Match ichthyoplankton to environmental data by scientific name

Relates net-tow ichthyoplankton (fish egg / larva counts, standardized to std_tally) to CTD-bottle environmental measurements, filtering the biological side by scientific name. Supersedes the retired /ichthyodata Plumber endpoint.

cc_match_ichthyo_by_name(
  scientific_name,
  env_var = "temperature",
  exact_match = TRUE,
  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

scientific_name

Character vector of scientific names to match against species.scientific_name.

env_var

Environmental measurement_type from the bottle_measurement table (default: "temperature"). See cc_list_measurement_types().

exact_match

If TRUE (default) match names exactly; if FALSE match case-insensitively as substrings (ILIKE '%name%').

life_stage

Optional character vector restricting ichthyo.life_stage (e.g. "larva", "egg").

date_min, date_max

Optional date bounds (Date or "YYYY-MM-DD" string) 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

Convenience flag mirroring the old API's relax_matching: widens 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{
# Pacific sardine larvae vs. temperature, Q1 2018, relaxed matching
# (note: CTD-bottle env data ends 2021-05, so Q1 2018 is used as the
#  recurring worked example across calcofi4r, int-app and the docs book)
d <- cc_match_ichthyo_by_name(
  "Sardinops sagax",
  env_var        = "temperature",
  life_stage     = "larva",
  date_min       = "2018-01-01",
  date_max       = "2018-03-31",
  relax_matching = TRUE)
} # }