Import data from SORMAS

The function returns the following columns by default: case_id, person_id, sex, date_of_birth, case_origin, country, city, latitude, longitude, case_status, date_onset, date_admission, outcome, date_outcome, contact_id, date_last_contact, date_first_contact, Ct_values.

Usage

read_sormas(login, disease, since = 0)

Arguments

login

A list with the user's authentication details

disease

A character with the target disease name

since

A Date value in ISO8601 format (YYYY-mm-dd). Default is 0 i.e. to fetch all cases from the beginning of data collection.

Value

A data frame with the case data of the specified disease.

Details

Note that the some values in the date_of_birth column of the output object might not have some missing elements such a missing year (NA-12-26), month (2025-NA-01) or date (2025-12-NA), or a combination of two missing elements.

Examples

# establish the connection to the SORMAS system
sormas_login <- login(
  type = "sormas",
  from = "https://demo.sormas.org/sormas-rest",
  user_name = "SurvSup",
  password = "Lk5R7JXeZSEc"
)
# fetch all COVID (coronavirus) cases from the test SORMAS instance
covid_cases <- read_sormas(
  login = sormas_login,
  disease = "coronavirus"
)
#> ℹ Checking whether the disease names are correct.
#> ✔ Checking whether the disease names are correct. [532ms]
#> 
#> ℹ Getting clinical data
#> ! outcomeDate not found for cases with the specified diseases.
#> ℹ Getting clinical data

#> ✔ Getting clinical data [403ms]
#> 
#> ℹ Getting socio-demographic data
#> ✔ Getting socio-demographic data [11.2s]
#> 
#> ℹ Getting contact data
#> ✔ Getting contact data [524ms]
#> 
#> ℹ Getting laboratory tests data
#> ✔ Getting laboratory tests data [231ms]
#>