Extract dengue case data from OpenDengue

A global database of publicly available dengue case data. The OpenDengue Project provides a harmonized, open-access repository of dengue surveillance data from national ministries of health across Latin America and other regions. This function enables programmatic access to weekly case counts by downloading, caching, unzipping, reading, and filtering national, spatial, or temporal extracts by region and country for a specified date range, returning a ready-to-use tibble.

Usage

l4h_dengue_cases(
  from,
  to,
  data_type = c("temporal", "spatial", "national"),
  region = NULL,
  country = "Peru",
  cache = TRUE,
  quiet = FALSE
)

Source

Data from the OpenDengue Project.

Arguments

from: Start date (YYYY-MM-DD).
to: End date (YYYY-MM-DD).
data_type: One of "national", "spatial", or "temporal".
region: Region code or full name (case-insensitive). Codes: "paho", "searo", "wpro", "afro", "emro", "euro". Full names: "Pan-American Region", "South-East Asia Region", "Western Pacific Region", "African Region", "Eastern Mediterranean Region", "European Region".
country: Country name (case-insensitive, e.g., "peru"), matched against adm_0_name.
cache: Logical. If TRUE, caches the downloaded ZIP locally.
quiet: Logical. If TRUE, prints progress status via cli.

Value

A tibble with columns: date_start, date_end, cases, state, area, plus other fields.

Credits

Pioneering geospatial health analytics and open‐science tools. Developed by the Innovalab Team, for more information send a email to imt.innovlab@oficinas-upch.pe

References

Morales, I. et al. (2024). OpenDengue: Harmonized dengue surveillance data for Latin America.

Examples

if (interactive()) {
  # National extract for Peru in 2019
  df_nat <- l4h_dengue_cases(
    from = "2019-01-01",
    to = "2019-12-31",
    data_type = "national",
    region = "paho",
    country = "peru",
    cache = TRUE,
    quiet = TRUE
  )
  head(df_nat)

  # Spatial extract for Brazil
  df_spat <- l4h_dengue_cases(
    from = "2021-01-01",
    to = "2021-12-31",
    data_type = "spatial",
    region = "Pan-American Region",
    country = "brazil",
    cache = TRUE,
    quiet = TRUE
  )
  head(df_spat)

  # Temporal extract for Argentina
  df_temp <- l4h_dengue_cases(
    from = "2020-01-01",
    to = "2020-12-31",
    data_type = "temporal",
    region = "PAHO",
    country = "Argentina",
    cache = TRUE,
    quiet = TRUE
  )
  head(df_temp)
}