tabledap {rerddap}

Get ERDDAP tabledap data.

Description

Get ERDDAP tabledap data.

Usage

tabledap(
  x,
  ...,
  fields = NULL,
  distinct = FALSE,
  orderby = NULL,
  orderbymax = NULL,
  orderbymin = NULL,
  orderbyminmax = NULL,
  units = NULL,
  url = eurl(),
  store = disk(),
  callopts = list()
)

Arguments

x

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()

...

Any number of key-value pairs in quotes as query constraints. See Details & examples

fields

Columns to return, as a character vector

distinct

If TRUE ERDDAP will sort all of the rows in the results table (starting with the first requested variable, then using the second requested variable if the first variable has a tie, ...), then remove all non-unique rows of data. In many situations, ERDDAP can return distinct values quickly and efficiently. But in some cases, ERDDAP must look through all rows of the source dataset.

orderby

If used, ERDDAP will sort all of the rows in the results table (starting with the first variable, then using the second variable if the first variable has a tie, ...). Normally, the rows of data in the response table are in the order they arrived from the data source. orderBy allows you to request that the results table be sorted in a specific way. For example, use orderby=c("stationID,time") to get the results sorted by stationID, then time. The orderby variables MUST be included in the list of requested variables in the fields parameter.

orderbymax

Give a vector of one or more fields, that must be included in the fields parameter as well. Gives back data given constraints. ERDDAP will sort all of the rows in the results table (starting with the first variable, then using the second variable if the first variable has a tie, ...) and then just keeps the rows where the value of the last sort variable is highest (for each combination of other values).

orderbymin

Same as orderbymax parameter, except returns minimum value.

orderbyminmax

Same as orderbymax parameter, except returns two rows for every combination of the n-1 variables: one row with the minimum value, and one row with the maximum value.

units

One of 'udunits' (units will be described via the UDUNITS standard (e.g.,degrees_C)) or 'ucum' (units will be described via the UCUM standard (e.g., Cel)).

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

callopts

Curl options passed on to crul::verb-GET (must be named parameters)

Details

For key-value pair query constraints, the valid operators are =, != (not equals), =~ (a regular expression test), <, <=, >, and >= . For regular expressions you need to add a regular expression. For others, nothing more is needed. Construct the entry like 'time>=2001-07-07' with the parameter on the left, value on the right, and the operator in the middle, all within a set of quotes. Since ERDDAP accepts values other than =, we can't simply do time = '2001-07-07' as we normally would.

Server-side functionality: Some tasks are done server side. You don't have to worry about what that means. They are provided via parameters in this function. See distinct, orderby, orderbymax, orderbymin, orderbyminmax, and units.

Data is cached based on all parameters you use to get a dataset, including base url, query parameters. If you make the same exact call in the same or a different R session, as long you don't clear the cache, the function only reads data from disk, and does not have to request the data from the web again.

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

Value

An object of class tabledap. This class is a thin wrapper around a data.frame, so the data you get back is a data.frame with metadata attached as attributes (datasetid, path (path where the csv is stored on your machine), url (url for the request))

References

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

Examples

## Not run: 
# Just passing the datasetid without fields gives all columns back
tabledap('erdCinpKfmBT')

# Pass time constraints
tabledap('erdCinpKfmBT', 'time>=2006-08-24')

# Pass in fields (i.e., columns to retrieve) & time constraints
tabledap('erdCinpKfmBT',
  fields = c('longitude', 'latitude', 'Aplysia_californica_Mean_Density'),
  'time>=2006-08-24'
)

# Get info on a datasetid, then get data given information learned
info('erdCalCOFIlrvsiz')$variables
tabledap('erdCalCOFIlrvsiz', fields=c('latitude','longitude','larvae_size',
   'itis_tsn'), 'time>=2011-10-25', 'time<=2011-10-31')

# An example workflow
## Search for data
(out <- ed_search(query='fish', which = 'table'))
## Using a datasetid, search for information on a datasetid
id <- out$alldata[[1]]$dataset_id
vars <- info(id)$variables
## Get data from the dataset
vars$variable_name[1:3]
tabledap(id, fields = vars$variable_name[1:3])

# Time constraint
## Limit by time with date only
(info <- info('erdCinpKfmBT'))
tabledap(info, fields = c(
  'latitude','longitude','Haliotis_fulgens_Mean_Density'),
  'time>=2001-07-14')

# Use distinct parameter - compare to distinct = FALSE
tabledap('sg114_3',
   fields=c('longitude','latitude','trajectory'),
   'time>=2008-12-05', distinct = TRUE)

# Use units parameter
## In this example, values are the same, but sometimes they can be different
## given the units value passed
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', units='udunits')
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', units='ucum')

# Use orderby parameter
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', orderby='temperature')
# Use orderbymax parameter
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', orderbymax='temperature')
# Use orderbymin parameter
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', orderbymin='temperature')
# Use orderbyminmax parameter
tabledap('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'),
   'time>=2007-09-19', 'time<=2007-09-21', orderbyminmax='temperature')
# Use orderbymin parameter with multiple values
tabledap('erdCinpKfmT',
   fields=c('longitude','latitude','time','depth','temperature'),
   'time>=2007-06-10', 'time<=2007-09-21',
   orderbymax=c('depth','temperature')
)

# Integrate with taxize
out <- tabledap('erdCalCOFIlrvcntHBtoHI',
   fields = c('latitude','longitude','scientific_name','itis_tsn'),
   'time>=2007-06-10', 'time<=2007-09-21'
)
tsns <- unique(out$itis_tsn[1:100])
library("taxize")
classif <- classification(tsns, db = "itis")
head(rbind(classif)); tail(rbind(classif))

# Write to memory (within R), or to disk
(out <- info('erdCinpKfmBT'))
## disk, by default (to prevent bogging down system w/ large datasets)
## the 2nd call is much faster as it's mostly just the time of reading
## in the table from disk
system.time( tabledap('erdCinpKfmBT', store = disk()) )
system.time( tabledap('erdCinpKfmBT', store = disk()) )
## memory
tabledap('erdCinpKfmBT', store = memory())

# use a different ERDDAP server
## NOAA IOOS NERACOOS
url <- "http://www.neracoos.org/erddap/"
tabledap("E01_optics_hist", url = url)

## End(Not run)