Extract malaria metrics from the Malaria Atlas Project GeoServer

Downloads modeled malaria raster surfaces from the Malaria Atlas Project (MAP) GeoServer via WCS 2.0.1, extracts zonal statistics for a user-defined region and time range, and returns an sf or tibble.

Available species: Plasmodium falciparum ("pf") and Plasmodium vivax ("pv"). Available measures: "incidence_rate", "incidence_count", "parasite_rate", "mortality_rate", "mortality_count". The function automatically selects the latest release available on the server for the requested species + measure combination.

Usage

l4h_malaria(
  from,
  to,
  species = "pf",
  measure = "incidence_rate",
  region,
  stat = "mean",
  sf = TRUE,
  quiet = FALSE,
  force = FALSE,
  ...
)

Arguments

from

Integer. Start year.

to

Integer. End year. Must be >= from.

species

Character. One of "pf" (Plasmodium falciparum) or "pv" (Plasmodium vivax). Default "pf".

measure

Character. One of "incidence_rate", "incidence_count", "parasite_rate", "mortality_rate", "mortality_count". Default "incidence_rate".

region

Spatial object defining the region of interest. Accepts an sf, sfc, or SpatVector object.

stat

Character. Summary statistic per pixel per year. One of "mean", "median", "min", "max". Default "mean".

sf

Logical. If TRUE, returns an sf; if FALSE, returns a tibble. Default TRUE.

quiet

Logical. If TRUE, suppresses progress messages. Default FALSE.

force

Logical. If TRUE, skips the representativity check. Default FALSE.

...

Additional arguments (currently unused).

Value

An sf or tibble with columns:

• date (Date, first day of year),

• species (character, "pf" or "pv"),

• measure (character, the requested measure),

• value (numeric, in native units), plus geometry if sf = TRUE, and any attributes from region.

Details

The MAP GeoServer provides modeled global raster surfaces at ~5 km resolution. Rates are expressed per person (0-1 scale for parasite rate, per 1,000 for incidence), and counts are absolute numbers. The function connects to the GeoServer via ows4R::WCSClient, downloads the coverage clipped to the region bounding box, and uses terra::extract() for zonal statistics.

Credits

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

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References

Malaria Atlas Project. https://malariaatlas.org/

Examples

# \donttest{
if (interactive()) {
library(land4health)

# ROI simple (EPSG:4326)
region <- st_as_sf(st_sfc(
  st_polygon(list(matrix(c(
    -74.1, -4.4,
    -74.1, -3.7,
    -73.2, -3.7,
    -73.2, -4.4,
    -74.1, -4.4
  ), ncol = 2, byrow = TRUE))), crs = 4326))

# Pf incidence rate 2015-2020
out <- l4h_malaria(
  from    = 2015,
  to      = 2020,
  species = "pf",
  measure = "incidence_rate",
  region  = region
)
head(out)

# Pv parasite rate
out_pv <- l4h_malaria(
  from    = 2020,
  to      = 2022,
  species = "pv",
  measure = "parasite_rate",
  region  = region,
  sf      = FALSE
)
head(out_pv)
}
# }