Skip to contents

Pull MPOX Case and Death Data

get_mpx_cases.Rd

This function provides a standardized interface to read in CDC Monkeypox line-list data from local path, Sharepoint/Teams, or Azure DataLake. The interface is liable to change as longer-term data storage changes.

Usage

get_mpx_cases(path, connection = NULL, include_endemic = TRUE)

get_mpx_deaths(path, connection = NULL, include_endemic = TRUE)

Arguments

path

character string path to MPX data

connection

(optional) an spoConnection or AzureStor::storage_container object

include_endemic

(boolean, default: TRUE) should data from MPX endemic countries be included?

Value

A data frame with n rows and 4 variables:

  • Country character English name for administrative region

  • date date reporting date

  • cases integer cumulative monkeypox cases

  • iso3code character ISO 3166-1 alpha-3 country code

Details

In the past, all MPOX data was "wide", where the first column is Country, and the following columns are dates. This was pivoted internally to "long", and ISO code inferred from Country column.

The default is now a "long" dataset, which doesn't require this processing (includes ISO code, country name, and date columns).

Examples

if (FALSE) {
# Using local path (on your PC or from shared drive)
path <- "<path_to_my_dir>/mpx_data.csv"

get_mpx_cases(path)

# From Sharepoint / MS Teams (remotely)
# In this case, path should be relative to the Shared Documents folder
spo_path <- "<My Sharepoint Folder>/mpx_data.csv"
spo_con <- spoConnection$new(
  tenant = "Tennant-Id",
  client_id = Sys.getenv("CLIENT-ID"),
  client_secret = Sys.getenv("CLIENT-SECRET"),
  teams_name = "My-Team-Name"
)

get_mpx_cases(spo_path, connection = spo_con)

# From Azure Data Lake

azdl_path <- "<path_to_azdl_folder>/mpx_data.csv"

# Retrieve token using app registration
token <- AzureRMR::get_azure_token(
  "https://storage.azure.com",
  tenant = Sys.getenv("AZURE_TENANT_ID"),
  app = Sys.getenv("AZURE_APP_ID"),
  password = Sys.getenv("AZURE_APP_SECRET")
)

# We use the Blob URL, but DFS should work too
azdl_con <- AzureStor::storage_container("https://<my_azdl_site>.blob.core.windows.net/<my_azdl_container>/", token = token)

get_mpx_cases(azdl_path, connection = azdl_con)
}