Extract the bottom available layer from a 3D netCDF variable

For each observation, this function extracts the full vertical profile at the nearest longitude, latitude and time cell, then returns the deepest non-missing value. This is useful when the bathymetry of the netCDF grid means that deeper layers are missing over shallow areas.

Usage

extract3d_bottom(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 extracted values appended. 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),
  date = as.Date(c("2020-01-01", "2020-01-03"))
)

extract3d_bottom(
  data = observations,
  nc = nc_file,
  var = "temp"
)
#>   lon lat       date temp
#> 1   0  40 2020-01-01 10.0
#> 2   1  41 2020-01-03 13.5