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Clean WHO administrative spatial data

Source: R/spatial.R
process_spatial.Rd

Reads the country (ADM0), province (ADM1) and district (ADM2) boundary layers from any source sf can open and turns each into a cleaned, validity-checked, reprojected sf object written to output_dir. For ADM1 and ADM2 a year-expanded "long" shape (one row per active year) is also written, ready for temporal point-in-polygon joins.

Usage

process_spatial(
  input_path,
  output_dir,
  layers = c(adm0 = "GLOBAL_ADM0", adm1 = "GLOBAL_ADM1", adm2 = "GLOBAL_ADM2"),
  transform = TRUE,
  crs = 4326,
  fix_issues = TRUE,
  sliver_area = 10000,
  output_format = "rds",
  verbose = TRUE
)

Arguments

input_path

Path to the spatial source: a .gdb / .gpkg dataset, or a folder of standalone .shp / .gpkg / .geojson files.

output_dir

Directory for cleaned outputs and the checks/ subfolder.

layers

Named character vector mapping admin levels to a layer name (for a .gdb / .gpkg) or a filename stem (for a folder of files). Names must be a subset of adm0 / adm1 / adm2; only the levels present are processed, so pass a single entry to clean one level. Matching is case-insensitive, preferring an exact match and otherwise the substring match. Defaults to all three WHO GLOBAL_ADM* layers.

transform

Whether to reproject each layer to crs. The reprojection is skipped automatically when a layer's CRS is already equivalent to crs (ignoring cosmetic CRS-label differences), so no coordinates are swept needlessly. Default TRUE.

crs

Target CRS as an EPSG code. Default 4326 (WGS84).

fix_issues

Whether to repair geometries (in addition to flagging them): drop Z/M dimensions, make invalid geometries valid (sf::st_make_valid()), and strip sliver holes and sliver polygon parts smaller than sliver_area. Real enclaves, lakes and islands above the threshold are kept, and a feature never loses its largest part. Set FALSE for the fastest run (flag-only). Default TRUE.

sliver_area

Area threshold in square metres below which interior holes and detached polygon parts are treated as digitising artifacts and removed when fix_issues = TRUE. Default 1e4 (1 hectare).

output_format

Serialization format for the cleaned shapes, "rds" or "qs2". "qs2" writes and reads large geometries far faster (needs the qs2 package). Default "rds".

verbose

Whether to print a cli progress summary. Default TRUE.

Value

output_dir, invisibly. The function's outputs are the files it writes ({ext} is output_format):

  • spatial_global_{level}.{ext}: cleaned per-level shapes;

  • spatial_{level}_long_shape.{ext}: year-expanded shapes (ADM1, ADM2);

  • checks/spatial_*_{level}_*.csv: any validity/duplicate issues.

Details

input_path may be any of:

  • an Esri geodatabase (.gdb) or GeoPackage (.gpkg) holding the three admin layers, matched by name via layers;

  • a folder of standalone files – shapefiles (.shp), GeoPackages (.gpkg) or GeoJSON (.geojson / .json) – one per level, matched by filename via layers.

Per layer the cleaner:

  • reads the layer and snake_cases its columns (via janitor);

  • parses startdate / enddate to lubridate::Date and derives year_start / year_end;

  • normalises the Cote d'Ivoire country name;

  • renames the admin name columns to the package's canonical adm0 / adm1 / adm2, the level GUID column to adm0_guid / adm1_guid / adm2_guid, and the geometry column to shape;

  • runs validity, empty-geometry and duplicate (GUID and name) checks, writing a CSV per issue found into a checks/ subfolder;

  • when fix_issues = TRUE, repairs geometries: drops Z/M, makes invalid geometries valid, and removes sliver holes and sliver polygon parts below sliver_area;

  • reprojects to crs when transform is TRUE.

Examples

if (FALSE) { # \dontrun{
# an Esri geodatabase with the GLOBAL_ADM* layers
process_spatial("path/to/who.gdb", output_dir = "outputs/spatial")

# a folder of shapefiles named adm0.shp / adm1.shp / adm2.shp
process_spatial(
  "path/to/shapefiles",
  output_dir = "outputs/spatial",
  layers = c(adm0 = "adm0", adm1 = "adm1", adm2 = "adm2")
)
} # }