Get ERDDAP gridded data

Usage

griddap(
  datasetx,
  ...,
  fields = "all",
  stride = 1,
  fmt = "nc",
  url = eurl(),
  store = disk(),
  read = TRUE,
  callopts = list()
)

Arguments

datasetx: Anything coercable to an object of class info. So the output of a call to info, or a datasetid, which will internally be passed through info
...: Dimension arguments. See examples. Can be any 1 or more of the dimensions for the particular dataset - and the dimensions vary by dataset. For each dimension, pass in a vector of length two, with min and max value desired. at least 1 required.
fields: (character) Fields to return, in a character vector.
stride: (integer) How many values to get. 1 = get every value, 2 = get every other value, etc. Default: 1 (i.e., get every value)
fmt: (character) One of csv or nc (for netcdf). Default: nc
url: A URL for an ERDDAP server. Default: https://upwell.pfeg.noaa.gov/erddap/ - See eurl() for more information
store: One of disk (default) or memory. You can pass options to disk. Beware: if you choose fmt="nc", we force store=disk() because nc files have to be written to disk.
read: (logical) Read data into memory or not. Does not apply when store parameter is set to memory (which reads data into memory). For large csv, or especially netcdf files, you may want to set this to FALSE, which simply returns a summary of the dataset - and you can read in data piecemeal later. Default: TRUE
callopts: Curl options passed on to verb-GET

Value

An object of class griddap_csv if csv chosen or griddap_nc if nc file format chosen.

griddap_csv: a data.frame created from the downloaded csv data
griddap_nc: a list, with slots "summary" and "data". "summary" is the unclassed output from ncdf4::nc_open, from which you can do any netcdf operations you like. "data" is a data.frame created from the netcdf data. the data.frame may be empty if there were problems parsing the netcdf data

Both have the attributes: datasetid (the dataset id), path (the path on file for the csv or nc file), url (the url requested to the ERDDAP server)

If read=FALSE, the data.frame for griddap_csv and the data.frame in the "data" slot is empty for griddap_nc

Details

Details:

If you run into an error like "HTTP Status 500 - There was a (temporary?) problem. Wait a minute, then try again.". it's likely they are hitting up against a size limit, and they should reduce the amount of data they are requesting either via space, time, or variables. Pass in config = verbose() to the request, and paste the URL into your browser to see if the output is garbled to examine if there's a problem with servers or this package

Dimensions and Variables

ERDDAP grid dap data has this concept of dimenions vs. variables. Dimensions are things like time, latitude, longitude, altitude, and depth. Whereas variables are the measured variables, e.g., temperature, salinity, air.

You can't separately adjust values for dimensions for different variables. So, here's how it's gonna work:

Pass in lower and upper limits you want for each dimension as a vector (e.g., c(1,2)), or leave to defaults (i.e., don't pass anything to a dimension). Then pick which variables you want returned via the fields parameter. If you don't pass in options to the fields parameter, you get all variables back.

To get the dimensions and variables, along with other metadata for a dataset, run info, and each will be shown, with their min and max values, and some other metadata.

Where does the data go?

You can choose where data is stored. Be careful though. You can easily get a single file of hundreds of MB's (upper limit: 2 GB) in size with a single request. To the store parameter, pass memory if you want to store the data in memory (saved as a data.frame), or pass disk if you want to store on disk in a file. Note that memory and disk are not character strings, but function calls. memory does not accept any inputs, while disk does. Possibly will add other options, like “sql” for storing in a SQL database.

Non-lat/lon grid data

Some gridded datasets have latitude/longitude components, but some do not. When nc format gridded datasets have latitude and longitude we "melt" them into a data.frame for easy downstream consumption. When nc format gridded datasets do not have latitude and longitude components, we do not read in the data, throw a warning saying so. You can readin the nc file yourself with the file path. CSV format is not affected by this issue as CSV data is easily turned into a data.frame regardless of whether latitude/longitude data are present.

References

https://upwell.pfeg.noaa.gov/erddap/rest.html

Examples

if (FALSE) { # \dontrun{
# single variable dataset
## You can pass in the outpu of a call to info
(out <- info('erdVHNchlamday'))
## Or, pass in a dataset id
(res <- griddap('erdVHNchlamday',
 time = c('2015-04-01','2015-04-10'),
 latitude = c(18, 21),
 longitude = c(-120, -119)
))

# multi-variable dataset
(out <- info('erdQMekm14day'))
(res <- griddap(out,
 time = c('2015-12-28','2016-01-01'),
 latitude = c(24, 23),
 longitude = c(88, 90)
))
(res <- griddap(out, time = c('2015-12-28','2016-01-01'),
   latitude = c(24, 23), longitude = c(88, 90), fields = 'mod_current'))
(res <- griddap(out, time = c('2015-12-28','2016-01-01'),
   latitude = c(24, 23), longitude = c(88, 90), fields = 'mod_current',
   stride = c(1,2,1,2)))
(res <- griddap(out, time = c('2015-12-28','2016-01-01'),
   latitude = c(24, 23), longitude = c(88, 90),
   fields = c('mod_current','u_current')))


# Write to memory (within R), or to disk
(out <- info('erdQSwindmday'))
## disk, by default (to prevent bogging down system w/ large datasets)
## you can also pass in path and overwrite options to disk()
(res <- griddap(out,
 time = c('2006-07-11','2006-07-20'),
 longitude = c(166, 170),
 store = disk()
))
## the 2nd call is much faster as it's mostly just the time of reading in
## the table from disk
system.time( griddap(out,
 time = c('2006-07-11','2006-07-15'),
 longitude = c(10, 15),
 store = disk()
) )
system.time( griddap(out,
 time = c('2006-07-11','2006-07-15'),
 longitude = c(10, 15),
 store = disk()
) )

## memory - you have to choose fmt="csv" if you use memory
(res <- griddap("erdMBchla1day",
 time = c('2015-01-01','2015-01-03'),
 latitude = c(14, 15),
 longitude = c(125, 126),
 fmt = "csv", store = memory()
))

## Use ncdf4 package to parse data
info("erdMBchla1day")
(res <- griddap("erdMBchla1day",
 time = c('2015-01-01','2015-01-03'),
 latitude = c(14, 15),
 longitude = c(125, 126)
))

# Get data in csv format
## by default, we get netcdf format data
(res <- griddap('erdMBchla1day',
 time = c('2015-01-01','2015-01-03'),
 latitude = c(14, 15),
 longitude = c(125, 126),
 fmt = "csv"
))

# Use a different ERDDAP server url
## NOAA IOOS PacIOOS
url = "https://cwcgom.aoml.noaa.gov/erddap/"
out <- info("miamiacidification", url = url)
(res <- griddap(out,
 time = c('2019-11-01','2019-11-03'),
 latitude = c(15, 16),
 longitude = c(-90, -88)
))
## pass directly into griddap() - if you pass a datasetid string directly
## you must pass in the url or you'll be querying the default ERDDAP url,
## which isn't the one you want if you're not using the default ERDDAP url
griddap("miamiacidification", url = url,
 time = c('2019-11-01','2019-11-03'),
 latitude = c(15, 16),
 longitude = c(-90, -88)
)

# Using 'last'
## with time
griddap('erdVHNchlamday',
 time = c('last-5','last'),
 latitude = c(18, 21),
 longitude = c(-120, -119)
)
## with latitude
griddap('erdVHNchlamday',
  time = c('2015-04-01','2015-04-10'),
  latitude = c('last', 'last'),
  longitude = c(-120, -119)
)
## with longitude
griddap('erdVHNchlamday',
  time = c('2015-04-01','2015-04-10'),
  latitude = c(18, 21),
  longitude = c('last', 'last')
)

# datasets without lat/lon grid and with fmt=nc
# FIXME: this dataset is gone
# (x <- info('glos_tds_5912_ca66_3f41'))
# res <- griddap(x,
#   time = c('2018-04-01','2018-04-10'),
#   ny = c(1, 2),
#   nx = c(3, 5)
# )
## data.frame is empty
# res$data
## read in from the nc file path
# ncdf4::nc_open(res$summary$filename)
} # }