Package index • obisindicators

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Functions for reading data.

Functions for calculating indicators.

calc_indicators(): Calculate Biodiversity Indicators, including ES50 (Hurlbert index)

Build an H3 grid, and serve indicators as H3 hexagon tiles.

make_hex_res(): Make hexagon feature
build_obis_h3_duckdb(): Build the OBIS H3 DuckDB store
obis_h3t_sql(): Build an h3t tile SQL query for an OBIS biodiversity indicator
obis_h3t_url(): Assemble an h3t tile (or stats) URL for an OBIS indicator

Resolve children taxa (any rank), close the WoRMS coverage gap from the REST API, and the sightings-per-unit-effort (SPUE) proxy.

calc_spue(): Sightings-per-unit-effort (SPUE) effort proxy, per H3 cell (R reference)
obis_spue_sql(): Build an h3t tile SQL query for the SPUE effort proxy
obis_taxon_children(): Resolve the descendant taxa of a WoRMS AphiaID
obis_taxon_fill_gaps(): Fill gaps in the taxon table from the WoRMS REST API
obis_taxon_orphans(): AphiaIDs present in occ_h3 but missing from the taxon table
obis_taxon_subtree_sql(): Standalone SQL for the AphiaID subtree (descendant taxonIDs)
wm_aphia_records(): Look up WoRMS taxon records by AphiaID

GOOS/IOOS biology & ecosystems EOVs as WoRMS AphiaID subtrees, per the IOOS Marine Life Data Network definitions.

obis_eov_aphiaid(): AphiaID seeds for one or more EOVs
obis_eov_bake(): Bake the EOV membership and precomputed-indicator layers into a store
obis_eov_label(): Human-readable EOV label with its taxonomic definition
obis_eov_seeds(): Essential Ocean Variable (EOV) taxonomic seeds
obis_eov_sql(): Build an h3t tile SQL query for an Essential Ocean Variable

Functions for visualizing indicators.

Locally available datasets for running examples.

occ_1960s: OBIS occurrences, temporal sample for the 1960s, limited to 1M records
occ_1970s: OBIS occurrences, temporal sample for the 1970s, limited to 1M records
occ_1980s: OBIS occurrences, temporal sample for the 1980s, limited to 1M records
occ_1990s: OBIS occurrences, temporal sample for the 1990s, limited to 1M records
occ_1M: OBIS occurrences, global sample of 1 million records
occ_2000s: OBIS occurrences, temporal sample for the 2000s, limited to 1M records
occ_2010s: OBIS occurrences, temporal sample for the 2010s, limited to 1M records
occ_SAtlantic: OBIS occurrences, South Atlantic full regional sample
occ_fk: OBIS occurrences, Florida Keys full regional sample