get_downloads — get_downloads • neotoma2

Download sites objects up to datum and chronology detail level.

get_downloads(x, verbose = TRUE, ...)

# S3 method for class 'numeric'
get_downloads(x, ...)

# S3 method for class 'sites'
get_downloads(x, verbose = TRUE, ...)

Arguments

x: Use a single number to extract site information
verbose: Status bar of items being downloaded
...: accepted arguments: sites, datasets

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites and datasets returned by the Neotoma API. Each "site" object contains 6 parameters that can be accessed as well:

siteid: site ID number
sitename: site's name
location: sf object that describes site's location
description
collunits: limited information on collunits

Each "collection unit" embedded in the "sites" object contains 6 parameters that can be accessed as well:

collunitid: collection unit ID number
handle: collection unit's handle
collunitname: collection unit's name
colldate: date in collection unit
substrate: substrate
location: sf object that describes site's location
datasets: detailed information regarding dataset

Each "dataset" nested in the "collection unit" contains the following detail of information:

datasetid: dataset ID number
datasetname: site's name
datasettype: type of data found
location: sf object that describes site's location
notes: notes on the dataset
taxa table: taxa table
pi list: P.I. info
analyst: analyst info
metadata: dataset metadata

Details

The get_downloads() command wraps the Neotoma API (api.neotomadb.org) call for downloads. The call itself uses a SQL query which accepts any one of the following parameters:

datasetid The unique dataset ID (integer) in Neotoma. Can be passed as a vector of dataset IDs.
all_data The API only downloads the first 25 records of the query. For the complete records, use all_data=TRUE

Author

Socorro Dominguez dominguezvid@wisc.edu

Examples

# \donttest{
# To find the downloads object of dataset 24:
tryCatch({
  downloads24 <- get_downloads(24)
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
# To find all downloads in Brazil
brazil <- '{"type": "Polygon",
"coordinates": [[
 [-73.125, -9.102096738726443],
 [-56.953125,-33.137551192346145],
 [-36.5625,-7.710991655433217],
 [-68.203125,13.923403897723347],
 [-73.125,-9.102096738726443]]]}'
tryCatch({
  brazil_datasets <- get_datasets(loc = brazil[1])
  brazil_downloads <- get_downloads(brazil_datasets)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
# }