Package 'roadoi'

R Client for the Unpaywall-API

Description

What is this client for?: roadoi interacts with the Unpaywall data service, which links DOIs representing scholarly works with open access versions.

Details

Use the oadoi_fetch() function in this package to get open access status information and full-text links from Unpaywall.

You are welcome to contribute to this package. Use GitHub's issue tracker for bug reporting and feature requests.

More details about the Unpaywall API: https://unpaywall.org/products/api.

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Fetch open access status information and full-text links using Unpaywall

Description

This is the main function to retrieve comprehensive open access status information from Unpaywall data service. Please play nice with the API. For each user, 100k calls per day are suggested. If you need to access more data, there is also a data dump available. For more info see https://unpaywall.org/products/snapshot.

Usage

oadoi_fetch(
  dois = NULL,
  email = Sys.getenv("roadoi_email"),
  .progress = "none",
  .flatten = FALSE
)

Arguments

dois	character vector, search by a single DOI or many DOIs. A rate limit of 100k requests per day is suggested. If you need to access more data, request the data dump https://unpaywall.org/dataset instead.
email	character vector, mandatory! Unpaywall requires your email address, so that they can track usage and notify you when something breaks. Set email address in your '.Renviron' file with the option 'roadoi_email' options(roadoi_email = "[email protected]"). You can open your '.Renviron' file calling 'file.edit("~/.Renviron")'. Save the file and restart your R session. To stop sharing your email when using rcrossref, delete it from your '.Renviron' file.
.progress	Shows the plyr-style progress bar. Options are "none", "text", "tk", "win", and "time". See create_progress_bar for details of each. By default, no progress bar is displayed.
.flatten	Simplify open access evidence output. If 'TRUE' it transforms the nested column oa_locations so that each open access evidence variable has its own column and each row represents a single full-text. Following these basic principles of "Tidy Data" makes data analysis and export as a spreadsheet more straightforward.

Value

The result is a tibble with each row representing a publication. Here are the returned columns and descriptions according to the API docu:

doi	DOI (always in lowercase).
best_oa_location	list-column describing the best OA location. Algorithm prioritizes publisher hosted content (eg Hybrid or Gold), then prioritizes versions closer to the version of record (PublishedVersion over AcceptedVersion), then more authoritative repositories (PubMed Central over CiteSeerX).
oa_locations	list-column of all the OA locations.
oa_locations_embargoed	list-column of locations expected to be available in the future based on information like license metadata and journals' delayed OA policies
data_standard	Indicates the data collection approaches used for this resource. 1 mostly uses Crossref for hybrid detection. 2 uses a more comprehensive hybrid detection methods.
is_oa	Is there an OA copy (logical)?
is_paratext	Is the item an ancillary part of a journal, like a table of contents? See here for more information https://support.unpaywall.org/support/solutions/articles/44001894783.
genre	Publication type
oa_status	Classifies OA resources by location and license terms as one of: gold, hybrid, bronze, green or closed. See here for more information https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-.
has_repository_copy	Is a full-text available in a repository?
journal_is_oa	Is the article published in a fully OA journal?
journal_is_in_doaj	Is the journal listed in the Directory of Open Access Journals (DOAJ).
journal_issns	ISSNs, i.e. unique numbers to identify journals.
journal_issn_l	Linking ISSN.
journal_name	Journal title, not normalized.
publisher	Publisher, not normalized.
published_date	Date published
year	Year published.
title	Publication title.
updated_resource	Time when the data for this resource was last updated.
authors	Lists author information (family name, given name and author role sequence), if available.

The columns best_oa_location. oa_locations and oa_locations_embargoed are list-columns that contain useful metadata about the OA sources found by Unpaywall.

If .flatten = TRUE the list-column oa_locations will be restructured in a long format where each OA fulltext is represented by one row.

These are:

endpoint_id	Unique repository identifier.
evidence	How the OA location was found and is characterized by Unpaywall?
host_type	OA full-text provided by publisher or repository.
is_best	Is this location the best_oa_location for its resource?
license	The license under which this copy is published, e.g. Creative Commons license.
pmh_id	OAI-PMH endpoint where we found this location.
repository institution	Hosting institution of the repository.
updated	Time when the data for this location was last updated.
url	The url_for_pdf if there is one; otherwise landing page URL.
url_for_landing_page	The URL for a landing page describing this OA copy.
url_for_pdf	The URL with a PDF version of this OA copy.
version	The content version accessible at this location following the DRIVER 2.0 Guidelines (https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings

Note that Unpaywall schema is only informally described. Check also https://unpaywall.org/data-format.

Examples

## Not run: 
oadoi_fetch("10.1038/nature12373", email = "[email protected]")
oadoi_fetch(dois = c("10.1016/j.jbiotec.2010.07.030",
"10.1186/1471-2164-11-245"), email = "[email protected]")
# flatten OA evidence
roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
                            "10.1103/physreve.88.012814",
                            "10.1093/reseval/rvaa038"),
                   email = "[email protected]", .flatten = TRUE)


## End(Not run)

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Get open access status information.

Description

In general, use oadoi_fetch instead. It calls this method, returning open access status information from all your requests.

Usage

oadoi_fetch_(doi = NULL, email = NULL)

Arguments

doi

character vector,a DOI

email

character vector, mandatory! Unpaywall requires your email address, so that they can track usage and notify you when something breaks. Set email address in your '.Renviron' file with the option 'roadoi_email' options(roadoi_email = "[email protected]"). You can open your '.Renviron' file calling 'file.edit("~/.Renviron")'. Save the file and restart your R session. To stop sharing your email when using rcrossref, delete it from your '.Renviron' file.

Value

A tibble

Examples

## Not run: 
oadoi_fetch_(doi = c("10.1016/j.jbiotec.2010.07.030"))

## End(Not run)

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Find OA copies with RStudio addin

Description

An RStudio addin to call oadoi_fetch(). Shows up as "Find free full-texts" in the RStudio addin menu.

Usage

roadoi_addin()

Details

The addin works as follows:

1. Copy up to ten line-separated DOIs into the text area

2. Press the button "Run!"

3. Click on the links in the table to download full-text

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