Indicators rolled up from H3 cells to places — calc_place

Fills each polygon with H3 cells at res, sums species records over those cells from occ_h3 (optionally restricted to an EOV, an AphiaID subtree, DwC rank values and/or a year range), and computes the indicators per place with calc_indicators(). Also reports the number of cells filled and the number with any record, so sparse places are visible.

Usage

calc_place_indicators(
  con,
  places,
  name_col = NULL,
  res = 7L,
  eov = NULL,
  aphiaid = NULL,
  taxon = NULL,
  years = NULL,
  esn = 50L
)

Arguments

con: connection from obis_store_connect().
places: an sf of polygons (lon/lat, EPSG:4326).
name_col: column naming each place; default the first non-geometry column.
res: H3 resolution (1-7).
eov: optional EOV name (one); see obis_eov_seeds().
aphiaid: optional WoRMS AphiaID(s) — the subtree filter.
taxon: optional named list of DwC rank values; see obis_h3t_sql().
years: optional c(min, max) year range.
esn: expected sample size for ES(n); default 50.

Value

data frame with place, n_cells, n_cells_occupied, and the calc_indicators() columns (n, sp, shannon, simpson, es, hill_1, hill_2, hill_inf).