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Sea Surface Temperature of the FAO Major Fishing Areas

Source: R/sst_data.R
fao_area_sst.Rd

This function returns the yearly sea surface temperature (SST) of the 19 FAO major marine fishing areas: the area mean, the range within the area and the seasonal range, one row per area and year, like the FAO catch statistics. It is used by mean_temperature_catch(). It always says which SST data it uses.

Usage

fao_area_sst(
  area = NULL,
  sst = fao_setting("sst"),
  level = c("area", "division"),
  variable = NULL,
  data_dir = fao_data_dir()
)

Arguments

area

FAO area codes (e.g. "34") or names as in the FAO data (e.g. "Atlantic, Eastern Central"). Default is NULL, all areas.

sst

The SST data: "ersst5" (built in), the name of a product downloaded with download_sst_data(), or the path of a NetCDF file or of a folder of NetCDF files. Default is the sst setting of fao_settings(), "ersst5" unless changed.

level

"area" (default) for the 19 FAO major marine areas, or "division" for the FAO subareas and divisions (e.g. "37.1.1", Balearic), as in the catch data of load_fao_divisions() (see Subareas and divisions).

variable

The name of the SST variable in your NetCDF files. Default is NULL, found from its name.

data_dir

The directory where downloaded data and computed tables are stored. Default is fao_data_dir().

Value

A data frame with one row per area and year: product, area_code, area_en, year, sst_mean, sst_p10, sst_p90, sst_min_month, sst_max_month (all in °C), n_cells (grid cells in the area), source (the SST data used) and downloaded (date the data were downloaded or computed).

Which SST data

Built in (default): NOAA ERSST v5

The package comes with the yearly SST of the 19 areas from 1950, computed from NOAA Extended Reconstructed SST version 5 (Huang et al. 2017): a monthly reconstruction on a 2° x 2° grid (about 220 km) from in situ observations only (ships and buoys of ICOADS, Argo floats from 1999). It is the smallest of the common SST products, needs no download, and is consistent over the whole period; its grid is coarse for small areas such as the Mediterranean and Black Sea (n_cells gives the number of grid cells of each area).

Your own NetCDF files

Give the path of a NetCDF file, or of a folder of NetCDF files, as sst, or once for the session with fao_settings(sst = "path"). The files must hold a gridded SST with longitude, latitude and time, monthly or daily (e.g. HadISST, COBE-SST2, OISST, ERSST, or a model output). The yearly area means are computed the first time, which can take a few minutes, and saved in the sst folder of data_dir; later calls with the same files read the saved table. Reading NetCDF files needs the ncdf4 package.

Downloaded with download_sst_data()

download_sst_data() downloads one of the products listed by fao_sst_products() (HadISST1, COBE-SST2, OISST v2.1, or the newest years of ERSST v5) and computes its table; it is then used by its name, e.g. sst = "hadisst1".

Subareas and divisions

With level = "division", the table has one row per FAO subarea and division of the FAO map in the package (inst/extdata/FAO_AREAS_CWP.shp): area_code is its code (e.g. "34.1.1" or the subarea "34.2") and area_en its name. The built-in ERSST v5 table covers the subareas and divisions of areas 34, 37, 47 and 51, those of the catch data by division (load_fao_divisions()); tables from downloaded products or your own files cover all of them. Many divisions are small for a 2° grid (see n_cells; e.g. the Sea of Azov or the Sea of Marmara have none or a few cells), so a finer SST product, given as the path of its NetCDF files, suits divisions better.

How the area means are computed

  • Files: the SST variable is found by its name ("sst", "analysed_sst", "tos", ...) unless given as variable; longitudes may run from -180 to 180 or from 0 to 360; values in kelvin are converted to °C; if there are several depths, the first (the surface) is used. Values below -5 °C, which some products use to mark sea ice (-1000 in HadISST1), are set to -1.8 °C, the value other products give under sea ice. Daily values are averaged by month.

  • Grids finer than 1° are first averaged to about 1° (mean of the cells with a value).

  • Each grid cell counts for each FAO major area it overlaps (inst/extdata/FAO_AREAS_CWP.shp, the 19 marine areas), weighted by the area of the overlap computed on the sphere, so cells on a boundary are shared and coastal cells count for their sea part only.

  • sst_mean is the mean of the 12 monthly area means; sst_p10 and sst_p90 are the weighted 10th and 90th percentiles of the yearly mean SST of the cells (the range within the area); sst_min_month and sst_max_month are the coldest and warmest monthly area means (the seasonal range; in areas on both sides of the equator the seasons of the two hemispheres partly cancel, so this range is narrow there). Only years with all 12 months are kept.

Values over the Arctic Sea and the Antarctic areas partly reflect sea ice rather than measured water temperature. SST products use different observations and methods, so their values and trends differ somewhat; repeating an analysis with a second product shows how much a result depends on the product.

References

Hirahara, S., Ishii, M. and Fukuda, Y. (2014). Centennial-scale sea surface temperature analysis and its uncertainty. Journal of Climate 27: 57-75. doi:10.1175/JCLI-D-12-00837.1

Huang, B., Thorne, P.W., Banzon, V.F., Boyer, T., Chepurin, G., Lawrimore, J.H., Menne, M.J., Smith, T.M., Vose, R.S. and Zhang, H.-M. (2017). Extended Reconstructed Sea Surface Temperature, Version 5 (ERSSTv5): Upgrades, Validations, and Intercomparisons. Journal of Climate 30: 8179-8205. doi:10.1175/JCLI-D-16-0836.1

Huang, B., Liu, C., Banzon, V., Freeman, E., Graham, G., Hankins, B., Smith, T. and Zhang, H.-M. (2021). Improvements of the Daily Optimum Interpolation Sea Surface Temperature (DOISST) Version 2.1. Journal of Climate 34: 2923-2939. doi:10.1175/JCLI-D-20-0166.1

Rayner, N.A., Parker, D.E., Horton, E.B., Folland, C.K., Alexander, L.V., Rowell, D.P., Kent, E.C. and Kaplan, A. (2003). Global analyses of sea surface temperature, sea ice, and night marine air temperature since the late nineteenth century. Journal of Geophysical Research 108 (D14): 4407. doi:10.1029/2002JD002670

HadISST1 dataset description, with the warning of 10 March 2016 and a link to the analysis by D. Chelton and C. Risien (https://ir.library.oregonstate.edu/xmlui/handle/1957/58385): https://coastwatch.pfeg.noaa.gov/erddap/info/erdHadISST/index.html

Web pages of the products: ERSST v5 https://www.ncei.noaa.gov/products/extended-reconstructed-sst; HadISST1 https://www.metoffice.gov.uk/hadobs/hadisst/; COBE-SST2 https://psl.noaa.gov/data/gridded/data.cobe2.html; OISST v2.1 https://www.ncei.noaa.gov/products/optimum-interpolation-sst

Examples

if (FALSE) { # \dontrun{
sst34 <- fao_area_sst("34")                          # built in: NOAA ERSST v5
plot(sst_mean ~ year, data = sst34, type = "l", ylim = range(sst34$sst_p10, sst34$sst_p90))
lines(sst_p10 ~ year, data = sst34, lty = 2)
lines(sst_p90 ~ year, data = sst34, lty = 2)

# Your own NetCDF file (e.g. HadISST_sst.nc downloaded from the Met Office), for one call ...
fao_area_sst("34", sst = "D:/data/HadISST_sst.nc")
# ... or for the whole session, including mean_temperature_catch()
fao_settings(sst = "D:/data/HadISST_sst.nc")

# Subareas and divisions, e.g. those of the Mediterranean and Black Sea
div <- fao_area_sst(level = "division")
subset(div, startsWith(area_code, "37.") & year == 2024)
} # }