Extract a specific variable from a fvcom format netCDF file for all provided geographical locations.

Usage

extract_site_grids_fvcom(
  nc_file,
  sites,
  nc_crs,
  nc_var_name,
  sites_crs = NULL,
  id = "site",
  dates_to_extract = NULL,
  time_var_name = "time",
  all_sigma = FALSE,
  pretty_dates = TRUE,
  grid_name_x = "",
  grid_name_y = ""
)

Arguments

nc_file: Filepath for the fvcom netCDF file to extract the data from.
sites: Simple features (or spatial) data frame of geographical areas to extract the variable values for. The data frame should contain a single row per buffer and have a unique identifier.
nc_crs: The numerical value for the crs of the netCDF file.
nc_var_name: The name of the variable to extract from the file.
sites_crs: The numerical value for the crs of sites, if different from the crs of the netCDF file.
id: The name of the identifier provided in the sites special features data frame.
dates_to_extract: Vector of dates to extract the variable for. If not provided, all available values will be returned.
time_var_name: Name of time/date variable to extract from the netCDF file. Defaults to "time" as that is by far the most common variable name used.
all_sigma: Boolean variable to allow users to specify whether all sigma layers or levels, often labelled siglay and siglev in fvcom files should be extracted. Defaults to FALSE, where the first (or top) layer/level will be extracted.
pretty_dates: Boolean variable to control whether to tidy the fvcom date/times to the nearest hour or not. Defaults to TRUE.
grid_name_x: Name of the geographical x coordinate to be extracted. If not specified, an attempt will be made to establish this from the netCDF file itself.
grid_name_y: Name of the geographical y coordinate to be extracted. If not specified, an attempt will be made to establish this from the netCDF file itself.

Value

A tibble of each location id, with the corresponding variable values depths and dates available.

Examples

if (FALSE) { # \dontrun{

 the_nc_file <- "path/to/netCDF/file.nc"

 # presuming we already have a set of spatial buffers to collect data
 # from and that the file contains a "temp" variable
 extract_site_grids_fvcom(the_nc_file, sites = buffers, nc_crs = 4326, nc_var_name = "temp")
} # }