get_downloads: get_downloads

In neotoma2: Working with the Neotoma Paleoecology Database

get_downloads

Description

Information for Fossil Datasets

Usage

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

Arguments

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

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

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:

\code{siteid}	site ID number
\code{sitename}	site's name
\code{location}	sf object that describes site's location
\code{description}
\code{collunits}	limited information on collunits

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

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

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

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

Author(s)

Socorro Dominguez [e-mail]

Examples

# To find the downloads object of dataset 24:
downloads24 <- get_downloads(24)

# 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]]]}'
brazil_datasets <- get_datasets(loc = brazil[1])
brazil_downloads <- get_downloads(brazil_datasets)

neotoma2 documentation built on May 29, 2024, 6:21 a.m.