Access CEFI regional MOM6 output

Reads the NOAA CEFI regional ocean model over OPeNDAP and returns it as an sf point object with one row per grid cell and time step — the same shape accessCopernicus(), accessFVCOM(), accessHYCOM(), accessCCMP() and accessERDDAP() return, so matchData() joins it unchanged.

Usage

accessCEFI(
  vars,
  years = NULL,
  months = NULL,
  bounding_box,
  dates = NULL,
  frequency = c("monthly", "daily"),
  experiment = "hindcast",
  init = NULL,
  member = NULL,
  release = "latest",
  archive = NULL,
  overwrite = FALSE
)

Arguments

vars: variables to read, from cefi_variables()
years: years to read. Required unless dates is given.
months: months to read. Required unless dates is given.
bounding_box: named list with xmin, xmax, ymin, ymax, or an sf/sfc object. Longitudes negative west.
dates: the exact dates to read, as YYYYMMDD strings, YYYY-MM-DD strings, or Date objects
frequency: "monthly" (the default) or "daily"
experiment: which CEFI experiment to read. "hindcast" is the default; "decadal_forecast" is experimental. The rest are refused with the reason — see cefi_experiments().
init: for a forecast, which initialisation to read, as "i198001" or "198001". Required for "decadal_forecast".
member: for a forecast, which ensemble member or members to read, from 1 to 10. Required for "decadal_forecast". Several may be given, and each arrives as its own block of rows carrying its own source tag.
release: a release directory such as "r20250715", or "latest" (the default), which follows whatever CEFI published last
archive: a spec from cefi_archive(), to read a domain this package does not ship. Overrides experiment, frequency and release.
overwrite: re-read time steps already cached

Value

one row per grid cell per time step, with YEAR, MONTH, DAY and a column per requested variable

Why reach for it, and why not

On the Northwest Atlantic shelf this is the highest-resolution coupled physics-and-biogeochemistry field available here: a twelfth of a degree for both, against a quarter degree for the Copernicus biogeochemical reanalysis. It carries nutrients, oxygen, pH, pCO2, phytoplankton carbon and mesozooplankton biomass on the same grid as the temperature and salinity, which no other source in this package does.

Against that: it is one region. Outside roughly 98W-36W and 5N-58N there is nothing to read, and a bounding box outside the domain is refused rather than returning an empty join. It is also a model throughout — its CHL is simulated, not retrieved, and is not the satellite CHL from accessERDDAP() under another name.

Forecasts are experimental

experiment = "decadal_forecast" reads a prediction rather than a reconstruction, and this package treats it as experimental: it warns on every call, and it will not choose for you between the things a forecast makes you choose.

A decadal file is ten years from one January, and there are sixty of them, so init says which initialisation to read. Each holds ten ensemble members, so member says which. Neither has a defensible default and neither is guessed:

The members are not repeats of one number. They are the model's own estimate of how uncertain it is, and averaging them is a modelling decision — a reasonable one, often the right one, but not one a fetch should make silently. Read the members you want and combine them yourself, so the combination is visible in your code.
A year covered by several initialisations is covered by several different forecasts of it, at different lead times. Which one you mean is a question about your analysis, not about the archive.

The source tag records both, so source_of() on the result says which initialisation and which member produced it.

What is monthly and what is also daily

The hindcast saves everything monthly. Its daily output is biogeochemistry only — see the section of the same name in cefi_variables() — and a daily request for SST is refused with the list of what is available daily rather than returning nothing.

Longitude and the domain

The regridded files are already on a -180 to 180 grid, so bounding_box is given negative west as everywhere else in this package and needs no conversion in either direction.

Examples

if (FALSE) { # \dontrun{
bb <- list(xmin = -70, xmax = -66, ymin = 41, ymax = 44)

# The hindcast, monthly
env <- accessCEFI(vars = c("SST", "BOTT", "BOTS"), years = 2015,
                  months = 1:12, bounding_box = bb)
source_of(env)
#> [1] "cefi:NWA12-hindcast-r20250715"

# Daily biogeochemistry on survey dates
bgc <- accessCEFI(vars = c("CHL", "NO3", "PH"), frequency = "daily",
                  dates = unique(observations$date), bounding_box = bb)

matched <- matchData(observations, bgc)
} # }