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Match biological to environmental observations

Source: R/match.R
cc_match_bio_env.Rd

Core engine relating biological observations to environmental observations by matching them on time and space. Builds a single DuckDB SQL string — a temporal interval join (within max_time_hr) plus a spatial filter (ST_Distance_Sphere within max_dist_km) — that reads directly from the Parquet files of a frozen CalCOFI release on Google Cloud Storage, runs it, and attaches the fully-interpolated SQL and query metadata as attributes.

Usage

cc_match_bio_env(
  bio,
  env,
  max_dist_km = 2,
  max_time_hr = 6,
  join_method = c("nearest_time", "nearest_dist", "average"),
  con = NULL,
  version = "latest",
  collect = TRUE,
  return_sql = FALSE
)

Arguments

bio

SQL SELECT string producing the biological side. Must yield columns bio_id (unique per observation), bio_datetime (TIMESTAMP), bio_lon, bio_lat (decimal degrees) and bio_value (DOUBLE). Any additional columns (e.g. scientific_name) are carried through to the output as grouping keys.

env

SQL SELECT string producing the environmental side. Must yield exactly env_id, env_datetime (TIMESTAMP), env_lon, env_lat, env_value (DOUBLE), env_depth_m (DOUBLE) and measurement_type.

max_dist_km

Maximum match distance in kilometers (default: 2).

max_time_hr

Maximum match time difference in hours (default: 6).

join_method

One of "nearest_time" (default — keep the env observation(s) closest in time, averaging ties), "nearest_dist" (closest in space) or "average" (average every env observation in the window).

con

Optional DuckDB connection. If NULL (default) a temporary in-memory connection is created (and closed again when collect = TRUE).

version

Release version string (e.g. "v2026.05.14") or "latest" (default). Recorded in the query metadata; the actual table URLs come from bio / env.

collect

If TRUE (default) execute and return a tibble; if FALSE return a lazy dplyr::tbl() reference.

return_sql

If TRUE, return the interpolated SQL string (with query_meta attached) without executing. Default: FALSE.

Value

When return_sql = TRUE, a length-1 character vector of SQL with attr(., "query_meta"). Otherwise a tibble (or lazy tbl) of one row per biological observation per measurement_type, with the matched env_value, env_value_sd, env_depth_m, n_env, dist_km and time_diff_hr, plus all bio columns. The result carries attr(., "sql") and attr(., "query_meta") (package + release version, parameters and GCS source URLs).

Details

Most users want a wrapper (cc_match_ichthyo_by_name(), cc_match_ichthyo_by_taxon() or cc_match_zooplankton_biomass()) rather than calling cc_match_bio_env() directly.

Examples

if (FALSE) { # \dontrun{
# build bio + env subqueries yourself, or use a wrapper
d <- cc_match_ichthyo_by_name("Sardinops sagax", env_var = "temperature")

# the exact, portable SQL that produced it
cat(attr(d, "sql"))
str(attr(d, "query_meta"))
} # }