Extracts time-series of selected variables from the bottom water-column cell at specified locations from eReefs output files

See also get_ereefs_ts() to extract from a specified layer instead of a depth-integrated value. By Barbara Robson (AIMS).

get_ereefs_bottom_ts(
  var_names = c("Chl_a_sum", "TN"),
  location_latlon = c(-23.39189, 150.88852),
  start_date = c(2010, 12, 31),
  end_date = c(2016, 12, 31),
  input_file = "menu",
  input_grid = NA,
  eta_stem = NA,
  override_positive = FALSE,
  verbosity = 1
)

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').

location_latlon

is a vector containing the decimal latitude and longitude of the desired location. If you want to specify an x-y grid coordinate instead of a latitude and longitude, you can: to do this, is.integer(location_latlon) must be TRUE. Defaults to c(-23.39189, 150.88852).

start_date

date for animation. Can either be a) a vector of integers in the format c(year, month, day); b) a date obtained e.g. from as.Date(); or c) a character string formatted for input to as.Date(). Defaults to c(2010,12,31).

input_file

is the URL or file location of any of the EMS output files or a THREDDS catalog URI. Defaults to a menu selection based on current NCI catalogs. Can also be set to "nci", "menu" or "catalog" for the same behaviour. Set to "old_menu" to provide old menu options instead of menu options from the NCI catalog. Numeric values are interpreted as references to selections available from the old menu. Short codes can be used for some options (codenames as used in https://research.csiro.au/ereefs/models/model-outputs/access-to-raw-model-output/ )

input_grid

Name of the locally-stored or opendap-served netcdf file that contains the grid coordinates for the top and bottom of each layer (z_grid). If not specified, the function will first look for z_grid can be found in the first INPUT_STEM file, and if not found, will check whether the size of the variables in the input file corresponds to the size expected for GBR4 or GBR1, and load an appropriate z grid from data files stored in this package. Alternatively, you can provide the location of a full (not simple-format) ereefs netcdf output file such as "http://dapds00.nci.org.au/thredds/dodsC/fx3/gbr4_hydro_all/gbr4_all_2016-09.nc" "http://dapds00.nci.org.au/thredds/dodsC/fx3/gbr4_hydro_all/gbr4_all_2016-09.nc".

eta_stem

The URI or file location of the model output files that contains the surface elevation (eta), minus the date components of the filename in the case of GBR1 or GBR4 files, and ommitting the file extension, ".nc". Needed only if eta is not in the files indicated by input_stem (e.g. some GBR1 bgc files).

override_positive

Reverse the value of the "positive" attribute of botz for BGC files, assuming that it is incorrect. Default FALSE

end

date for animation. Can either be a) a vector of integers in the format c(year, month, day); b) a date obtained e.g. from as.Date(); or c) a character string formatted for input to as.Date(). Defaults to c(2016,12,31).

Value

a data frame containing the dates and values of extracted variables

Examples

if (FALSE) {
get_ereefs_bottom_ts(c('Chl_a_sum', 'NH4'), location_latlon=data.frame(latitide=-23.39189, longitude=150.88852), layer='surface', start_date=c(2010,12,31),end_date=c(2011,1,5), input_file=2)
}