SQL for a WoRMS subtree's indicators from the exported species table — obis_h3_species_subtree

What a browser runs against the release instead of asking h3t: the species files of one resolution joined to the lookup, filtered to the aphiaids whose lineage contains a seed, and summarized per cell with the store's own indicator SQL (.h3t_indicators_sql(), species counted by name_key). It reproduces the h3t subtree (the recursive CTE down taxon from the seeds) cell for cell: n and sp exactly, Shannon, Simpson and ES to floating point.

Usage

obis_h3_species_subtree_sql(
  release_dir,
  aphiaid,
  res,
  esn = 50L,
  classes = NULL
)

Arguments

release_dir: the release directory written by obis_h3_export_parquet() (holding species/).
aphiaid: one or more seed WoRMS AphiaIDs (e.g. 2, Animalia).
res: a resolution of the species table.
esn: expected sample size for ES(n) (default 50).
classes: optional classes to read (the partitions a class-bounded taxon needs; NA reads the _none file); NULL reads every partition.

Value

a SQL string with columns h3, cell_id, n, sp, shannon, simpson, es, ordered by cell_id.