R/mers_korea_2015.R
mers_korea_2015.RdThese datasets correspond to the initial information collected by the Epidemic Intelligence group at European Centre for Disease Prevention and Control (ECDC) during the first weeks of the outbreak of Middle East respiratory syndrome (MERS-CoV) outbreak (South Korea) in 2015. The data were used to follow the daily evolution of this outbreak using public information available.
mers_korea_2015
A list of two dataframes:
$linelist: A dataframe of MERS-CoV cases and their attributes
id: Unique identifier
age: Age
age_class: Age using 10-year groups
sex: Sex
place_infect: Probable region of infection
reporting_ctry: Country reporting the case
loc_hosp: Local hospital name where the case was hospitalized
dt_onset: Date of onset of symptoms
dt_report: Date of reporting
week_report: Week number of date of reporting
dt_start_exp: Date of first probable exposure to another MERS Co-V case
dt_end_exp: Date of last probable exposure to another MERS Co-V case
dt_diag: Date of MERS Co-V diagnosis
outcome: Outcome (alive or dead)
dt_death: Date of death
$contacts: A dataframe describing the relationship between MERS Co-V cases
from: Unique identifier of the probably source patient
to: Unique identifier of the secondary case
exposure: Probable place of exposure
diff_dt_onset: Time in days between two successive cases
This dataset is meant for teaching purposes; it represents neither the final outbreak investigation results nor a consolidated and complete description of the transmission chain.
More information on the intial stage of the outbreak in the following reference: Penttinen PM, Kaasik-Aaslav K, Friaux A, Donachie A, Sudre B, Amato-Gauci AJ, Memish ZA, Coulombier D. Taking stock of the first 133 MERS coronavirus cases globally--Is the epidemic changing? Euro Surveill. 2013 Sep 26;18(39). pii: 20596. PubMed PMID: 24094061.
Data collected by the European Centre for Disease Prevention and Control (Epidemic Intelligence and Response section, contact: Bertrand Sudre ( ) and Kaja Kaasik Aaslav(Kaja.KaasikAaslav@ecdc.europa.eu). Transfer to R and documentation by Bertrand Sudre ( bertrand.sudre@ecdc.europa.eu).
## show the line list describing MERS Co-V cases and their attributes head(mers_korea_2015$linelist)#> id age age_class sex place_infect reporting_ctry #> 1 SK_1 68 60-69 M Middle East South Korea #> 2 SK_2 63 60-69 F Outside Middle East South Korea #> 3 SK_3 76 70-79 M Outside Middle East South Korea #> 4 SK_4 46 40-49 F Outside Middle East South Korea #> 5 SK_5 50 50-59 M Outside Middle East South Korea #> 6 SK_6 71 70-79 M Outside Middle East South Korea #> loc_hosp dt_onset dt_report #> 1 Pyeongtaek St. Mary, Hospital, Pyeongtaek, Gyeonggi 2015-05-11 2015-05-19 #> 2 Pyeongtaek St. Mary, Hospital, Pyeongtaek, Gyeonggi 2015-05-18 2015-05-20 #> 3 Pyeongtaek St. Mary, Hospital, Pyeongtaek, Gyeonggi 2015-05-20 2015-05-20 #> 4 Pyeongtaek St. Mary, Hospital, Pyeongtaek, Gyeonggi 2015-05-25 2015-05-26 #> 5 365 Yeollin Clinic, Seoul 2015-05-25 2015-05-27 #> 6 Pyeongtaek St. Mary, Hospital, Pyeongtaek, Gyeonggi 2015-05-24 2015-05-28 #> week_report dt_start_exp dt_end_exp dt_diag outcome dt_death #> 1 2015_21 2015-04-18 2015-05-04 2015-05-20 Alive <NA> #> 2 2015_21 2015-05-15 2015-05-20 2015-05-20 Alive <NA> #> 3 2015_21 2015-05-16 2015-05-16 2015-05-21 Dead 2015-06-04 #> 4 2015_22 2015-05-16 2015-05-20 2015-05-26 Alive <NA> #> 5 2015_22 2015-05-17 2015-05-17 2015-05-26 Alive <NA> #> 6 2015_22 2015-05-15 2015-05-17 2015-05-28 Dead 2015-06-01#> from to exposure diff_dt_onset #> 1 SK_14 SK_113 Emergency room 10 #> 2 SK_14 SK_116 Emergency room 13 #> 3 SK_14 SK_41 Emergency room 14 #> 4 SK_14 SK_112 Emergency room 14 #> 5 SK_14 SK_100 Emergency room 15 #> 6 SK_14 SK_114 Emergency room 15