Package index • obisindicators

Read

Functions for reading data.

Connect to, summarize, query and benchmark an obis_h3 DuckDB store from R.

Calculate indicators, and the paper’s analyses: scale curves, rank-column vs subtree, EOV totals, SPUE vs SDM, periods, and place roll-ups.

calc_eov_totals(): Records, species and cells per Essential Ocean Variable
calc_indicators(): Calculate Biodiversity Indicators, including ES50 (Hurlbert index)
calc_period_change(): Change in an indicator between two periods, where both are reliable
calc_period_indicators(): Indicators per period (e.g. decade) and cell
calc_place_indicators(): Indicators rolled up from H3 cells to places
calc_rank_vs_subtree(): Records and species by DwC rank column vs by AphiaID subtree
calc_scale_curves(): Scale curves: indicator summaries across H3 resolutions
calc_spue_cells(): SPUE effort proxy per cell at one resolution
calc_spue_scale(): Scale curves for the SPUE effort proxy
compare_eov_totals(): Compare EOV totals between two stores (e.g. before/after taxonomy gap-fill)
compare_spue_sdm(): Compare the SPUE effort proxy with modeled suitability
h3_raster_to_cells(): Aggregate a raster (e.g. an SDM) to H3 cells
obis_cell_indicators(): Per-cell indicators for a filter at one resolution
obis_rank_presets(): Default taxon-group presets for the rank-vs-subtree comparison
place_cells(): H3 cells covering each place polygon

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