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

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

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