Files in epiforecasts/covid-rt-estimates
Forecasting and nowcasting Covid-19 related metrics Globally and Subnationally.
.Rbuildignore
.Renviron
.dockerignore
.github/workflows/docker-build.yaml
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NEWS.md
R/case-manipulation-utils.R
R/collate-derivative.R
R/entities/abstract-dataset.R
R/entities/collated-derivative.R
R/entities/dataset-location.R
R/entities/publication-metadata.R
R/entities/region.R
R/entities/super-region.R
R/get_estimates.R
R/lists/collated-derivative-list.R
R/lists/dataset-list.R
R/lists/dataverse-countries.R
R/publish-data.R
R/run-collate-derivative.R
R/run-region-updates.R
R/run-republish.R
R/run-resummarise.R
R/update-delays.R
R/update-regional.R
R/utils.R
README.md
SMG.md
bin/install_azcopy.sh
bin/update-docker.sh
bin/update-estimates.sh
bin/update-via-docker.sh
bin/update-via-ssh.sh
covid-rt-estimates.Rproj
data/cocin_onset_to_death_delay.rds
data/generation_time.rds
data/incubation_period.rds
data/onset_to_admission_delay.rds
data/onset_to_death_delay.rds
data/runtime/example-config.R
data/runtime/known-author-affiliations.R
data/uk_onset_to_case.rds
last-update/belgium.rds
last-update/brazil.rds
last-update/canada-full.rds
last-update/canada.rds
last-update/cases.rds
last-update/colombia.rds
last-update/deaths.rds
last-update/germany.rds
last-update/india.rds
last-update/italy.rds
last-update/regional-cases.rds
last-update/regional-deaths.rds
last-update/russia.rds
last-update/united-kingdom-admissions.rds
last-update/united-kingdom-deaths.rds
last-update/united-kingdom-local-admissions.rds
last-update/united-kingdom-local-deaths.rds
last-update/united-kingdom-local.rds
last-update/united-kingdom.rds
last-update/united-states.rds
last_warning.rds
national/cases/summary/cases_by_infection.csv
national/cases/summary/cases_by_report.csv
national/cases/summary/growth_rate.csv
national/cases/summary/latest_date.rds
national/cases/summary/reported_cases.csv
national/cases/summary/rt.csv
national/cases/summary/summary_data.csv
national/cases/summary/summary_table.csv
national/deaths-all-time/summary/cases_by_infection.csv
national/deaths-all-time/summary/cases_by_report.csv
national/deaths-all-time/summary/growth_rate.csv
national/deaths-all-time/summary/latest_date.rds
national/deaths-all-time/summary/reported_cases.csv
national/deaths-all-time/summary/rt.csv
national/deaths-all-time/summary/summary_data.csv
national/deaths-all-time/summary/summary_table.csv
national/deaths/summary/cases_by_infection.csv
national/deaths/summary/cases_by_report.csv
national/deaths/summary/growth_rate.csv
national/deaths/summary/latest_date.rds
national/deaths/summary/reported_cases.csv
national/deaths/summary/rt.csv
national/deaths/summary/summary_data.csv
national/deaths/summary/summary_table.csv
region/cases-all-time/summary/cases_by_infection.csv
region/cases-all-time/summary/cases_by_report.csv
region/cases-all-time/summary/growth_rate.csv
region/cases-all-time/summary/latest_date.rds
region/cases-all-time/summary/reported_cases.csv
region/cases-all-time/summary/rt.csv
region/cases-all-time/summary/summary_data.csv
region/cases-all-time/summary/summary_table.csv
region/cases/summary/cases_by_infection.csv
region/cases/summary/cases_by_report.csv
region/cases/summary/growth_rate.csv
region/cases/summary/latest_date.rds
region/cases/summary/reported_cases.csv
region/cases/summary/rt.csv
region/cases/summary/summary_data.csv
region/cases/summary/summary_table.csv
region/deaths/summary/cases_by_infection.csv
region/deaths/summary/cases_by_report.csv
region/deaths/summary/growth_rate.csv
region/deaths/summary/latest_date.rds
region/deaths/summary/reported_cases.csv
region/deaths/summary/rt.csv
region/deaths/summary/summary_data.csv
region/deaths/summary/summary_table.csv
subnational/belgium/cases/summary/cases_by_infection.csv
subnational/belgium/cases/summary/cases_by_report.csv
subnational/belgium/cases/summary/growth_rate.csv
subnational/belgium/cases/summary/latest_date.rds
subnational/belgium/cases/summary/reported_cases.csv
subnational/belgium/cases/summary/rt.csv
subnational/belgium/cases/summary/summary_data.csv
subnational/belgium/cases/summary/summary_table.csv
subnational/brazil/cases/summary/cases_by_infection.csv
subnational/brazil/cases/summary/cases_by_report.csv
subnational/brazil/cases/summary/growth_rate.csv
subnational/brazil/cases/summary/latest_date.rds
subnational/brazil/cases/summary/reported_cases.csv
subnational/brazil/cases/summary/rt.csv
subnational/brazil/cases/summary/summary_data.csv
subnational/brazil/cases/summary/summary_table.csv
subnational/canada-full/cases/summary/cases_by_infection.csv
subnational/canada-full/cases/summary/cases_by_report.csv
subnational/canada-full/cases/summary/growth_rate.csv
subnational/canada-full/cases/summary/latest_date.rds
subnational/canada-full/cases/summary/reported_cases.csv
subnational/canada-full/cases/summary/rt.csv
subnational/canada-full/cases/summary/summary_data.csv
subnational/canada-full/cases/summary/summary_table.csv
subnational/canada/cases/summary/cases_by_infection.csv
subnational/canada/cases/summary/cases_by_report.csv
subnational/canada/cases/summary/growth_rate.csv
subnational/canada/cases/summary/latest_date.rds
subnational/canada/cases/summary/reported_cases.csv
subnational/canada/cases/summary/rt.csv
subnational/canada/cases/summary/summary_data.csv
subnational/canada/cases/summary/summary_table.csv
subnational/colombia/cases-all-time/summary/cases_by_infection.csv
subnational/colombia/cases-all-time/summary/cases_by_report.csv
subnational/colombia/cases-all-time/summary/growth_rate.csv
subnational/colombia/cases-all-time/summary/latest_date.rds
subnational/colombia/cases-all-time/summary/reported_cases.csv
subnational/colombia/cases-all-time/summary/rt.csv
subnational/colombia/cases-all-time/summary/summary_data.csv
subnational/colombia/cases-all-time/summary/summary_table.csv
subnational/colombia/cases/summary/cases_by_infection.csv
subnational/colombia/cases/summary/cases_by_report.csv
subnational/colombia/cases/summary/growth_rate.csv
subnational/colombia/cases/summary/latest_date.rds
subnational/colombia/cases/summary/reported_cases.csv
subnational/colombia/cases/summary/rt.csv
subnational/colombia/cases/summary/summary_data.csv
subnational/colombia/cases/summary/summary_table.csv
subnational/germany/cases/summary/cases_by_infection.csv
subnational/germany/cases/summary/cases_by_report.csv
subnational/germany/cases/summary/growth_rate.csv
subnational/germany/cases/summary/latest_date.rds
subnational/germany/cases/summary/reported_cases.csv
subnational/germany/cases/summary/rt.csv
subnational/germany/cases/summary/summary_data.csv
subnational/germany/cases/summary/summary_table.csv
subnational/india/cases/summary/cases_by_infection.csv
subnational/india/cases/summary/cases_by_report.csv
subnational/india/cases/summary/growth_rate.csv
subnational/india/cases/summary/latest_date.rds
subnational/india/cases/summary/reported_cases.csv
subnational/india/cases/summary/rt.csv
subnational/india/cases/summary/summary_data.csv
subnational/india/cases/summary/summary_table.csv
subnational/italy/cases-all-time/summary/cases_by_infection.csv
subnational/italy/cases-all-time/summary/cases_by_report.csv
subnational/italy/cases-all-time/summary/growth_rate.csv
subnational/italy/cases-all-time/summary/latest_date.rds
subnational/italy/cases-all-time/summary/reported_cases.csv
subnational/italy/cases-all-time/summary/rt.csv
subnational/italy/cases-all-time/summary/summary_data.csv
subnational/italy/cases-all-time/summary/summary_table.csv
subnational/italy/cases/summary/cases_by_infection.csv
subnational/italy/cases/summary/cases_by_report.csv
subnational/italy/cases/summary/growth_rate.csv
subnational/italy/cases/summary/latest_date.rds
subnational/italy/cases/summary/reported_cases.csv
subnational/italy/cases/summary/rt.csv
subnational/italy/cases/summary/summary_data.csv
subnational/italy/cases/summary/summary_table.csv
subnational/russia/cases/summary/cases_by_infection.csv
subnational/russia/cases/summary/cases_by_report.csv
subnational/russia/cases/summary/growth_rate.csv
subnational/russia/cases/summary/latest_date.rds
subnational/russia/cases/summary/reported_cases.csv
subnational/russia/cases/summary/rt.csv
subnational/russia/cases/summary/summary_data.csv
subnational/russia/cases/summary/summary_table.csv
subnational/south-africa/cases/summary/cases_by_infection.csv
subnational/south-africa/cases/summary/cases_by_report.csv
subnational/south-africa/cases/summary/growth_rate.csv
subnational/south-africa/cases/summary/latest_date.rds
subnational/south-africa/cases/summary/reported_cases.csv
subnational/south-africa/cases/summary/rt.csv
subnational/south-africa/cases/summary/summary_data.csv
subnational/south-africa/cases/summary/summary_table.csv
subnational/south-africa/deaths/summary/cases_by_infection.csv
subnational/south-africa/deaths/summary/cases_by_report.csv
subnational/south-africa/deaths/summary/growth_rate.csv
subnational/south-africa/deaths/summary/latest_date.rds
subnational/south-africa/deaths/summary/reported_cases.csv
subnational/south-africa/deaths/summary/rt.csv
subnational/south-africa/deaths/summary/summary_data.csv
subnational/south-africa/deaths/summary/summary_table.csv
subnational/test/cases/summary/cases_by_infection.csv
subnational/test/cases/summary/cases_by_report.csv
subnational/test/cases/summary/growth_rate.csv
subnational/test/cases/summary/latest_date.rds
subnational/test/cases/summary/reported_cases.csv
subnational/test/cases/summary/rt.csv
subnational/test/cases/summary/summary_data.csv
subnational/test/cases/summary/summary_table.csv
subnational/united-kingdom-local/admissions/summary/cases_by_infection.csv
subnational/united-kingdom-local/admissions/summary/cases_by_report.csv
subnational/united-kingdom-local/admissions/summary/growth_rate.csv
subnational/united-kingdom-local/admissions/summary/latest_date.rds
subnational/united-kingdom-local/admissions/summary/reported_cases.csv
subnational/united-kingdom-local/admissions/summary/rt.csv
subnational/united-kingdom-local/admissions/summary/summary_data.csv
subnational/united-kingdom-local/admissions/summary/summary_table.csv
subnational/united-kingdom-local/cases/summary/cases_by_infection.csv
subnational/united-kingdom-local/cases/summary/cases_by_report.csv
subnational/united-kingdom-local/cases/summary/growth_rate.csv
subnational/united-kingdom-local/cases/summary/latest_date.rds
subnational/united-kingdom-local/cases/summary/reported_cases.csv
subnational/united-kingdom-local/cases/summary/rt.csv
subnational/united-kingdom-local/cases/summary/summary_data.csv
subnational/united-kingdom-local/cases/summary/summary_table.csv
subnational/united-kingdom-local/deaths/summary/cases_by_infection.csv
subnational/united-kingdom-local/deaths/summary/cases_by_report.csv
subnational/united-kingdom-local/deaths/summary/growth_rate.csv
subnational/united-kingdom-local/deaths/summary/latest_date.rds
subnational/united-kingdom-local/deaths/summary/reported_cases.csv
subnational/united-kingdom-local/deaths/summary/rt.csv
subnational/united-kingdom-local/deaths/summary/summary_data.csv
subnational/united-kingdom-local/deaths/summary/summary_table.csv
subnational/united-kingdom/admissions/summary/cases_by_infection.csv
subnational/united-kingdom/admissions/summary/cases_by_report.csv
subnational/united-kingdom/admissions/summary/growth_rate.csv
subnational/united-kingdom/admissions/summary/latest_date.rds
subnational/united-kingdom/admissions/summary/reported_cases.csv
subnational/united-kingdom/admissions/summary/rt.csv
subnational/united-kingdom/admissions/summary/summary_data.csv
subnational/united-kingdom/admissions/summary/summary_table.csv
subnational/united-kingdom/cases-all-time/summary/latest_date.rds
subnational/united-kingdom/cases-all-time/summary/reported_cases.csv
subnational/united-kingdom/cases/summary/cases_by_infection.csv
subnational/united-kingdom/cases/summary/cases_by_report.csv
subnational/united-kingdom/cases/summary/growth_rate.csv
subnational/united-kingdom/cases/summary/latest_date.rds
subnational/united-kingdom/cases/summary/reported_cases.csv
subnational/united-kingdom/cases/summary/rt.csv
subnational/united-kingdom/cases/summary/summary_data.csv
subnational/united-kingdom/cases/summary/summary_table.csv
subnational/united-kingdom/deaths/summary/cases_by_infection.csv
subnational/united-kingdom/deaths/summary/cases_by_report.csv
subnational/united-kingdom/deaths/summary/growth_rate.csv
subnational/united-kingdom/deaths/summary/latest_date.rds
subnational/united-kingdom/deaths/summary/reported_cases.csv
subnational/united-kingdom/deaths/summary/rt.csv
subnational/united-kingdom/deaths/summary/summary_data.csv
subnational/united-kingdom/deaths/summary/summary_table.csv
subnational/united-states/cases/summary/cases_by_infection.csv
subnational/united-states/cases/summary/cases_by_report.csv
subnational/united-states/cases/summary/growth_rate.csv
subnational/united-states/cases/summary/latest_date.rds
subnational/united-states/cases/summary/reported_cases.csv
subnational/united-states/cases/summary/rt.csv
subnational/united-states/cases/summary/summary_data.csv
subnational/united-states/cases/summary/summary_table.csv
subnational/vietnam/cases/summary/cases_by_infection.csv
subnational/vietnam/cases/summary/cases_by_report.csv
subnational/vietnam/cases/summary/growth_rate.csv
subnational/vietnam/cases/summary/latest_date.rds
subnational/vietnam/cases/summary/reported_cases.csv
subnational/vietnam/cases/summary/rt.csv
subnational/vietnam/cases/summary/summary_data.csv
subnational/vietnam/cases/summary/summary_table.csv
tests/testthat.R
tests/testthat/test-lists.R
tests/testthat/test-utils.R
utils/runtime_analysis.py
