Extracts time series at specified locations from eReefs model output files

Create a time-series of values of one or more selected model output variables in a specified layer of the water column or sediment store at one or more geographic locations. The active extraction path supports local NetCDF files, live OPeNDAP URLs, and THREDDS catalog-backed workflows.

get_ereefs_ts(
  var_names = c("Chl_a_sum", "TN"),
  geocoordinates = c(-23.39189, 150.88852),
  layer = "surface",
  start_date = c(2016, 2, 4),
  end_date = c(2016, 3, 2),
  input_file = "catalog",
  input_grid = NA,
  eta_stem = NA,
  override_positive = FALSE,
  verbosity = 0,
  default_to_bottom = TRUE
)

Arguments

var_names: either a single character value or a vector specifying the short names for variables that you want from the netcdf file. Defaults to c('Chl_a_sum', 'TN').
geocoordinates: A tibble of decimal latitude and longitude pairs, or a length-two vector containing a single location. `geocoordinates` can also be set to `"mmp"` to extract time-series at all Marine Monitoring Program sites. Additional columns are preserved, for example site names.
layer: Layer selector. Use a positive layer index, `"surface"`, `"bottom"`, or a negative value to indicate depth below mean sea level in metres. Use [get_ereefs_depth_specified_ts()] instead if you need depth below the free surface.
start_date: Start of the extraction period. Can be a vector such as `c(year, month, day)`, a `Date`/`POSIXct`, or a character string accepted by [get_date_time()].
end_date: End of the extraction period, specified as for `start_date`.
input_file: NetCDF file path, OPeNDAP URL, or THREDDS catalog URI. THREDDS catalogs are preferred for live multi-file requests. Legacy shortcuts such as `"nci"`, `"menu"`, `"catalog"`, `"old_menu"`, and old numeric menu selections are still accepted for backward compatibility.
input_grid: Optional alternative source for vertical grid metadata (`z_grid`). This can be a local or remote NetCDF file that carries the required layer-interface information.
eta_stem: Legacy fallback for locating surface elevation (`eta`) when it is not in the main file. Usually unnecessary for catalog-driven workflows.
override_positive: Reverse the value of the "positive" attribute of botz for BGC files, assuming that it is incorrect. Default FALSE. Not normally needed.
verbosity: How much information to display along the way (0 to 2. Default is 1).
default_to_bottom: Whether to fall back to the bottom wet layer if the requested layer contains `NA` values. Defaults to `TRUE`.

Value

a data tibble containing extracted variables, including dates and locations

Details

All variables to be extracted must have the same number of dimensions (e.g., either all 2D or all 3D variables).

If you run into memory constraints, consider grouping points to be extracted within regions, and calling this once for each region.

Examples

if (FALSE) { # \dontrun{
get_ereefs_ts('Chl_a_sum', geocoordinates=tibble(latitude=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer='surface', start_date=c(2010,12,31),end_date=c(2011,1,5), input_file=2)
get_ereefs_ts(var_names=c('Tricho_N', 'DIP', 'TP'), geocoordinates=tibble(latitude=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer='bottom', start_date="2012-07-03",end_date="2012-07-05", input_file='GBR4_BGC-v2.0 Chyb Dcrt')
get_ereefs_ts(var_names=c('ZooL_N', 'ZooS_N'), geocoordinates=tibble(latitude=c(-23.39189,-18), longitude=c(150.88852, 147.5)), layer=45, start_date=c(2010,12,31),end_date=c(2011,1,5), input_file="https://dapds00.nci.org.au/thredds/dodsC/fx3/gbr4_bgc_GBR4_H2p0_B2p0_Cpre_Dcrt/gbr4_bgc_simple_2016-06.nc")
} # }