This function downloads, processes, and extracts variables from the Bio-ORACLE v3.0 dataset.
Usage
biooracle(
x,
vars,
realm = "surface",
years = "2000-2010",
ssp = NULL,
algorithm = "mean",
...
)Arguments
- x
The output from `par_set()` defining the area or locations. It must have been created with `res = 6` (Bio-ORACLE's native 0.05-degree grid).
- vars
Character vector of one or more variables or synonyms to download.
- realm
Character. One of "surface" (default), "benthic_minimum", "benthic_average", or "benthic_maximum".
- years
Character. The time period for the data in "YYYY-YYYY" format. Use "2000-2010" or "2010-2020" for baseline current conditions (default is "2000-2010"). For future projections, specify the decade (e.g., "2040-2050", "2090-2100") and provide the `ssp` argument.
- ssp
numeric or character. Shared Socioeconomic Pathway (119, 126, 245, 370, 460, 585). Required if `years` is in the future (>= 2020).
- algorithm
Character. Statistic to apply (max, mean, min, ltmax, ltmin, range). Default "mean".
- ...
Additional arguments.
Value
If `par_set()` contained a raster/polygon/points with buffer: a `SpatRaster` stack of processed variables. If `par_set()` contained spatial points or data.frame of points without buffer: a `data.frame` of x, y, and extracted values.
Details
Available variables (working synonyms in parentheses and ""):
1 - "thetao" (Ocean temperature; [ºC]) ("temperature", "temp", "sea temperature")
2 - "so" (Salinity; [-]) ("sal", "salt", "saltiness")
3 - "sws" (Sea water velocity; [m.s-1]) ("velocity", "current speed", "speed")
4 - "swd" (Sea water direction; [degree]) ("direction", "current direction")
5 - "no3" (Nitrate; [mmol . m-3]) ("nitrate")
6 - "po4" (Phosphate; [mmol . m-3]) ("phosphate")
7 - "si" (Silicate; [mmol . m-3]) ("silicate", "silicon")
8 - "o2" (Dissolved molecular oxygen; [mmol . m-3]) ("oxygen", "dissolved oxygen", "o2")
9 - "dfe" (Iron; [mmol . m-3]) ("iron", "fe")
10 - "phyc" (Primary productivity; [mmol . m-3]) ("productivity", "pp", "primary production")
11 - "ph" (pH; [-]) ("acidity")
12 - "chl" (Chlorophyll; [mg . m-3]) ("chlorophyll", "chla")
13 - "sithick" (Sea ice thickness; [m]) ("ice thickness")
14 - "siconc" (Sea ice cover; [Fraction]) ("ice cover", "sea ice")
15 - "clt" (Cloud cover; [
16 - "mlotst" (Mixed layer depth; [m]) ("mld", "mixed layer")
17 - "tas" (Air temperature; [ºC]) ("air temperature", "air temp")
18 - "par" (Photosynt. Avail. Radiation; [E.m-2.day-1]) ("light", "radiation")
19 - "kdpar" (Diffuse attenuation; [m-1]) ("attenuation", "turbidity")
20 - "bathymetry" (Bathymetry; [m]) ("depth", "elevation", "altitude")
21 - "slope" (Topographic slope; [-]) ("topographic slope")
22 - "aspect" (Topographic aspect; [-]) ("topographic aspect")
23 - "tpi" (Topographic position index; [-]) ("topographic position index")
24 - "tri" (Terrain ruggedness index; [-]) ("terrain ruggedness index", "ruggedness")
Citation:
Assis J, Fernández Bejarano SJ, Salazar VW, Schepers L, Gouvêa L, Fragkopoulou E, Leclercq F, Vanhoorne B, Tyberghein L, Serrão EA, Verbruggen H, De Clerck O (2024). "Bio-ORACLE v3.0. Pushing marine data layers to the CMIP6 Earth system models of climate change research." Global Ecology and Biogeography, 33, e13813.
https://doi.org/10.1111/geb.13813
Resolution
Bio-ORACLE layers are distributed on a 0.05-degree grid (~5.5 km at the
equator). Because res is a multiplier of the 30 arc-second base grid,
the value that reproduces this grid exactly is res = 6
(\(6 \times 30''= 0.05^{\circ}\)). You must therefore call par_set()
with res = 6; any other value (including the default) raises an error.
Examples
# \donttest{
# Example 1: Current conditions (Baseline)
current_env <- par_set(country = "Italy", crs = 3035, res = 6) %>%
biooracle(vars = c("temperature", "salinity"),
years = "2000-2010")
# Example 2: Future projections (2050, SSP 585)
future_env <- par_set(country = "Italy", crs = 3035, res = 6) %>%
biooracle(vars = c("temperature", "salinity"),
years = "2040-2050",
ssp = 585)
# }