get_ereefs_bottom_ts: Extracts time-series of selected variables from the bottom...

In BarbaraRobson/ereefs: Useful Functions to Handle eReefs and EMS model Output

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

Description

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

Usage

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

## Not run: 
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)

## End(Not run)

BarbaraRobson/ereefs documentation built on April 23, 2023, 5:47 a.m.