Package index • appliedepidata

Functions

list_data(): List Datasets in a Package
search_data(): Search and Filter Datasets Available in appliedepidata
get_data(): Retrieve and Load Datasets
save_data(): Save Data Files to a Specified Directory
create_desc(): Create Description of Variables for Roxygen Documentation

Data

AJS in Am Timan, Chad (2016) - English

AJS_AmTiman: Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
AJS_AmTiman_population: Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
Blocksshape: Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
Quartiersshape: Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016

Feveriosis surveillance data, Feveria (2025) - English

feveriosis_main: Feveriosis surveillance data from Viraland from Jan 1 2025 to Aug 31 2026
feveriosis_recent: Recent feveriosis surveillance data from Viraland from Aug 31 2026 to Sep 4 2026

Feveriosis surveillance data, Feveria (2025) - French

feveriosis_main_fr: Feveriosis surveillance data from Viraland from Jan 1 2025 to Aug 31 2026 \(French\)
feveriosis_recent_fr: Recent feveriosis surveillance data from Viraland from Aug 31 2026 to Sep 4 2026 \(French\)

Feveriosis surveillance data, Feveria (2025) - Spanish

feveriosis_main_es: Feveriosis surveillance data from Viraland from Jan 1 2025 to Aug 31 2026 \(Spanish\)
feveriosis_recent_es: Recent feveriosis surveillance data from Viraland from Aug 31 2026 to Sep 4 2026 \(Spanish\)

Feveriosis surveillance data, Feveria (2025) - Portuguese

feveriosis_main_pt: Feveriosis surveillance data from Viraland from Jan 1 2025 to Aug 31 2026 \(Portuguese\)
feveriosis_recent_pt: Recent feveriosis surveillance data from Viraland from Aug 31 2026 to Sep 4 2026 \(Portuguese\)

Feveriosis surveillance data, Feveria (2025) - Russian

feveriosis_main_ru: Feveriosis surveillance data from Viraland from Jan 1 2025 to Aug 31 2026 \(Russian\)
feveriosis_recent_ru: Recent feveriosis surveillance data from Viraland from Aug 31 2026 to Sep 4 2026 \(Russian\)

Multidisease lab and surveillance data, Feveria (2024) - English

multidisease_tests: Test results for notifiable disease surveillance cases in Feveria in 2024
multidisease_notifications: Notifiable disease surveillance data from Feveria in 2024

Multidisease lab and surveillance data, Feveria (2024) - French

multi_maladies_tests: Test results for notifiable disease surveillance cases in Feveria in 2024 \(French\)
multi_maladies_notifications: Notifiable disease surveillance data from Feveria in 2024 \(French\)

Multidisease lab and surveillance data, Feveria (2024) - Spanish

pruebas_multienfermedad: Test results for notifiable disease surveillance cases in Feveria in 2024 \(Spanish\)
notificaciones_multienfermedad: Notifiable disease surveillance data from Feveria in 2024 \(Spanish\)

Multidisease lab and surveillance data, Feveria (2024) - Portuguese

testes_multidoencas: Test results for notifiable disease surveillance cases in Feveria in 2024 \(Portuguese\)
notificacoes_multidoencas: Notifiable disease surveillance data from Feveria in 2024 \(Portuguese\)

Sitrep example datasets - English

mortality_survey_data: Fake data for a mortality survey
mortality_survey_dict: Fake data dictionary for a mortality survey

COVID-19 data in Fulton County, USA (2020) - English

fulton_data: Anonymized COVID-19 linelist data from Fulton County (USA), 2020
fulton_data_clean: Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020
fulton_population: Zip-code population data Fulton County (USA), 2020

Fictional Mpox data from 5 European countries (2022) - English

mpox_linelist: Fictional mpox linelist data from five European countries, 2022
mpox_aggregate_table: Fictional cumulative mpox case totals from five European countries, 2022

Fictional linelist data from Salmonella outbreak in Stegen, Germany (1998) - English

stegentira_data: Linelist for fictionalized salmonella outbreak in Stegen, Germany

Influenza A H7N9 data in China (2013) - English

fluH7N9_China_2013: Linelist data from an outbreak of influenza A H7N9 in China 2013.

Fictional linelist data from Ebola outbreak in Sierra Leone (2014) - English

linelist_raw: Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
linelist_cleaned_excel: Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
linelist_cleaned_rds: Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
hospital_linelists: Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
linelist_cleaned_with_adm3: Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
linelist_cleaned: Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 (plain copy)
cleaning_dict: Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014
sle_adm3: Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange
sle_admpop_adm3_2020: Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange
epinow_res epinow_res_small generation_time incubation_period: Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014

Fictional case data for a generic disease to demonstrate contact tracing (2020) - English

cases_clean contacts_clean followups_clean relationships_clean: Fictional case data for a generic disease to demonstrate contact tracing

Fictional counts of malaria cases from Mozambique (2019) - English

district_weekly_count_data: Fictional counts of malaria cases from Mozambique in 2019
malaria_facility_count_data: Fictional counts of malaria cases from Mozambique in 2019

Next generation sequencing data of Shigella surveillance samples from Belgium (2013-2019) - English

Shigella_tree: Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019
sample_data_Shigella_tree: Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019
Shigella_subtree_2: Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019

Fictional country demographic and mortality data to demonstrate standardisation (2020) - English

country_demographics country_demographics_2 deaths_countryA deaths_countryB: Fictional country demographic and mortality data to demonstrate standardisation
world_standard_population_by_sex: World “standard population” by sex

Other fictional example data

likert_data: Fictional likert data for demonstration purposes

Fictional data for a mortality survey - English

survey_data: Fake data for a mortality survey
survey_dict: Fake data dictionary for a mortality survey
population: Fake population data for a mortality survey

Campylobacter surveillance data from Germany (2001-2011) - English

campylobacter_germany: Linelist data of Campylobacter surveillance in Germany 2001-2011.
germany_weather: Weather data for Germany from 2001-2011
campylobacter_germany_epirh: Full linelist data of Campylobacter surveillance in Germany 2001-2011

Cholera surveillance data, Viraland (2021) - English

viraland_cholera_20210525_linelist: Clean cholera surveillance data for Viraland, 25 May 2021
viraland_cholera_20210617_linelist: Clean cholera surveillance data for Viraland, 17 June 2021
viraland_cholera_20210721_linelist: Clean cholera surveillance data for Viraland, 21 July 2021
viraland_cholera_20210721_linelist_raw: Raw cholera surveillance data for Viraland, 21 July 2021
viraland_cholera_20210721_labs: Lab data with cholera test results for Viraland, 21 July 2021

Case linelist cleaning bundle, Ebola outbreak in Sierra Leone (2014) - English

case_linelists_linelist_raw: Fictional case linelist data simulating properties from the West African Ebola outbreak of 2014
case_linelists_linelist_cleaned_excel: Cleaned fictional case linelist data (Excel) simulating properties from the West African Ebola outbreak of 2014
case_linelists_linelist_cleaned_rds: Cleaned fictional case linelist data (rds) simulating properties from the West African Ebola outbreak of 2014
case_linelists_cleaning_dict: Example data dictionary for fictional case linelist data simulating properties from the West African Ebola outbreak of 2014

Iteration/loops example - hospital linelists, Ebola outbreak in Sierra Leone (2014) - English

example_case_linelist_2020_10_08: Dated snapshot of fictional case linelist data simulating properties from the West African Ebola outbreak of 2014
example_hospital_linelists: Combined hospital linelists example, fictional Ebola Virus Disease data (West Africa, 2014)
example_central_hospital: Central Hospital subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)
example_military_hospital: Military Hospital subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)
example_port_hospital: Port Hospital subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)
example_st_marks_maternity_hospital: St. Mark's Maternity Hospital (SMMH) subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)
example_missing: Missing-hospital subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)
example_other: Other-hospital subset, fictional Ebola Virus Disease case linelist (West Africa, 2014)

Iteration/loops example - Influenza A H7N9 data in China (2013) - English

example_fluH7N9_China_2013: Linelist data from an outbreak of influenza A H7N9 in China 2013 (example copy)

Iteration/loops example - malaria cases from Mozambique (2019) - English

example_district_weekly_count_data: Fictional counts of malaria cases from Mozambique (example copy)

GIS basics mapping example, Sierra Leone (2020) - English

gis_population_sle_admpop_adm3_2020: Population data at admin level 3 for Sierra Leone (GIS basics example)
gis_linelist_cleaned_with_adm3: Cleaned fictional Ebola linelist joined with admin-3 spatial data (GIS basics example)
gis_covid_incidence: Fictional cumulative COVID-19 incidence by country (GIS basics example)
gis_population_sle_population_statistics_sierraleone_2020: Age/sex population proportions for Sierra Leone (GIS basics example)

GIS basics mapping example, Africa (2020) - English

gis_africa_countries: Africa country boundaries (GIS basics example)

Epidemic models example, Ebola outbreak in Sierra Leone (2014) - English

epidemic_models_epinow_res epidemic_models_epinow_res_small epidemic_models_generation_time epidemic_models_incubation_period: Outputs from epinow2, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_estimate_samples: Posterior estimate samples, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_estimated_reported_cases_samples: Posterior estimated-reported-cases samples, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_latest_date: Latest observation date, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_reported_cases: Reported case counts, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_summarised_estimated_reported_cases: Summarised estimated-reported-cases, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_summarised_estimates: Summarised estimates, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example
epidemic_models_summary: Model run summary, fictional Ebola outbreak in Sierra Leone (2014) - epidemic models example