Match ichthyoplankton to environmental data by WoRMS taxon subtree

Source: R/match.R

Relates net-tow ichthyoplankton to CTD-bottle environmental measurements, filtering the biological side to a taxon and all of its descendants. The subtree is resolved with a recursive walk of taxon.parentNameUsageID over the WoRMS authority. Supersedes the retired /itis_ichthyodata endpoint, replacing the dead ITIS path regex with the WoRMS worms_id hierarchy.

cc_match_ichthyo_by_taxon(
  worms_id,
  env_var = "temperature",
  life_stage = NULL,
  date_min = NULL,
  date_max = NULL,
  depth_m_min = NULL,
  depth_m_max = NULL,
  max_dist_km = NULL,
  max_time_hr = NULL,
  relax_matching = FALSE,
  join_method = c("nearest_time", "nearest_dist", "average"),
  con = NULL,
  version = "latest",
  collect = TRUE,
  return_sql = FALSE
)

Arguments

worms_id

Integer vector of WoRMS taxonID(s); the match includes each id and every descendant taxon.

env_var

Environmental measurement_type (default: "temperature").

life_stage

Optional character vector restricting ichthyo.life_stage.

date_min, date_max

Optional date bounds on the tow start time.

depth_m_min, depth_m_max

Optional depth bounds (meters) on the bottle environmental observations.

max_dist_km, max_time_hr

Match tolerances. Default to 2 km / 6 hr, or 5 km / 72 hr when relax_matching = TRUE; an explicit value always wins.

relax_matching

Widen the default tolerances to 5 km / 72 hr.

join_method, con, version, collect, return_sql

Passed to cc_match_bio_env().

Value

See cc_match_bio_env().

Examples

if (FALSE) { # \dontrun{
# Engraulis (anchovies) — WoRMS taxonID 125620 — and all descendants
d <- cc_match_ichthyo_by_taxon(125620, env_var = "salinity")
} # }