├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENCE.md ├── NAMESPACE ├── R ├── download_book.R ├── get_data.R └── handbookfiles-package.R ├── README.Rmd ├── README.md ├── epirhandbook.Rproj ├── inst ├── extdata │ ├── cache │ │ └── epidemic_models │ │ │ ├── 2015-04-30 │ │ │ ├── estimate_samples.rds │ │ │ ├── estimated_reported_cases_samples.rds │ │ │ ├── latest_date.rds │ │ │ ├── reported_cases.rds │ │ │ ├── summarised_estimated_reported_cases.rds │ │ │ ├── summarised_estimates.rds │ │ │ └── summary.rds │ │ │ ├── epinow_res.rds │ │ │ ├── epinow_res_small.rds │ │ │ ├── generation_time.rds │ │ │ └── incubation_period.rds │ ├── campylobacter_germany.xlsx │ ├── case_linelists │ │ ├── cleaning_dict.csv │ │ ├── linelist_cleaned.rds │ │ ├── linelist_cleaned.xlsx │ │ └── linelist_raw.xlsx │ ├── example │ │ ├── Central Hospital.csv │ │ ├── Military Hospital.csv │ │ ├── Missing.csv │ │ ├── Other.csv │ │ ├── Port Hospital.csv │ │ ├── St. Mark's Maternity Hospital (SMMH).csv │ │ ├── district_weekly_count_data.xlsx │ │ ├── fluH7N9_China_2013.csv │ │ ├── hospital_linelists.xlsx │ │ └── linelists │ │ │ ├── 20201007linelist.csv │ │ │ ├── case_linelist20201006.csv │ │ │ ├── case_linelist_2020-10-02.csv │ │ │ ├── case_linelist_2020-10-03.csv │ │ │ ├── case_linelist_2020-10-04.csv │ │ │ ├── case_linelist_2020-10-05.csv │ │ │ └── case_linelist_2020-10-08.xlsx │ ├── flexdashboard │ │ ├── outbreak_dashboard.Rmd │ │ ├── outbreak_dashboard_test.Rmd │ │ └── outbreak_dashboard_test.html │ ├── gis │ │ ├── africa_countries.geo.json │ │ ├── covid_incidence.csv │ │ ├── covid_incidence_map.R │ │ ├── linelist_cleaned_with_adm3.rds │ │ ├── population │ │ │ ├── sle_admpop_adm3_2020.csv │ │ │ └── sle_population_statistics_sierraleone_2020.xlsx │ │ └── shp │ │ │ ├── README.txt │ │ │ ├── sle_adm3.CPG │ │ │ ├── sle_adm3.dbf │ │ │ ├── sle_adm3.prj │ │ │ ├── sle_adm3.sbn │ │ │ ├── sle_adm3.sbx │ │ │ ├── sle_adm3.shp │ │ │ ├── sle_adm3.shp.xml │ │ │ ├── sle_adm3.shx │ │ │ ├── sle_hf.CPG │ │ │ ├── sle_hf.dbf │ │ │ ├── sle_hf.prj │ │ │ ├── sle_hf.sbn │ │ │ ├── sle_hf.sbx │ │ │ ├── sle_hf.shp │ │ │ └── sle_hf.shx │ ├── likert_data.csv │ ├── linelist_cleaned.xlsx │ ├── make_evd_dataset.R │ ├── malaria_facility_count_data.rds │ ├── phylo │ │ ├── Shigella_subtree_2.nwk │ │ ├── Shigella_subtree_2.txt │ │ ├── Shigella_tree.txt │ │ └── sample_data_Shigella_tree.csv │ ├── standardization │ │ ├── country_demographics.csv │ │ ├── country_demographics_2.csv │ │ └── world_standard_population_by_sex.csv │ └── weather │ │ ├── germany_weather2002.nc │ │ ├── germany_weather2003.nc │ │ ├── germany_weather2004.nc │ │ ├── germany_weather2005.nc │ │ ├── germany_weather2006.nc │ │ ├── germany_weather2007.nc │ │ ├── germany_weather2008.nc │ │ ├── germany_weather2009.nc │ │ ├── germany_weather2010.nc │ │ └── germany_weather2011.nc ├── file_lookup.R └── file_lookup.rds └── man ├── download_book.Rd ├── epirhandbook-package.Rd └── 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