sciSpatialR: Spatial Harmonization and Covariate Extraction

Provides tools for harmonizing spatial layers (masking, resampling, aggregating) and extracting covariates at point locations for Alberta-focused biodiversity and species distribution modelling workflows.

Reference Layers

Harmonization defaults to the Alberta provincial boundary and the ABMI 1 km grid, both in NAD83 / Alberta 10-TM (Forest), EPSG:3400. Every function below that takes a reference grid or boundary falls back to these, so layers harmonized with this package share one CRS, extent, resolution, and origin unless a caller opts out.

• ab_crs() — default CRS, "EPSG:3400"

• ab_boundary() — Alberta provincial boundary (2020 revision)

• ab_grid() — ABMI 1 km reference grid, 1234 x 695 cells

Input and Validation

• check_alignment() — test CRS, extent, resolution, and origin congruence against a reference grid

• harmonize_crs() — transform points to raster CRS; warn if raster reprojection would be implied

Inspection

• raster_stats() — per-layer cell counts, missingness, and value summaries

• plot_raster() — quick-look ggplot2 map with a quantile-stretched colour scale and boundary overlay

• plot_hist() — histogram of cell values

• theme_science_map() — the ggplot2 theme those maps use

Harmonization

• mask_to_boundary() — mask to Alberta or a user-supplied polygon

• resample_to_grid() — align to a reference grid, choosing the resampling method from the resolution ratio and whether the layer is categorical

Extraction

• extract_points() — point-in-cell raster extraction

• extract_vector() — point-in-polygon attribute join

• extract_proportion() — class proportions within buffer for categorical layers

• extract_buffer() — summary statistic within one or more radii

Catalogue and Metadata

The catalogue is built by scanning the spatial data share and parsing the readme stored beside each dataset, so it is always a description of the data as it actually sits on disk. Readmes follow the ABMI spatial metadata template documented in the geospatial catalog and management guide at https://github.com/bgcasey/geospatial_catalog_and_management_guide.

• spatial_root() — location of the data share

• build_catalogue() — scan the share into a manifest

• list_layers() — list catalogue contents

• list_themes() — list ISO 19115 theme folders

• find_layer() — filter by theme, keyword, year, extent, resolution, CRS

• get_layer() — return a SpatRaster, SpatVector, or path

• layer_files() — list a layer's data files

• layer_meta() — source, vintage, licence, caveats, contact

• read_metadata() — parse one readme

• as_metadata_row() — flatten metadata to a data.frame row

• check_metadata() — audit metadata completeness

See also

Useful links:

• https://ABbiodiversity.github.io/sciSpatialR/

• https://github.com/ABbiodiversity/sciSpatialR

• Report bugs at https://github.com/ABbiodiversity/sciSpatialR/issues

Author

Maintainer: Brendan Casey brendan.casey@ualberta.ca

Other contributors:

• Alberta Biodiversity Monitoring Institute [copyright holder, funder]