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Clean polygon topology in a GeoPackage layer using GDAL and Mapshaper

Source: R/clean_geom.R
clean_gpkg_layer.Rd

Extracts a polygon layer from a GeoPackage, reprojects it to EPSG:4326, runs `mapshaper -clean` to repair polygon topology, reprojects the cleaned output back to the original coordinate reference system, and overwrites the original layer in the source GeoPackage.

Usage

clean_gpkg_layer(
  gpkg,
  layer,
  mapshaper = "mapshaper",
  ogr2ogr = "ogr2ogr",
  gdalsrsinfo = "gdalsrsinfo",
  snap_interval = NULL,
  gap_fill_area = NULL,
  overlap_rule = NULL,
  verbose = FALSE
)

Arguments

gpkg

Character scalar. Path to the input GeoPackage.

layer

Character scalar. Name of the layer in `gpkg` to clean.

mapshaper

Character scalar. Path to the `mapshaper` executable. Defaults to `"mapshaper"`, assuming it is available on the system path.

ogr2ogr

Character scalar. Path to the `ogr2ogr` executable. Defaults to `"ogr2ogr"`.

gdalsrsinfo

Character scalar. Path to the `gdalsrsinfo` executable. Defaults to `"gdalsrsinfo"`.

snap_interval

Optional numeric or character scalar. Passed to `mapshaper -clean` as `snap-interval=...`. Use this to snap nearby vertices before topology repair. Because cleaning occurs in EPSG:4326, this value is interpreted in decimal degrees.

gap_fill_area

Optional numeric or character scalar. Passed to `mapshaper -clean` as `gap-fill-area=...`. Controls the maximum enclosed gap area that will be filled.

overlap_rule

Optional character scalar. Passed to `mapshaper -clean` as `overlap-rule=...`. Controls how overlap areas are assigned. Common values include `"max-area"`, `"min-area"`, `"max-id"`, and `"min-id"`.

verbose

Logical scalar. If `TRUE`, print step-by-step progress, commands, and captured CRS detection output.

Value

Invisibly returns a named list with:

gpkg

Path to the GeoPackage that was modified.

layer

Layer name that was cleaned.

original_srs

The CRS definition used to project the cleaned layer back to its original coordinate system.

tmp_files

Named character vector of temporary intermediate files used during processing. These are scheduled for deletion on exit.

Details

This function is intended for polygon datasets that may contain small overlaps, enclosed gaps, or minor boundary misalignments that prevent a clean polygon mosaic. The topology repair is performed in geographic coordinates because `mapshaper -clean` is often more reliable there for mixed-source inputs, after which the data are restored to their original CRS.

The function relies on external command line tools:

  • `ogr2ogr` for layer extraction, reprojection, and overwrite

  • `gdalsrsinfo` for recovering the original CRS definition

  • `mapshaper` for polygon cleaning

CRS detection prefers an EPSG code, then a PROJ string, and finally a simple WKT representation as a fallback.

The processing steps are:

  1. Extract the requested layer from the source GeoPackage into a temporary single-layer GeoPackage.

  2. Detect the original CRS using `gdalsrsinfo`, preferring EPSG output.

  3. Reproject the temporary layer to EPSG:4326 and write it as GeoJSON.

  4. Run `mapshaper -clean` on the EPSG:4326 GeoJSON.

  5. Reproject the cleaned output back to the original CRS.

  6. Overwrite the original layer in the input GeoPackage.

Temporary files are created in `tempdir()` and removed with `on.exit()`.

The function assumes the target layer contains polygonal data appropriate for `mapshaper -clean`. It may still run on other geometry types, but the repair behavior is designed for polygon topology.

Requirements

The following executables must be installed and available:

  • GDAL tools: `ogr2ogr`, `gdalsrsinfo`

  • Mapshaper CLI

On many systems, Mapshaper can be installed with:


npm install -g mapshaper

Caveats

  • Cleaning is performed in EPSG:4326, so `snap_interval` is interpreted in angular units, not the source layer's native units.

  • Overwriting replaces the original layer in the GeoPackage.

  • Attribute preservation depends on the behavior of `ogr2ogr` and `mapshaper`; field ordering and some metadata may change.

  • Very large layers may require substantial temporary disk space.

Examples

if (FALSE) { # \dontrun{
clean_gpkg_layer(
  gpkg = "data/hydrofabric.gpkg",
  layer = "divides"
)

clean_gpkg_layer(
  gpkg = "data/hydrofabric.gpkg",
  layer = "catchments",
  snap_interval = 1e-7,
  overlap_rule = "max-area",
  verbose = TRUE
)

clean_gpkg_layer(
  gpkg = "data/hydrofabric.gpkg",
  layer = "basins",
  gap_fill_area = 0,
  mapshaper = "/usr/local/bin/mapshaper",
  ogr2ogr = "/opt/homebrew/bin/ogr2ogr",
  gdalsrsinfo = "/opt/homebrew/bin/gdalsrsinfo"
)
} # }