Package 'rscopus' reference manual

Title:	Scopus Database 'API' Interface
Description:	Uses Elsevier 'Scopus' API <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.
Authors:	John Muschelli [aut, cre]
Maintainer:	John Muschelli <[email protected]>
License:	GPL-2
Version:	0.7.2
Built:	2024-10-25 04:01:54 UTC
Source:	https://github.com/muschellij2/rscopus

SCOPUS Abstract Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an abstract from the Elsevier Abstract Retrieval API

Usage

abstract_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id", "pui", "group_id"),
  http_end = NULL,
  ...
)
abstract_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id", "pui", "group_id"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for abstract
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   view = "FULL",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   view = "FULL",
   verbose = FALSE)
}

Search Affiliation Content on SCOPUS

Description

Searches SCOPUS to get information about documents on an affiliation

Usage

affil_df(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  facets = NULL,
  sort = "document-count",
  ...
)

affil_data(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  facets = NULL,
  sort = "document-count",
  ...
)
affil_df(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  facets = NULL,
  sort = "document-count",
  ...
)

affil_data(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  facets = NULL,
  sort = "document-count",
  ...
)

Arguments

`affil_id`	Affiliation ID number.
`affil_name`	affiliation name. Disregarded if `affil_id` is specified
`api_key`	Elsevier API key
`verbose`	Print diagnostic messages
`facets`	Facets sent in query. See https://dev.elsevier.com/api_docs.html
`sort`	sorting sent to query
`...`	Arguments to be passed to `author_search`

Value

List of entries from SCOPUS

Note

The affil_data command will return the list of all entries as well as the data.frame

List of SCOPUS Entries to List of Affiliations Data Frames

Description

Take a SCOPUS entry and transform it to a data frame of affiliations

Usage

affil_list_to_df(affils)
affil_list_to_df(affils)

Arguments

affils

List of affiliations, from entries_to_affil_list

Value

A data.frame of affiliation information. A column named "index" denotes the element of the object affils that the row corresponds to

Search Author Content on SCOPUS

Description

Searches SCOPUS to get information about documents on an author.

Usage

affil_search(
  affil_id,
  searcher = "AF-ID",
  http = "https://api.elsevier.com/content/search/affiliation",
  facets = "affilcountry(sort=document-count)",
  count = 200,
  ...
)
affil_search(
  affil_id,
  searcher = "AF-ID",
  http = "https://api.elsevier.com/content/search/affiliation",
  facets = "affilcountry(sort=document-count)",
  count = 200,
  ...
)

Arguments

`affil_id`	Affiliation ID number
`searcher`	Identifier for Affiliation ID. Do not change unless you know exactly what the API calls for.
`http`	Address for scopus api
`facets`	Facets sent in query. See https://dev.elsevier.com/api_docs.html
`count`	number of records to retrieve (below 200, see https://dev.elsevier.com/api_key_settings.html)
`...`	Arguments to be passed to `author_search`

Value

List of entries from SCOPUS

SCOPUS Affiliation Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an affiliation from the Elsevier Affiliation Retrieval API

Usage

affiliation_retrieval(
  id,
  identifier = c("affiliation_id", "eid"),
  http_end = NULL,
  ...
)
affiliation_retrieval(
  id,
  identifier = c("affiliation_id", "eid"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for affiliation
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = affiliation_retrieval("60006183", identifier = "affiliation_id",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = affiliation_retrieval("60006183", identifier = "affiliation_id",
   verbose = FALSE)
}

Find all affiliations

Description

Take a SCOPUS entry and transform it to a data frame of all affiliations listed in there

Usage

all_possible_affils(entries)
all_possible_affils(entries)

Arguments

entries

list of entries from SCOPUS, usually from author_search result

Value

A data.frame of affiliations

ScienceDirect Article Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an article from the Elsevier Article Retrieval API

Usage

article_retrieval(
  id,
  view = c("META", "META_ABS", "META_ABS_REF", "FULL", "REF", "ENTITLED"),
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  http_end = NULL,
  ...
)
article_retrieval(
  id,
  view = c("META", "META_ABS", "META_ABS_REF", "FULL", "REF", "ENTITLED"),
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for article
`view`	Which view to see. See https://dev.elsevier.com/guides/ArticleRetrievalViews.htm
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
    x = article_retrieval("S1053811915002700", identifier = "pii",
    verbose = FALSE, view = "FULL")
    gen = x$content$`full-text-retrieval-response`
    ot = gen$originalText
} else {
 x = article_retrieval("S1053811915002700",
   identifier = "pii",
   api_key_error = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
    x = article_retrieval("S1053811915002700", identifier = "pii",
    verbose = FALSE, view = "FULL")
    gen = x$content$`full-text-retrieval-response`
    ot = gen$originalText
} else {
 x = article_retrieval("S1053811915002700",
   identifier = "pii",
   api_key_error = FALSE)
}

Search Author Content on SCOPUS

Description

Searches SCOPUS to get information about documents on an author. Note, author_list returns a list of the entries from author_search, but allows you to put in a name.

Usage

author_df(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  all_author_info = FALSE,
  http = "https://api.elsevier.com/content/search/scopus",
  view = "COMPLETE",
  count = 25,
  general = TRUE,
  scrub = FALSE,
  headers = NULL,
  ...
)

author_df_orig(..., general = FALSE)

author_list(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  http = "https://api.elsevier.com/content/search/scopus",
  view = "COMPLETE",
  count = 25,
  headers = NULL,
  ...
)

author_data(
  ...,
  verbose = TRUE,
  all_author_info = FALSE,
  general = TRUE,
  scrub = FALSE
)
author_df(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  all_author_info = FALSE,
  http = "https://api.elsevier.com/content/search/scopus",
  view = "COMPLETE",
  count = 25,
  general = TRUE,
  scrub = FALSE,
  headers = NULL,
  ...
)

author_df_orig(..., general = FALSE)

author_list(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  api_key = NULL,
  verbose = TRUE,
  http = "https://api.elsevier.com/content/search/scopus",
  view = "COMPLETE",
  count = 25,
  headers = NULL,
  ...
)

author_data(
  ...,
  verbose = TRUE,
  all_author_info = FALSE,
  general = TRUE,
  scrub = FALSE
)

Arguments

`au_id`	Author ID number. Overrides any first/last name argument
`last_name`	last name of author
`first_name`	first name of author
`api_key`	Elsevier API key
`verbose`	Print diagnostic messages
`all_author_info`	Should all author info be recorded instead of that just to the author given
`http`	Address for scopus api
`view`	type of view to give, see https://api.elsevier.com/documentation/ScopusSearchAPI.wadl
`count`	number of records to retrieve (below 25, see https://dev.elsevier.com/api_key_settings.html)
`general`	Should `gen_entries_to_df` instead of the way before version 0.5.10.9001
`scrub`	Should 'scrub_identifier' be run on the identifier?
`headers`	Headers passed to `add_headers`, passed to `GET`
`...`	Arguments to be passed to `author_search`

Value

List of entries from SCOPUS

Note

The author_data command will return the list of all entries as well as the data.frame.

Examples

if (is_elsevier_authorized()) {
res = author_df(last_name = "Muschelli", first_name = "John",
verbose = FALSE)
}
if (is_elsevier_authorized()) {
res = author_df(last_name = "Muschelli", first_name = "John",
verbose = FALSE)
}

SCOPUS Author Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an author from the Elsevier Author Retrieval API

Usage

author_retrieval_id(
  id,
  identifier = c("author_id", "eid"),
  http_end = NULL,
  ...
)

multi_author_retrieval(
  id,
  identifier = c("author_id", "eid"),
  http_end = NULL,
  ...
)

author_retrieval(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  view = c("LIGHT", "STANDARD", "ENHANCED", "METRICS", "ENTITLED"),
  self_cite = c("include", "exclude"),
  http_end = NULL,
  verbose = TRUE,
  api_key = NULL,
  headers = NULL,
  ...
)
author_retrieval_id(
  id,
  identifier = c("author_id", "eid"),
  http_end = NULL,
  ...
)

multi_author_retrieval(
  id,
  identifier = c("author_id", "eid"),
  http_end = NULL,
  ...
)

author_retrieval(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  view = c("LIGHT", "STANDARD", "ENHANCED", "METRICS", "ENTITLED"),
  self_cite = c("include", "exclude"),
  http_end = NULL,
  verbose = TRUE,
  api_key = NULL,
  headers = NULL,
  ...
)

Arguments

`id`	Identifier for author
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`
`au_id`	Author ID number. Overrides any first/last name argument
`last_name`	last name of author
`first_name`	first name of author
`view`	Which view to see. See https://api.elsevier.com/documentation/AuthorRetrievalAPI.wadl
`self_cite`	Should self-citations be included?
`verbose`	Print diagnostic messages
`api_key`	Elsevier API key
`headers`	Headers passed to `add_headers`, passed to `GET`

Value

List of elements, similar to generic_elsevier_api

Note

See https://api.elsevier.com/documentation/AuthorRetrievalAPI.wadl for documentation

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = author_retrieval(au_id = "40462056100",
   verbose = FALSE)
   x = author_retrieval_id("40462056100", identifier = "author_id",
   verbose = FALSE)
} else {
 x = author_retrieval_id(
 "40462056100",
 identifier = "author_id",
   api_key_error = FALSE, verbose = FALSE)
 x = author_retrieval(
 au_id = "40462056100",
   api_key_error = FALSE, verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = author_retrieval(au_id = "40462056100",
   verbose = FALSE)
   x = author_retrieval_id("40462056100", identifier = "author_id",
   verbose = FALSE)
} else {
 x = author_retrieval_id(
 "40462056100",
 identifier = "author_id",
   api_key_error = FALSE, verbose = FALSE)
 x = author_retrieval(
 au_id = "40462056100",
   api_key_error = FALSE, verbose = FALSE)
}

Search Author Content on SCOPUS

Description

Searches SCOPUS to get information about documents on an author.

Usage

author_search(
  au_id,
  api_key = NULL,
  http = "https://api.elsevier.com/content/search/author",
  count = 200,
  start = 0,
  verbose = TRUE,
  facets = "subjarea(sort=fd,count=350)",
  searcher = "AU-ID",
  max_count = Inf,
  view = c("STANDARD", "COMPLETE"),
  add_query = NULL,
  headers = NULL,
  wait_time = 0,
  ...
)
author_search(
  au_id,
  api_key = NULL,
  http = "https://api.elsevier.com/content/search/author",
  count = 200,
  start = 0,
  verbose = TRUE,
  facets = "subjarea(sort=fd,count=350)",
  searcher = "AU-ID",
  max_count = Inf,
  view = c("STANDARD", "COMPLETE"),
  add_query = NULL,
  headers = NULL,
  wait_time = 0,
  ...
)

Arguments

`au_id`	Author ID number
`api_key`	API Key for Elsevier
`http`	Address for scopus api
`count`	number of records to retrieve (below 200, see https://dev.elsevier.com/api_key_settings.html)
`start`	where should the records start gathering
`verbose`	Print diagnostic messages
`facets`	Facets sent in query. See https://dev.elsevier.com/api_docs.html
`searcher`	Identifier for author ID. Do not change unless you know exactly what the API calls for.
`max_count`	Maximum count of records to be returned.
`view`	type of view to give, see https://api.elsevier.com/documentation/AuthorSearchAPI.wadl
`add_query`	Things to add to the query parameter for the request
`headers`	additional headers to be added to `add_headers`
`wait_time`	The time in seconds to wait across consecutive requests of a single search (when records > 25)
`...`	Arguments to be passed to the query list for `GET`

Value

List of entries from SCOPUS

Examples

## Not run: 
author_search(au_id = "Smith", searcher = "affil(princeton) and authlast")
berk = author_search(au_id = "berkeley", searcher = "affil", count =100)

## End(Not run)
## Not run: 
author_search(au_id = "Smith", searcher = "affil(princeton) and authlast")
berk = author_search(au_id = "berkeley", searcher = "affil", count =100)

## End(Not run)

Search Authors by Affiliation on SCOPUS

Description

Searches SCOPUS to get information about authors with a certain affiliation

Usage

author_search_by_affil(affil_id, searcher = "AF-ID", ...)
author_search_by_affil(affil_id, searcher = "AF-ID", ...)

Arguments

`affil_id`	Affiliation ID number
`searcher`	Identifier for Affiliation ID. Do not change unless you know exactly what the API calls for.
`...`	Arguments to be passed to `GET`

Value

List of entries from SCOPUS

Makes a `bibtex` entry from an output of `abstract_retrieval` or `article_retrieval`

Description

Makes a bibtex entry from an output of abstract_retrieval or article_retrieval

Usage

bibtex_core_data(x)
bibtex_core_data(x)

Arguments

`x`	output of `abstract_retrieval` or `article_retrieval`, with both `get_statement` and `content`

Value

A character vector of bibtex values

Note

Adapted from https://github.com/pybliometrics-dev/pybliometrics/blob/master/pybliometrics/scopus/abstract_retrieval.py

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   res = bibtex_core_data(x)
   cat(res)
   x = abstract_retrieval("84929707579", identifier = "scopus_id",
   verbose = FALSE)
   res2 = bibtex_core_data(x)
   cat(res2)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = abstract_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   res = bibtex_core_data(x)
   cat(res)
   x = abstract_retrieval("84929707579", identifier = "scopus_id",
   verbose = FALSE)
   res2 = bibtex_core_data(x)
   cat(res2)
}

SCOPUS Citation Retrieval

Description

SCOPUS Citation Retrieval

Usage

citation_retrieval(
  scopus_id = NULL,
  pii = NULL,
  doi = NULL,
  pubmed_id = NULL,
  date_range = NULL,
  exclude = NULL,
  ...
)

parse_citation_retrieval(result)
citation_retrieval(
  scopus_id = NULL,
  pii = NULL,
  doi = NULL,
  pubmed_id = NULL,
  date_range = NULL,
  exclude = NULL,
  ...
)

parse_citation_retrieval(result)

Arguments

`scopus_id`	Scopus Identifier
`pii`	Scopus Identifier
`doi`	Scopus Identifier
`pubmed_id`	PubMed Identifier
`date_range`	date range to specify, must be length 2
`exclude`	either exclude-self or exclude-books for exclusion of citation
`...`	Arguments to be passed to `generic_elsevier_api`
`result`	result from `citation_retrieval`, which has an element of `content`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = Sys.getenv("Elsevier_API_Interactive")
set_api_key(api_key)
if (!is.null(api_key) & nchar(api_key) > 0){
   result = citation_retrieval(pii = c("S0140673616324102",
   "S0014579301033130"),
   verbose = FALSE)
   if (httr::status_code(result$get_statement) < 400) {
      res = parse_citation_retrieval(result)
   }

}
set_api_key(NULL)
api_key = Sys.getenv("Elsevier_API_Interactive")
set_api_key(api_key)
if (!is.null(api_key) & nchar(api_key) > 0){
   result = citation_retrieval(pii = c("S0140673616324102",
   "S0014579301033130"),
   verbose = FALSE)
   if (httr::status_code(result$get_statement) < 400) {
      res = parse_citation_retrieval(result)
   }

}
set_api_key(NULL)

Collapse Affiliations to one row

Description

Take an individual SCOPUS entry and transform it to a data frame of affiliations

Usage

collapse_affil(affils, collapse = ";")
collapse_affil(affils, collapse = ";")

Arguments

`affils`	Data frame of affiliations to be collapsed usually from `author_search`
`collapse`	What should values be collapsed using as a separator

Value

A data.frame of affiliation information

Get Complete Author Information and ID from Scopus

Description

Get Complete Author Information and ID from Scopus

Usage

complete_multi_author_info(au_id = NULL, api_key = NULL, verbose = TRUE, ...)
complete_multi_author_info(au_id = NULL, api_key = NULL, verbose = TRUE, ...)

Arguments

`au_id`	vector of Author IDs
`api_key`	Elsevier API key
`verbose`	Print messages from specification
`...`	options to pass to `generic_elsevier_api`

Value

List of information

Authenticate API Key and get Token

Description

Authenticate API Key and get Token

Usage

elsevier_authenticate(
  api_key = NULL,
  api_key_error = TRUE,
  choice = NULL,
  verbose = TRUE,
  headers = NULL,
  ...
)

is_elsevier_guest(...)

is_elsevier_authorized(...)
elsevier_authenticate(
  api_key = NULL,
  api_key_error = TRUE,
  choice = NULL,
  verbose = TRUE,
  headers = NULL,
  ...
)

is_elsevier_guest(...)

is_elsevier_authorized(...)

Arguments

`api_key`	Elsevier API key
`api_key_error`	Should there be an error if no API key?
`choice`	Choice of which registered See https://dev.elsevier.com/tecdoc_api_authentication.html
`verbose`	Print messages from specification
`headers`	Headers passed to `add_headers`, passed to `GET`
`...`	Additional arguments to send to `GET`.

Value

List of content, the GET request, and the token

Examples

if (have_api_key()) {
   auth = elsevier_authenticate()
}
if (have_api_key()) {
   auth = elsevier_authenticate()
}

SCOPUS Embase Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an Embase Entry from the Elsevier Embase Retrieval API

Usage

embase_retrieval(
  id,
  identifier = c("lui", "pii", "doi", "embase", "pubmed_id", "medline"),
  http_end = NULL,
  ...
)
embase_retrieval(
  id,
  identifier = c("lui", "pii", "doi", "embase", "pubmed_id", "medline"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for abstract
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = embase_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = embase_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}

ScienceDirect Text Entitlement Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an entitlement from the Elsevier Text Entitlement API

Usage

entitlement_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  http_end = NULL,
  ...
)
entitlement_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for entitlement
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = entitlement_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = entitlement_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}

List of SCOPUS Entries to List of Affiliations Data Frames

Description

Take a SCOPUS entry and transform it to a data frame of affiliations

Usage

entries_to_affil_list(entries)
entries_to_affil_list(entries)

Arguments

entries

list of entries from SCOPUS, usually from author_search result

Value

A data.frame of affiliation information

List of SCOPUS Entries to Data Frame of Citations

Description

Take a SCOPUS entry list and transform it to a data frame of citation and article information

Usage

entries_to_citation_df(entries)
entries_to_citation_df(entries)

Arguments

entries

list of entries from SCOPUS, usually from author_search result

Value

A data.frame of citation information

Convert Entries into a data.frame

Description

Converts a list of entries into a data.frame of records

Usage

entries_to_df(entries, au_id = NULL, verbose = TRUE)

entries_to_df2(entries, verbose = TRUE)
entries_to_df(entries, au_id = NULL, verbose = TRUE)

entries_to_df2(entries, verbose = TRUE)

Arguments

`entries`	Entries from the output of a command
`au_id`	Author ID number. Overrides any first/last name argument
`verbose`	Print diagnostic messages

Value

Data frame of records

SCOPUS Entry to Affiliation

Description

Take an individual SCOPUS entry and transform it to a data frame of affiliations

Usage

entry_to_affil(x, all_affils)
entry_to_affil(x, all_affils)

Arguments

`x`	individual entry from SCOPUS, usually from `author_search`
`all_affils`	Affiliation data.frame from `all_possible_affils`

Value

A data.frame of affiliation information

Generally Convert Entries into a list of `data.frame`s

Description

Generally Convert Entries into a list of data.frames

Usage

gen_entries_to_df(entries, scrub = FALSE)
gen_entries_to_df(entries, scrub = FALSE)

Arguments

`entries`	Entries from the output of a command
`scrub`	Should 'scrub_identifier' be run on the identifier?

Value

List of data.frames from entries

Generic Elsevier Search

Description

Runs GET on generic Elsevier Search

Usage

generic_elsevier_api(
  query = NULL,
  type = c("search", "article", "entitlement", "recommendation", "object", "fragment",
    "abstract", "affiliation", "embase", "author", "serial", "nonserial", "subject",
    "holdings", "citation-count", "citations", "metadata", "ev", "ev_records",
    "analytics"),
  search_type = c("affiliation", "author", "scopus", "scidir", "scidir-object",
    "sciencedirect", "plumx"),
  api_key = NULL,
  headers = NULL,
  content_type = c("content", "feedback"),
  root_http = "https://api.elsevier.com",
  http_end = NULL,
  verbose = TRUE,
  api_key_error = TRUE,
  ...
)
generic_elsevier_api(
  query = NULL,
  type = c("search", "article", "entitlement", "recommendation", "object", "fragment",
    "abstract", "affiliation", "embase", "author", "serial", "nonserial", "subject",
    "holdings", "citation-count", "citations", "metadata", "ev", "ev_records",
    "analytics"),
  search_type = c("affiliation", "author", "scopus", "scidir", "scidir-object",
    "sciencedirect", "plumx"),
  api_key = NULL,
  headers = NULL,
  content_type = c("content", "feedback"),
  root_http = "https://api.elsevier.com",
  http_end = NULL,
  verbose = TRUE,
  api_key_error = TRUE,
  ...
)

Arguments

`query`	Query to run, not overall query, but 'queryParam' query
`type`	Type of search. See https://dev.elsevier.com/api_docs.html
`search_type`	Type of search if `type = "search"`. See https://dev.elsevier.com/api_docs.html
`api_key`	Elsevier API key
`headers`	Headers passed to `add_headers`, passed to `GET`
`content_type`	Is the data content or feedback?
`root_http`	address to use for query
`http_end`	string to add to end of http specification (done using `paste0`)
`verbose`	Print messages from specification
`api_key_error`	Should there be an error if no API key?
`...`	Options passed to queryParam for `GET`

Value

List of elements, content and the GET request

Examples

## Not run: 
query_string = "affil(hopkins)"
# Use affiliation query
s = generic_elsevier_api(query = query_string,
                         type = "search", search_type = "affiliation",
                         api_key = api_key,
                      verbose = FALSE)

# Use author query
s = generic_elsevier_api(query = query_string,
type = "search", search_type = "author",
api_key = api_key,
                      verbose = FALSE)

# Query abstract by pii
s = generic_elsevier_api(query = "",
                      type = "abstract", http_end = "pii/S1053811915002700",
                      api_key = api_key,
                      verbose = FALSE)

## End(Not run)
## Not run: 
query_string = "affil(hopkins)"
# Use affiliation query
s = generic_elsevier_api(query = query_string,
                         type = "search", search_type = "affiliation",
                         api_key = api_key,
                      verbose = FALSE)

# Use author query
s = generic_elsevier_api(query = query_string,
type = "search", search_type = "author",
api_key = api_key,
                      verbose = FALSE)

# Query abstract by pii
s = generic_elsevier_api(query = "",
                      type = "abstract", http_end = "pii/S1053811915002700",
                      api_key = api_key,
                      verbose = FALSE)

## End(Not run)

Get Affiliation Information and ID from Scopus

Description

Uses SCOPUS affiliation search to identify affiliation identification information

Usage

get_affiliation_info(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = FALSE,
  headers = NULL
)
get_affiliation_info(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = FALSE,
  headers = NULL
)

Arguments

`affil_id`	ID of affiliation
`affil_name`	name of affiliation
`api_key`	Elsevier API key
`verbose`	Print messages from specification
`headers`	Headers passed to `add_headers`, passed to `GET`

Value

A data.frame of affiliation information

Get all Co-Authors

Description

Get all Co-Authors

Usage

get_all_coauthors(...)
get_all_coauthors(...)

Arguments

...

arguments to pass to author_df

Value

A list of output, incluing a vector of author_ids

Examples

 ## Not run: 
 get_all_coauthors(last_name = "muschelli")
 
## End(Not run)
## Not run: 
 get_all_coauthors(last_name = "muschelli")
 
## End(Not run)

Find API Key for Elsevier

Description

Determines if option(elsevier_api_key) or option(elsevier_api_key_filename) is set. If not, it stops and returns an error. If so, returns the value.

Usage

get_api_key(api_key = NULL, error = TRUE)

have_api_key(api_key = NULL)
get_api_key(api_key = NULL, error = TRUE)

have_api_key(api_key = NULL)

Arguments

`api_key`	Elsevier API key
`error`	Should the function error if `api_key = NULL`?

Value

API key

Note

You can either set the API key using option(elsevier_api_key) or have it accessible by api_key = Sys.getenv('Elsevier_API').

Examples

res = get_api_key(error = FALSE)
res = get_api_key(error = FALSE)

Get Relevant Author Information and ID from Scopus in Data Frame

Description

Uses SCOPUS author search to identify author identification information in a workable format

Usage

get_author_info(...)
get_author_info(...)

Arguments

...

Arguments passed to get_complete_author_info

Value

Data.frame of information

Examples

## Not run: 
get_author_info(au_id = "40462056100")

## End(Not run)
## Not run: 
get_author_info(au_id = "40462056100")

## End(Not run)

Get Complete Author Information and ID from Scopus

Description

Uses SCOPUS author search to identify author identification information

Usage

get_complete_author_info(
  last_name = NULL,
  first_name = NULL,
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  http = "https://api.elsevier.com/content/search/author",
  query = NULL,
  count = 200,
  start = 0,
  verbose = TRUE,
  au_id = NULL,
  headers = NULL,
  ...
)
get_complete_author_info(
  last_name = NULL,
  first_name = NULL,
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  http = "https://api.elsevier.com/content/search/author",
  query = NULL,
  count = 200,
  start = 0,
  verbose = TRUE,
  au_id = NULL,
  headers = NULL,
  ...
)

Arguments

`last_name`	last name of author
`first_name`	first name of author
`affil_id`	ID of affiliation (optional)
`affil_name`	name of affiliation
`api_key`	Elsevier API key
`http`	Author API http
`query`	Additional query info, added using `+AND+` to original query
`count`	maximum number of records to retrieve
`start`	index to start on. Only necessary if a large number of records retrieved
`verbose`	Print messages from specification
`au_id`	Author ID number, will override first/last combination if specified
`headers`	Headers passed to `add_headers`, passed to `GET`
`...`	options to pass to `GET`

Value

List of information

Examples

if (is_elsevier_authorized()) {
res = get_complete_author_info(
last_name = "Muschelli",
first_name = "John",
verbose = FALSE)
}
if (is_elsevier_authorized()) {
res = get_complete_author_info(
last_name = "Muschelli",
first_name = "John",
verbose = FALSE)
}

Get Links for next/first/last query

Description

Get Links for next/first/last query

Usage

get_links(result)

get_url(result, type = c("self", "first", "prev", "next", "last"))

next_url(result)

last_url(result)

prev_url(result)

self_url(result)

first_url(result)

get_link_type(result, ..., type = c("self", "first", "prev", "next", "last"))

get_first(result, ...)

get_last(result, ...)

get_prev(result, ...)

get_next(result, ...)

get_self(result, ...)
get_links(result)

get_url(result, type = c("self", "first", "prev", "next", "last"))

next_url(result)

last_url(result)

prev_url(result)

self_url(result)

first_url(result)

get_link_type(result, ..., type = c("self", "first", "prev", "next", "last"))

get_first(result, ...)

get_last(result, ...)

get_prev(result, ...)

get_next(result, ...)

get_self(result, ...)

Arguments

`result`	Object (list) with an element named `content`, usually from `generic_elsevier_api`
`type`	The type of link requested
`...`	Options passed to `GET`

Value

A data.frame or a vector of characters

Examples

## Not run: 
result <- generic_elsevier_api(
query = "ISSN(0004-3702) AND YEAR(2001)",
search_type = "scopus")
next_result = get_next(result)


## End(Not run)

## Not run: 
result <- generic_elsevier_api(
query = "ISSN(0004-3702) AND YEAR(2001)",
search_type = "scopus")
next_result = get_next(result)


## End(Not run)

Add Institution or Authorization Token

Description

Add Institution or Authorization Token

Usage

inst_token_header(token)

auth_token_header(token)
inst_token_header(token)

auth_token_header(token)

Arguments

token

Elsevier API token, usually from elsevier_authenticate

Value

An object of class token, but really a character

SCOPUS Citation Retrieval

Description

SCOPUS Citation Retrieval

Usage

metadata_retrieval(query = NULL, view = c("STANDARD", "COMPLETE"), ...)
metadata_retrieval(query = NULL, view = c("STANDARD", "COMPLETE"), ...)

Arguments

`query`	Query to run, not overall query, but 'queryParam' query
`view`	Type of view to have. See https://dev.elsevier.com/guides/ArticleMetadataViews.htm
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = metadata_retrieval(query = "heart attack",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = metadata_retrieval(query = "heart attack",
   verbose = FALSE)
}

Get Relevant Authors Information from IDs from Scopus

Description

Get Relevant Authors Information from IDs from Scopus

Usage

multi_author_info(...)

process_complete_multi_author_info(res)
multi_author_info(...)

process_complete_multi_author_info(res)

Arguments

`...`	Arguments passed to `get_complete_author_info`
`res`	result from `complete_multi_author_info`

Value

Data.frame of information

Examples

## Not run: 
multi_author_info(au_id =  c("22968535800", "40462056100"))

## End(Not run)
## Not run: 
multi_author_info(au_id =  c("22968535800", "40462056100"))

## End(Not run)

Remove NULL

Description

Removes NULL values from a vector from a list

Usage

nonull(x, replace = NA)
nonull(x, replace = NA)

Arguments

`x`	Vector from a list
`replace`	Value to replace NULL with

Value

Vector

ScienceDirect Object Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of an object from the Elsevier Object Retrieval API

Usage

object_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  ref = NULL,
  http_end = NULL,
  ...
)

process_object_retrieval(res)

download_object(
  url,
  api_key = NULL,
  api_key_error = TRUE,
  verbose = TRUE,
  headers = NULL,
  ...
)

download_objects(url, ...)
object_retrieval(
  id,
  identifier = c("scopus_id", "eid", "doi", "pii", "pubmed_id"),
  ref = NULL,
  http_end = NULL,
  ...
)

process_object_retrieval(res)

download_object(
  url,
  api_key = NULL,
  api_key_error = TRUE,
  verbose = TRUE,
  headers = NULL,
  ...
)

download_objects(url, ...)

Arguments

`id`	Identifier for object
`identifier`	Type of identifier to use
`ref`	document reference
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api` or `GET`
`res`	result from `object_retrieval`
`url`	url to download from `object_retrieval`
`api_key`	Elsevier API key
`api_key_error`	Should there be an error if no API key?
`verbose`	Print messages from specification
`headers`	Headers passed to `add_headers`, passed to `GET`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
authorized = is_elsevier_authorized()
if (have_api_key()){
   x = object_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   df = process_object_retrieval(x)
   df = df[ grepl("image/jpeg", df$mime_type),,drop = FALSE ]
   df = df[ df$type %in% "IMAGE-HIGH-RES",,drop = FALSE ]
}
if (authorized) {
   res = download_object(df$url[1])
   if (interactive()) {
      browseURL(res$outfile)
   } else {
     img = res$content
     dims = dim(img)[1:2]
     mdim = max(dims)
     graphics::plot(c(0, ncol(img)), c(0, nrow(img)), type='n')
     graphics::rasterImage(img, 1, 1, ncol(img), nrow(img))
   }
}
api_key = get_api_key(NULL, error = FALSE)
authorized = is_elsevier_authorized()
if (have_api_key()){
   x = object_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
   df = process_object_retrieval(x)
   df = df[ grepl("image/jpeg", df$mime_type),,drop = FALSE ]
   df = df[ df$type %in% "IMAGE-HIGH-RES",,drop = FALSE ]
}
if (authorized) {
   res = download_object(df$url[1])
   if (interactive()) {
      browseURL(res$outfile)
   } else {
     img = res$content
     dims = dim(img)[1:2]
     mdim = max(dims)
     graphics::plot(c(0, ncol(img)), c(0, nrow(img)), type='n')
     graphics::rasterImage(img, 1, 1, ncol(img), nrow(img))
   }
}

Retrieve PlumX metrics for Scopus documents and other related artifacts

Description

Retrieve PlumX metrics for Scopus documents and other related artifacts

Usage

plumx_metrics(value, type = plumx_types(), ...)

plumx_types()
plumx_metrics(value, type = plumx_types(), ...)

plumx_types()

Arguments

`value`	The value of the identifier to search for.
`type`	The type of identifier to search for.
`...`	Additional arguments to pass to `generic_elsevier_api`, other than `http_end`, `type`, `search_type`, and `content_type`

Value

List of elements, content and the GET request

Note

See https://dev.elsevier.com/documentation/PlumXMetricsAPI.wadl for more information

Examples

if (have_api_key()) {
type = "doi"
value = "10.1016/j.nicl.2018.10.013"
res = plumx_metrics(value, type)
}
if (have_api_key()) {
type = "doi"
value = "10.1016/j.nicl.2018.10.013"
res = plumx_metrics(value, type)
}

Print method for Scopus API key

Description

Print method for Scopus API key

Usage

## S3 method for class 'scopus_api_key'
print(x, reveal = FALSE, ...)
## S3 method for class 'scopus_api_key'
print(x, reveal = FALSE, ...)

Arguments

`x`	an object used to select a method.
`reveal`	Should the API key be revealed
`...`	further arguments passed to or from other methods

Examples

x = "asdf"
class(x) = "scopus_api_key"
print(x)
print(x, reveal = TRUE)
x = "asdf"
class(x) = "scopus_api_key"
print(x)
print(x, reveal = TRUE)

Print method for token

Description

Print method for token

Usage

## S3 method for class 'token'
print(x, reveal = FALSE, ...)

reveal(x, ...)
## S3 method for class 'token'
print(x, reveal = FALSE, ...)

reveal(x, ...)

Arguments

`x`	an object used to select a method.
`reveal`	Should the token be revealed
`...`	further arguments passed to or from other methods

Examples

x = "asdf"
class(x) = "token"
print(x)
print(x, reveal = TRUE)
x = "asdf"
class(x) = "token"
print(x)
print(x, reveal = TRUE)

Process Affiliation Name

Description

Process Affiliation ID and names for generic use

Usage

process_affiliation_name(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE
)
process_affiliation_name(
  affil_id = NULL,
  affil_name = NULL,
  api_key = NULL,
  verbose = TRUE
)

Arguments

`affil_id`	Affiliation ID number.
`affil_name`	affiliation name
`api_key`	Elsevier API key
`verbose`	Print diagnostic messages

Value

List of affiliation name and affiliation ID

Process Author Name

Description

Process author ID and names for generic use

Usage

process_author_name(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  affil_id = NULL,
  api_key = NULL,
  verbose = TRUE,
  headers = NULL
)
process_author_name(
  au_id = NULL,
  last_name = NULL,
  first_name = NULL,
  affil_id = NULL,
  api_key = NULL,
  verbose = TRUE,
  headers = NULL
)

Arguments

`au_id`	Author ID number. Overrides any first/last name argument
`last_name`	last name of author
`first_name`	first name of author
`affil_id`	ID of affiliation (optional)
`api_key`	Elsevier API key
`verbose`	Print diagnostic messages
`headers`	Headers passed to `add_headers`, passed to `GET`

Value

List of first/last name and author ID

Note

This function is really to avoid duplication

Read Citation Overview (CTO) File

Description

Read Citation Overview (CTO) File

Usage

read_cto(file)

read_cto_long(file)
read_cto(file)

read_cto_long(file)

Arguments

file

CSV of CTO export from Scopus

Value

A list of the data, year columns, and header information

Examples

file = system.file("extdata", "CTOExport.csv", package = "rscopus")
citations_over_time = read_cto(file)
citations_over_time = citations_over_time$data
file = system.file("extdata", "CTOExport.csv", package = "rscopus")
citations_over_time = read_cto(file)
citations_over_time = citations_over_time$data

ScienceDirect Article Recommendation Retrieval

Description

This function wraps generic_elsevier_api to give a retrieval of a recommendation from the Elsevier Article Recommendation API

Usage

recommendation_retrieval(
  id,
  identifier = c("eid", "pii"),
  http_end = NULL,
  ...
)
recommendation_retrieval(
  id,
  identifier = c("eid", "pii"),
  http_end = NULL,
  ...
)

Arguments

`id`	Identifier for recommendation
`identifier`	Type of identifier to use
`http_end`	any additional end to http statement. See `generic_elsevier_api`
`...`	Arguments to be passed to `generic_elsevier_api`

Value

List of elements, similar to generic_elsevier_api

Examples

api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = recommendation_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
   x = recommendation_retrieval("S1053811915002700", identifier = "pii",
   verbose = FALSE)
}

Replace non-ASCII characters

Description

Replaces non-ASCII characters from a last or first name

Usage

replace_non_ascii(string)
replace_non_ascii(string)

Arguments

string

Character vector of values to be replaced

Value

Character vector

SCOPUS Search

Description

This function wraps generic_elsevier_api to give a scopus search from the Elsevier Scopus Search API

Searches SCOPUS to get information about documents on an author.

Usage

scopus_search(
  query,
  api_key = NULL,
  count = 200,
  view = c("STANDARD", "COMPLETE"),
  start = 0,
  verbose = TRUE,
  max_count = 20000,
  http = "https://api.elsevier.com/content/search/scopus",
  headers = NULL,
  wait_time = 0,
  ...
)

sciencedirect_search(count = 100, ...)

scidir_search(count = 100, ...)
scopus_search(
  query,
  api_key = NULL,
  count = 200,
  view = c("STANDARD", "COMPLETE"),
  start = 0,
  verbose = TRUE,
  max_count = 20000,
  http = "https://api.elsevier.com/content/search/scopus",
  headers = NULL,
  wait_time = 0,
  ...
)

sciencedirect_search(count = 100, ...)

scidir_search(count = 100, ...)

Arguments

`query`	Query string to search on SCOPUS
`api_key`	API Key for Elsevier
`count`	number of records to retrieve (below 200 for STANDARD, below 25 for COMPLETE views, see https://dev.elsevier.com/api_key_settings.html).
`view`	type of view to give, see https://api.elsevier.com/documentation/ScopusSearchAPI.wadl
`start`	where should the records start gathering
`verbose`	Print diagnostic messages
`max_count`	Maximum count of records to be returned.
`http`	Address for scopus API
`headers`	additional headers to be added to `add_headers`
`wait_time`	The time in seconds to wait across consecutive requests of a single search (when records > 25)
`...`	Arguments to be passed to the query list for `GET`

Value

List of entries from SCOPUS

Examples

if (have_api_key()) {
  authorized = is_elsevier_authorized()
  if (authorized) {
    res = scopus_search(query = "all(gene)", max_count = 20,
                        count = 10)
    df = gen_entries_to_df(res$entries)
    head(df$df)
    sci_res = sciencedirect_search(query = "heart+attack AND text(liver)",
                                   max_count = 30, count = 25)
    sci_df = gen_entries_to_df(sci_res$entries)
    Sys.sleep(2)
    nt = sciencedirect_search(query = "title(neurotoxin)", max_count = 20,
                              count = 10, wait_time = 1)
    nt_df = gen_entries_to_df(nt$entries)
    nt_df = nt_df$df
  }
}
if (have_api_key()) {
  authorized = is_elsevier_authorized()
  if (authorized) {
    res = scopus_search(query = "all(gene)", max_count = 20,
                        count = 10)
    df = gen_entries_to_df(res$entries)
    head(df$df)
    sci_res = sciencedirect_search(query = "heart+attack AND text(liver)",
                                   max_count = 30, count = 25)
    sci_df = gen_entries_to_df(sci_res$entries)
    Sys.sleep(2)
    nt = sciencedirect_search(query = "title(neurotoxin)", max_count = 20,
                              count = 10, wait_time = 1)
    nt_df = gen_entries_to_df(nt$entries)
    nt_df = nt_df$df
  }
}

Set API Key for Elsevier

Description

Sets Elsevier API key using if option(elsevier_api_key)

Usage

set_api_key(api_key)
set_api_key(api_key)

Arguments

api_key

Elsevier API key

Subject Areas

Description

Subject Areas

Usage

subject_areas()

subject_area_codes()
subject_areas()

subject_area_codes()

Value

Character vector of subject areas

Note

See https://service.elsevier.com/app/answers/detail/a_id/15181/supporthub/scopus/related/1/

Package 'rscopus'

Help Index

SCOPUS Abstract Retrieval

Description

Usage

Arguments

Value

See Also

Examples

Search Affiliation Content on SCOPUS

Description

Usage

Arguments

Value

Note

See Also

List of SCOPUS Entries to List of Affiliations Data Frames

Description

Usage

Arguments

Value

Search Author Content on SCOPUS

Description

Usage

Arguments

Value

See Also

SCOPUS Affiliation Retrieval

Description

Usage

Arguments

Value

See Also

Examples

Find all affiliations

Description

Usage

Arguments

Value

ScienceDirect Article Retrieval

Description

Usage

Arguments

Value

See Also

Examples

Search Author Content on SCOPUS

Description

Usage

Arguments

Value

Note

See Also

Examples

SCOPUS Author Retrieval

Description

Usage

Arguments

Value

Note

See Also

Examples

Search Author Content on SCOPUS

Description

Usage

Arguments

Value

See Also

Examples

Search Authors by Affiliation on SCOPUS

Description

Usage

Arguments

Value

See Also

Makes a bibtex entry from an output of abstract_retrieval or article_retrieval

Description

Usage

Arguments

Value

Makes a `bibtex` entry from an output of `abstract_retrieval` or `article_retrieval`

Generally Convert Entries into a list of `data.frame`s