Package 'scholidonline'

Convert scholarly identifiers across systems

Description

Convert scholarly identifiers across registries, for example from PMID to DOI.

Usage

id_convert(
  x,
  to = scholidonline_types(),
  from = NULL,
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

x	A character vector of scholarly identifiers.
to	A single target identifier type string, such as "doi" or "pmid". See scholidonline_types() for all supported values.
from	A single source identifier type string, or NULL to infer the source type for each element of x.
provider	A single provider string specifying which online service to use for the conversion. Use "auto" to use the default provider for the requested conversion. In most cases, "auto" is appropriate.
...	Reserved for future provider-specific arguments.
quiet	A single logical value; if TRUE, suppress provider warnings and messages where possible.

Value

A character vector of converted identifiers. Elements that cannot be identified, normalized, or converted return NA_character_.

Examples

id_convert("12345678", to = "doi", from = "pmid")
  id_convert("10.1038/nature12373", to = "pmid", from = "doi")

---

Check whether scholarly identifiers exist

Description

Check whether scholarly identifiers are found in their respective registries.

Usage

id_exists(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

x	A character vector of identifiers.
type	A single identifier type string, or "auto" to infer the type for each element of x. See scholidonline_types() for supported values.
provider	A single provider string specifying which online service to use for the lookup. Use "auto" to use the default provider for the resolved identifier type. In most cases, "auto" is appropriate.
...	Reserved for future provider-specific arguments.
quiet	A single logical value; if TRUE, suppress provider warnings and messages where possible.

Value

A logical vector. TRUE indicates that the identifier was found, FALSE indicates that it was not found, and NA indicates that the input could not be identified, normalized, or checked reliably.

Examples

id_exists("10.1038/nature12373", type = "doi")
  id_exists(c("31452104", "PMC6784763"))

---

Return identifiers linked to the same scholarly record

Description

Return identifiers that external registries link to the same scholarly record or to a closely corresponding version of it.

Usage

id_links(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

x	A character vector of identifiers.
type	A single identifier type string, or "auto" to infer the type for each element of x. See scholidonline_types() for supported values.
provider	A single provider string specifying which online service to use. Use "auto" to use the default provider for the resolved identifier type. In most cases, "auto" is appropriate.
...	Reserved for future provider-specific arguments.
quiet	A single logical value; if TRUE, suppress provider warnings and messages where possible.

Details

id_links() is vectorized over x and returns a long data.frame with one row per discovered identifier link.

Typical links include DOI <-> PMID, DOI <-> PMCID, PMID <-> PMCID, arXiv ID <-> DOI, and ORCID -> DOI for works recorded in ORCID.

Only identifier links explicitly exposed by the queried provider are returned. id_links() does not retrieve general metadata or broader related records unless the provider represents them as direct identifier links.

Trivial self-links are excluded from the result.

Value

A data.frame with columns query, query_type, linked_type, linked_id, and provider. If no links are found, a zero-row data.frame with these columns is returned.

Examples

out <- id_links("31452104", provider = "epmc")
  knitr::kable(out)

---

Retrieve scholarly metadata

Description

Retrieve structured metadata for scholarly identifiers from external registries.

Usage

id_metadata(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  fields = NULL,
  ...,
  quiet = FALSE
)

Arguments

x	A character vector of identifiers.
type	A single identifier type string, or "auto" to infer the type for each element of x. See scholidonline_types() for supported values.
provider	A single provider string specifying which online service to use. Use "auto" to use the default provider for the resolved identifier type. In most cases, "auto" is appropriate.
fields	An optional character vector naming the columns to return. If NULL, all default columns are returned. Unknown field names are ignored.
...	Reserved for future provider-specific arguments.
quiet	A single logical value; if TRUE, suppress provider warnings and messages where possible.

Details

id_metadata() is vectorized over x and returns a data.frame with one row per input identifier.

For providers that support batch lookup, such as arXiv, multiple identifiers may be resolved using a single provider request. This does not change the public return shape: the output still contains one row per input identifier.

The function returns a consistent cross-provider subset of core bibliographic metadata, such as title, publication year, container title, linked DOI, PMID, PMCID, and a canonical URL when available.

Value

A data.frame with one row per input identifier. By default, the returned columns are input, type, provider, title, year, container, doi, pmid, pmcid, and url. Inputs that cannot be identified, normalized, or resolved are returned as rows with missing metadata fields.

Examples

out <- id_metadata("10.1038/nature12373", type = "doi")
  knitr::kable(out)
  out <- id_metadata(c("31452104", "PMC6821181"))
  knitr::kable(out)
  out <- id_metadata(
    "10.1038/nature12373",
     fields = c("title", "year", "doi")
     )
  knitr::kable(out)

---

Supported scholidonline capabilities

Description

Return a summary of the capabilities supported by the scholidonline package.

The returned table describes, for each supported identifier type:

• which single-identifier operations are available (exists, links, meta),

• which identifier conversions are available,

• which providers support each capability, and

• which provider is used by default when provider = "auto".

This function is useful for discovering what scholidonline can do for a given identifier type or conversion pair.

Usage

scholidonline_capabilities()

Value

A data.frame with one row per supported capability and the following columns:

• type: source identifier type

• operation: operation name (exists, links, meta, or convert)

• target: target identifier type for conversion operations, otherwise NA

• providers: comma-separated names of providers supporting the capability

• default_provider: default provider used when provider = "auto"

Examples

caps <- scholidonline_capabilities()

subset(caps, type == "pmid" & operation == "convert")

subset(caps, type == "doi" & target == "pmcid")

---

Supported scholidonline identifier types

Description

Return the set of identifier types supported by the scholidonline package.

This is the set of identifier types for which scholidonline provides registry-backed functionality, including existence checks, identifier conversion, metadata retrieval, and link discovery.

Usage

scholidonline_types()

Value

A character vector of supported identifier type strings.

Examples

scholidonline_types()
"doi" %in% scholidonline_types()

---