Type: Package
Title: Access for Dryad Web Services
Description: Interface to the Dryad "Solr" API, their "OAI-PMH" service, and fetch datasets. Dryad (https://datadryad.org/) is a curated host of data underlying scientific publications.
Version: 1.0.0
License: MIT + file LICENSE
URL: https://docs.ropensci.org/rdryad, https://github.com/ropensci/rdryad
BugReports: https://github.com/ropensci/rdryad/issues
Encoding: UTF-8
Language: en-US
Imports: crul, curl, tibble, hoardr, zip, jsonlite, mime
Suggests: testthat, vcr
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-06-24 21:45:04 UTC; sckott
Author: Karthik Ram ORCID iD [aut], Scott Chamberlain ORCID iD [aut, cre], Carl Boettiger ORCID iD [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2020-06-25 06:00:02 UTC

Interface to the Dryad Web services

Description

Includes access to Dryad's Solr API, OAI-PMH service, and part of their REST API.

Package API

The functions match the three major sets of Dryad API routes for datasets, fiiles and versions.

Datasets:

Files:

Versions:

Defunct

The Dryad Solr API is no longer being updated, so the functions that used to work with it are all defunct, see solr-defunct

The Dryad OAI-PMH service is no longer being updated, so the functions that used to work with it are all defunct, see oai-defunct

More defunct functions:

Get a Dryad DOI from a handle, and vice versa

Description

These functions are defunct

Usage

doi2handle(...)

handle2doi(...)

Arguments

...

ignored

Download metadata for individual Dryad id's

Description

This function changed name to dr_get_records()

Usage

download_dryadmetadata(...)

Download url

Description

This function changed name to dryad_files

Usage

download_url(...)

Get datasets by DOI(s)

Description

Get datasets by DOI(s)

Usage

dryad_dataset(dois, ...)

Arguments

dois

(character) one or more DOIs, required

...

Further args passed on to crul::verb-GET

Value

a list of lists, each named by the input DOI

See Also

Other dryad-datasets: dryad_dataset_versions(), dryad_datasets()

Examples

## Not run: 
dryad_dataset(doi = "10.5061/dryad.f385721n")
dois <- c("10.5061/dryad.f385721n", "10.5061/dryad.7ct1n", "10.5061/dryad.1g626")
dryad_dataset(dois = dois)

## End(Not run)

Get dataset versions by DOI(s)

Description

Get dataset versions by DOI(s)

Usage

dryad_dataset_versions(dois, ...)

Arguments

dois

(character) one or more DOIs, required

...

Further args passed on to crul::verb-GET

Value

a list of lists, each named by the input DOI

See Also

Other dryad-datasets: dryad_datasets(), dryad_dataset()

Examples

## Not run: 
x = dryad_dataset_versions(dois = "10.5061/dryad.f385721n")
x
dois <- c("10.5061/dryad.f385721n", "10.5061/dryad.7ct1n", "10.5061/dryad.1g626")
dryad_dataset_versions(dois = dois)

## End(Not run)

List datasets

Description

List datasets

Usage

dryad_datasets(...)

Arguments

...

Further args passed on to crul::verb-GET

Value

a tibble

See Also

Other dryad-datasets: dryad_dataset_versions(), dryad_dataset()

Examples

## Not run: 
(x <- dryad_datasets())
x$meta
x$links
x$data

## End(Not run)

dryad_download

Description

Download datasets by their DOI(s)

Usage

dryad_download(dois, ...)

Arguments

dois

(character) one or more DOIs, required

...

Further args passed on to crul::verb-GET

Value

file path for the file

Examples

## Not run: 
dryad_download(dois = "10.5061/dryad.f385721n")
dois <- c("10.5061/dryad.f385721n", "10.5061/dryad.7ct1n", "10.5061/dryad.1g626")
dryad_download(dois = dois)

## End(Not run)

Download Dryad files

Description

This function is defunct

Usage

dryad_fetch(...)

Arguments

...

ignored

Get metadata information about a file

Description

Get metadata information about a file

Usage

dryad_files(ids, ...)

Arguments

ids

(numeric) one or more file ids, required

...

Further args passed on to crul::verb-GET

Value

a list of lists, each named by the input DOI

See Also

Other dryad-files: dryad_files_download()

Examples

## Not run: 
dryad_files(ids = 61859)
dryad_files(ids = 61858)
dryad_files(ids = c(61858, 61859))

## End(Not run)

Download a specific file

Description

Download a specific file

Usage

dryad_files_download(ids, ...)

Arguments

ids

(numeric) one or more file ids, required

...

Further args passed on to crul::verb-GET

Value

a list of lists, each named by the input DOI

Note

there's no use of cached files here because we can't determine what the file path will be before making the request, which requires knowing what the data type the file will be

See Also

Other dryad-files: dryad_files()

Examples

## Not run: 
dryad_files_download(ids = 61858)
dryad_files_download(ids = 61859)

## End(Not run)

Download Dryad file metadata

Description

This function is defunct

Usage

dryad_metadata(doi, ...)

Arguments

...

ignored

Get file DOIs for a Dryad package DOI

Description

This function is defunct

Usage

dryad_package_dois(doi, ...)

Arguments

...

ignored

Download metadata for all Dryad oai's for defined time period

Description

This function is defunct

Usage

getalldryad_metadata(...)

Defunct OAI-PMH functions

Description

Defunct OAI-PMH functions

Download metadata for individual Dryad id's

Learn about the Dryad OAI-PMH service.

List Dryad records

Gets OAI Dryad identifiers

Get available Dryad metadata formats

List the sets in the Dryad metadata repository.

Usage

dr_get_records(...)

dr_identify(...)

dr_list_records(
  prefix = "oai_dc",
  from = NULL,
  until = NULL,
  set = "hdl_10255_3",
  token = NULL,
  as = "df",
  ...
)

dr_list_identifiers(
  prefix = "oai_dc",
  from = NULL,
  until = NULL,
  set = "hdl_10255_3",
  token = NULL,
  as = "df",
  ...
)

dr_list_metadata_formats(...)

dr_list_sets(token = NULL, as = "df", ...)

Arguments

...

ignored

Details

The Dryad OAI-PMH service is no longer being updated See http://wiki.datadryad.org/Old:Dryad_API#OAI-PMH

Defunct functions:

Search metadata for search terms using regex

Description

This function is defunct

Usage

search_dryad(...)

Defunct Solr functions

Description

Defunct Solr functions

Search the Dryad Solr endpoint

Usage

d_solr_search(...)

d_solr_facet(...)

d_solr_group(...)

d_solr_highlight(...)

d_solr_mlt(...)

d_solr_stats(...)

Arguments

...

ignored

Details

The Dryad Solr service is no longer being updated See http://wiki.datadryad.org/Old:Dryad_API#SOLR_search_access

Defunct functions:

Get a dataset version by version ID

Description

Get a dataset version by version ID

Usage

dryad_versions(ids, ...)

dryad_versions_files(ids, ...)

dryad_versions_download(ids, ...)

Arguments

ids

(numeric/integer) one or more version ids, required

...

Further args passed on to crul::verb-GET

Details

dryad_versions() and dryad_versions_files() use async http requests, while dryad_versions_download() does not use async

Value

a list of lists, each named by the input DOI

Examples

## Not run: 
dryad_versions(ids = 18774)
dryad_versions_files(ids = 18774)
dryad_versions_download(ids = 18774)

## End(Not run)