Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling 'rhs(lhs)'.

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

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",
  ...
)

Arguments

Value

List of entries from SCOPUS

Note

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

See Also

get_author_info

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)

Arguments

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,
  ...
)

Arguments

Value

List of entries from SCOPUS

See Also

get_author_info

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

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)

Arguments

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

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
)

Arguments

Value

List of entries from SCOPUS

Note

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

See Also

get_author_info

Examples

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

Note

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

See Also

generic_elsevier_api

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)
}

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,
  ...
)

Arguments

Value

List of entries from SCOPUS

See Also

get_author_info

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)

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", ...)

Arguments

Value

List of entries from SCOPUS

See Also

get_author_info

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)

Arguments

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)
}

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)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)

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 = ";")

Arguments

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, ...)

Arguments

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(...)

Arguments

Value

List of content, the GET request, and the token

Examples

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

Value

A data.frame of affiliation information

Generally Convert Entries into a list of data.frames

Description

Generally Convert Entries into a list of data.frames

Usage

gen_entries_to_df(entries, scrub = FALSE)

Arguments

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,
  ...
)

Arguments

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)

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
)

Arguments

Value

A data.frame of affiliation information

Get all Co-Authors

Description

Get all Co-Authors

Usage

get_all_coauthors(...)

Arguments

Value

A list of output, including a vector of author_ids

Examples

 ## 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)

Arguments

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)

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(...)

Arguments

Value

Data.frame of information

See Also

get_complete_author_info

Examples

## 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,
  ...
)

Arguments

Value

List of information

Examples

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, ...)

Arguments

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)

Add Institution or Authorization Token

Description

Add Institution or Authorization Token

Usage

inst_token_header(token)

auth_token_header(token)

Arguments

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"), ...)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

generic_elsevier_api, https://dev.elsevier.com/documentation/ArticleMetadataAPI.wadl

Examples

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)

Arguments

Value

Data.frame of information

See Also

get_complete_author_info

Examples

## 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)

Arguments

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, ...)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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))
   }
}

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()

Arguments

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)
}

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, ...)

Arguments

Examples

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, ...)

Arguments

Examples

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
)

Arguments

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
)

Arguments

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)

Arguments

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

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,
  ...
)

Arguments

Value

List of elements, similar to generic_elsevier_api

See Also

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)
}

Replace non-ASCII characters

Description

Replaces non-ASCII characters from a last or first name

Usage

replace_non_ascii(string)

Arguments

Value

Character vector

See Also

Taken from https://stackoverflow.com/questions/20495598/replace-accented-characters-in-r-with-non-accented-counterpart-utf-8-encoding

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, ...)

Arguments

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
  }
}

Set API Key for Elsevier

Description

Sets Elsevier API key using if option(elsevier_api_key)

Usage

set_api_key(api_key)

Arguments

Subject Areas

Description

Subject Areas

Usage

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/