial_intervals.Rd
man/dist_fit.Rd
man/dist_skel.Rd
man/epi_measures_pipeline.Rd
man/estimate_R0.Rd
man/estimate_doubling_time.Rd
man/estimate_little_r.Rd
man/estimate_r_in_window.Rd
man/estimate_time_varying_r.Rd
man/gamma_dist_def.Rd
man/generate_pseudo_linelist.Rd
man/get_dist_def.Rd
man/get_local_import_case_counts.Rd
man/get_regions.Rd
man/get_timeseries.Rd
man/global_map.Rd
man/growth_to_R.Rd
man/linelist_from_case_counts.Rd
man/load_nowcast_result.Rd
man/lognorm_dist_def.Rd
man/make_conf.Rd
man/map_prob_change.Rd
man/nowcast_pipeline.Rd
man/plot_confidence.Rd
man/plot_forecast.Rd
man/plot_grid.Rd
man/plot_pipeline.Rd
man/plot_summary.Rd
man/pull_max_var.Rd
man/rbinom_size.Rd
man/regional_rt_pipeline.Rd
man/regional_summary.Rd
man/report_cases.Rd
man/report_littler.Rd
man/report_nowcast.Rd
man/report_reff.Rd
man/report_summary.Rd
man/rt_pipeline.Rd
man/sample_approx_dist.Rd
man/sample_delay.Rd
man/simulate_cases.Rd
man/split_linelist_by_day.Rd
man/summarise_cast.Rd
man/summarise_results.Rd
man/summarise_to_csv.Rd
man/theme_map.Rd
src/EpiNow.so
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/RcppExports.o
src/stanExports_exp_fit.cc
src/stanExports_exp_fit.h
src/stanExports_exp_fit.o
src/stanExports_gamma_fit.cc
src/stanExports_gamma_fit.h
src/stanExports_gamma_fit.o
vignettes/.gitignore
vignettes/getting-started.Rmd
