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Seasonal climatology for one or more measurement types

Source: R/transect.R
cc_climatology.Rd

The baseline every CalCOFI anomaly is a departure from: a plain mean per (site_key — the real station, the cruise's month, 10 m floor depth bin, measurement type) across a window of years, kept where at least min_cruises distinct cruises contribute. Calendar month is the finest season CalCOFI's design supports — quarterly-ish cruises over decades give many years per month at a station but only a handful of days — and the coarsest that works: a mean over all months is a map of the seasonal cycle, not an anomaly. A plain mean rather than harmonics: Rudnick et al. (2017) fit annual and semiannual harmonics for the CUGN glider climatology, which suits continuous glider sampling; CalCOFI's is episodic, and a monthly mean is something a reader can state exactly.

Usage

cc_climatology(
  con,
  variables = "temperature_ave",
  years = c(1993, 2013),
  dataset_key = "calcofi_ctd-cast",
  depth_max = 500,
  depth_bin = 10,
  min_cruises = 3,
  season = FALSE
)

Arguments

con

DuckDB connection to a release (cc_get_db()).

variables

measurement_types.

years

two-element baseline range, inclusive, e.g. c(1993, 2013). Recorded on the result as the baseline attribute so a plot can state it.

dataset_key, depth_max

as in cc_transect_section().

depth_bin

bin width, m (default 10; floor bins, labelled by the shallow edge). The release table is only used at 10.

min_cruises

minimum distinct cruises for a cell to be returned (default 3). A floor in cruises rather than observations because a nearshore grid cell holds several stations' casts from one cruise.

season

FALSE (default) for the monthly baseline; TRUE for the seasonal one — the quarter of the cruise's month (Q1 Jan–Mar, Q2 Apr–Jun, Q3 Jul–Sep, Q4 Oct–Dec) — returned on each month of the quarter under the same column names, so cc_anomaly() uses it unchanged. Fills stations whose months are each below min_cruises but whose quarter is not (the northern lines 60–73.3). Read from the release's season_* columns (calcofi4db= 4.24.0) or computed the same way. The period attribute says which.

Value

Tibble: site_key (the station; absent only when reading a release table from before v2026.09.2x, which was grained on the grid cell), grid_key (the station's modal cell — the inshore cells hold 2–4 stations, so key on site_key), month, depth_m, variable, clim_mean, clim_sd, clim_n, n_cruises; attributes baseline (the years), source ("release" or "computed") and period ("month" or "season").

Details

Since the releases of 2026-09 the database ships this table — climatology, built by calcofi4db::build_climatology() at release time with exactly this definition, the window stamped on every row — and ctd-transects and the CalCOFI Explorer subtract it. When con holds that table and years is its window, this returns its cells (source attribute "release"), so an R user, the two apps and any notebook see one baseline. Otherwise (an older release, or another window) it computes the same thing from obs (source = "computed").