Extract nearest, surface and bottom values from a 3D netCDF variable

For each observation, this function extracts the full vertical profile at the nearest longitude, latitude and time cell. It then returns three summary columns: nearest valid depth, surface and bottom.

Usage

extract3d_all(data, nc, var = NULL, ...)

Arguments

data

Object containing observation points. Can be a data frame, tibble, sf object with POINT geometries, matrix with column names, or named list.

nc

netCDF source. Can be a file path, vector of file paths, list of file paths, opened ncdf4 object, list of opened objects, or a data frame with a file column.

var

Name of the variable to extract from the netCDF file. If NULL, the function tries to detect the variable automatically from each file. This only works when each netCDF file contains one single variable.

...

Additional arguments passed to extract_to_point().

Value

The input observations with three extracted columns: nearest_*, surface_* and seabottom_*. Data frames, tibbles and sf objects retain their structure; matrices and named lists are returned as data frames.

Examples

nc_file <- system.file(
  "extdata", "example_3d.nc",
  package = "ocean3d"
)

observations <- data.frame(
  lon = c(0, 1),
  lat = c(40, 41),
  depth = c(60, 100),
  date = as.Date(c("2020-01-01", "2020-01-03"))
)

extract3d_all(
  data = observations,
  nc = nc_file,
  var = "temp"
)
#>   lon lat depth       date nearest_temp surface_temp seabottom_temp
#> 1   0  40    60 2020-01-01         15.0         20.0           10.0
#> 2   1  41   100 2020-01-03         13.5         23.5           13.5