R/oa2df.R
In massimoaria/openalexR: Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL' API
Defines functions
snowball2df
topics2df
publishers2df
sources2df
funders2df
keywords2df
concepts2df
institutions2df
authors2df
works2df
oa2df
Documented in
authors2df
concepts2df
funders2df
institutions2df
keywords2df
oa2df
publishers2df
snowball2df
sources2df
topics2df
works2df
#' Convert OpenAlex collection from list to data frame
#'
#' It converts bibliographic collections gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a collection of records about works, authors, institutions, venues or keywords obtained using \code{oa_request} into a data frame/tibble.
#'
#' @param data List. Output of \code{oa_request}.
#' @param entity Character. Scholarly entity of the search.
#' The argument can be one of
#' c("works", "authors", "institutions", "keywords", "funders", "sources", "publishers", "topics").
#' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
#' Ignored if entity is different from "works". Defaults to TRUE.
#' @param verbose Logical.
#' If TRUE, print information about the dataframe conversion process.
#' Defaults to TRUE.
#'
#' @inheritParams oa_query
#' @inheritParams oa_request
#' @return A tibble/dataframe result of the original OpenAlex result list.
#'
#' @examples
#' \dontrun{
#'
#' # Query to search all works citing the article:
#' # Aria, M., & Cuccurullo, C. (2017). bibliometrix:
#' # An R-tool for comprehensive science mapping analysis.
#' # Journal of informetrics, 11(4), 959-975.
#'
#' # published in 2021.
#' # The paper is associated to the OpenAlex id W2755950973.
#'
#' # Results have to be sorted by relevance score in a descending order.
#'
#' query <- oa_query(
#' entity = "works",
#' cites = "W2755950973",
#' from_publication_date = "2021-01-01",
#' to_publication_date = "2021-04-30"
#' )
#'
#' res <- oa_request(
#' query_url = query,
#' count_only = FALSE,
#' verbose = FALSE
#' )
#'
#' oa2df(res, entity = "works")
#' }
#'
#' @export
oa2df <- function(data, entity, options = NULL, count_only = FALSE, group_by = NULL, abstract = TRUE, verbose = TRUE) {
if (rlang::is_interactive()) {
rlang::warn(
"Note: `oa_fetch` and `oa2df` now return new names for some columns in openalexR v2.0.0.
See NEWS.md for the list of changes.
Call `get_coverage()` to view the all updated columns and their original names in OpenAlex.",
.frequency = "regularly",
.frequency_id = "oa2df_column_change"
)
}
if (length(data) == 0) {
return(NULL)
}
if (!is.null(group_by)) {
return(do.call(rbind.data.frame, data))
}
if (count_only && length(data) < 8) { # assuming less than 8 fields in output$meta
return(unlist(data))
}
if (entity != "snowball") {
ch <- ifelse(is.null(options$select), "id", options$select[[1]])
if (!is.null(data[[ch]])) {
data <- list(data)
}
}
switch(entity,
works = works2df(data, abstract, verbose),
authors = authors2df(data, verbose),
institutions = institutions2df(data, verbose),
concepts = concepts2df(data, verbose),
keywords = keywords2df(data, verbose),
funders = funders2df(data, verbose),
sources = sources2df(data, verbose),
publishers = publishers2df(data, verbose),
topics = topics2df(data, verbose),
snowball = snowball2df(data)
)
}
#' Convert OpenAlex collection of works from list format to data frame
#'
#' It converts bibliographic collection of works gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of works obtained using \code{oa_request} into a data frame/tibble.
#'
#' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
#' Defaults to TRUE.
#' @param pb Progress bar object. If verbose, computed from `oa_progress`.
#' NULL otherwise.
#' @inheritParams oa2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#' @importFrom stats setNames
#'
#' @examples
#' \dontrun{
#'
#' # Query to search all works citing the article:
#' # Aria, M., & Cuccurullo, C. (2017). bibliometrix:
#' # An R-tool for comprehensive science mapping analysis.
#' # Journal of informetrics, 11(4), 959-975.
#'
#' # published in 2021.
#' # The paper is associated to the OpenAlex id W2755950973.
#'
#' # Results have to be sorted by relevance score in a descending order.
#'
#' query <- oa_query(
#' identifier = NULL,
#' entity = "works",
#' cites = "W2755950973",
#' from_publication_date = "2021-01-01",
#' to_publication_date = "2021-12-31",
#' search = NULL,
#' endpoint = "https://api.openalex.org"
#' )
#'
#' res <- oa_request(
#' query_url = query,
#' count_only = FALSE,
#' verbose = FALSE
#' )
#'
#' df <- oa2df(res, entity = "works")
#'
#' df
#' }
#'
#' @export
#'
works2df <- function(data, abstract = TRUE, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
col_order <- c(
"id", "title", "display_name", "authorships", "abstract", "doi",
"publication_date", "publication_year", "relevance_score", "fwci",
"cited_by_count", "counts_by_year", "cited_by_api_url", "ids", "type",
"is_oa", "is_oa_anywhere", "oa_status", "oa_url",
"any_repository_has_fulltext", "source_display_name", "source_id", "issn_l",
"host_organization", "host_organization_name",
"landing_page_url", "pdf_url", "license", "version", "referenced_works",
"referenced_works_count", "related_works", "concepts", "topics", "keywords",
"is_paratext", "is_retracted", "language", "grants", "apc",
"first_page", "last_page", "volume", "issue"
)
works_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "title",
"identical", "publication_date",
"identical", "doi",
"identical", "type",
"identical", "cited_by_count",
"identical", "publication_year",
"identical", "cited_by_api_url",
"identical", "is_paratext",
"identical", "is_retracted",
"identical", "relevance_score",
"identical", "language",
"identical", "fwci",
"identical", "referenced_works_count",
"flat", "grants",
"flat", "referenced_works",
"flat", "related_works",
"rbind_df", "keywords",
"rbind_df", "counts_by_year",
"rbind_df", "concepts",
"flat", "apc_list",
"flat", "apc_paid",
"flat", "ids"
)
so_cols <- c(
source_id = "id",
source_display_name = "display_name",
issn_l = "issn_l",
host_organization = "host_organization",
host_organization_name = "host_organization_name"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
paper <- data[[i]]
fields <- works_process[works_process$field %in% names(paper), ]
sim_fields <- mapply(
function(x, y) subs_na(paper[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
if (!is.null(sim_fields$publication_date)) {
sim_fields$publication_date <- as.Date(sim_fields$publication_date)
}
authorships <- process_paper_authors(paper$authorships)
ab <- abstract_build(paper$abstract_inverted_index, abstract)
paper_biblio <- replace_w_na(paper$biblio)
open_access <- replace_w_na(paper$open_access)
if (length(open_access) > 0) {
names(open_access)[[1]] <- "is_oa_anywhere"
}
so_info <- paper$primary_location
venue <- so_info[names(so_info) != "source"]
source <- so_info$source
if (!is.null(source)){
source <- setNames(source[so_cols], names(so_cols))
}
# Process APC
apc <- NULL
if (any(lengths(paper[c("apc_list", "apc_paid")]) > 0)) {
apc_fields <- list(
value = NA_real_, currency = NA_character_,
value_usd = NA_real_, provenance = NA_character_
)
apc_list <- paper$apc_list[lengths(paper$apc_list) != 0]
apc_paid <- paper$apc_paid[lengths(paper$apc_paid) != 0]
apc <- list(rbind.data.frame(
c(type = "list", utils::modifyList(apc_fields, as.list(apc_list))),
c(type = "paid", utils::modifyList(apc_fields, as.list(apc_paid)))
))
}
topics <- process_topics(paper, "score")
out_ls <- c(sim_fields, venue, source, open_access, paper_biblio,
list(authorships = authorships, abstract = ab, apc = apc), topics)
out_ls[sapply(out_ls, is.null)] <- NULL
list_df[[i]] <- out_ls
}
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of authors' records from list format to data frame
#'
#' It converts bibliographic collection of authors' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of authors' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all authors affiliated to the University of Naples Federico II
#' # which have authored at least 100 publications:
#'
#' # University of Naples Federico II is associated to the OpenAlex id I71267560.
#'
#'
#' res <- oa_fetch(
#' entity = "authors",
#' last_known_institutions.id = "I71267560",
#' works_count = ">700",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "authors")
#'
#' df
#' }
#'
#' @export
authors2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
n <- length(data)
list_df <- vector(mode = "list", length = n)
author_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "works_count",
"identical", "display_name",
"identical", "orcid",
"identical", "works_api_url",
"identical", "cited_by_count",
"identical", "relevance_score",
"flat", "display_name_alternatives",
"rbind_df", "counts_by_year",
"flat", "ids"
)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- author_process[author_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
# current affiliations
if (!is.null(item$last_known_institutions)) {
l_inst <- item$last_known_institutions
affs <- list(last_known_institutions = process_affil(l_inst))
} else {
affs <- NULL
}
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, affs, item$summary_stats, topics)
}
col_order <- c(
"id", "display_name", "display_name_alternatives", "relevance_score",
"ids", "orcid", "works_count", "cited_by_count", "counts_by_year",
"2yr_mean_citedness", "h_index", "i10_index",
"last_known_institutions", "topics", "works_api_url"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of institutions' records from list format to data frame
#'
#' It converts bibliographic collection of institutions' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of institutions' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#' res <- oa_fetch(
#' entity = "institutions",
#' country_code = "it",
#' type = "education",
#' output = "list"
#' )
#'
#' oa2df(res, entity = "institutions")
#' }
#'
#' @export
institutions2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
n <- length(data)
list_df <- vector(mode = "list", length = n)
institution_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "ror",
"identical", "works_api_url",
"identical", "type",
"identical", "works_count",
"identical", "display_name",
"identical", "country_code",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "cited_by_count",
"identical", "updated_date",
"identical", "created_date",
"identical", "relevance_score",
"flat", "summary_stats",
"flat", "display_name_alternatives",
"flat", "display_name_acronyms",
"row_df", "geo",
"rbind_df", "counts_by_year",
"rbind_df", "associated_institutions",
"flat", "ids"
)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- institution_process[institution_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
interna <- NULL
if (!is.null(item$international)) {
interna <- list(
international_display_name = subs_na(
item$international$display_name,
type = "flat"
)
)
}
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, interna, topics)
}
col_order <- c(
"id", "display_name", "display_name_alternatives", "display_name_acronyms",
"international_display_name", "ror", "ids", "country_code", "geo", "type",
"homepage_url", "image_url", "image_thumbnail_url",
"associated_institutions", "relevance_score", "works_count",
"cited_by_count", "counts_by_year", "summary_stats",
"works_api_url", "topics", "updated_date", "created_date"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of concepts' records from list format to data frame
#'
#' It converts bibliographic collection of concepts' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of concepts' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#'
#' res <- oa_query(
#' entity = "concepts",
#' display_name.search = "electrodynamics",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "concepts")
#'
#' df
#' }
#'
#' @export
concepts2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
concept_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "wikidata",
"identical", "level",
"identical", "description",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "works_count",
"identical", "cited_by_count",
"identical", "works_api_url",
"identical", "relevance_score",
"rbind_df", "counts_by_year",
"rbind_df", "ancestors",
"rbind_df", "related_concepts",
"flat", "ids"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- concept_process[concept_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
intern_fields <- NULL
if (!is.null(item$international)) {
intern_fields <- lapply(
item$international[c("display_name", "description")],
subs_na,
type = "flat"
)
names(intern_fields) <- paste(names(intern_fields), "international", sep = "_")
}
list_df[[i]] <- c(sim_fields, intern_fields)
}
col_order <- c(
"id", "display_name", "display_name_international", "description",
"description_international", "wikidata", "level", "ids",
"image_url", "image_thumbnail_url", "ancestors",
"related_concepts", "relevance_score", "works_count",
"cited_by_count", "counts_by_year",
"works_api_url"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert keywords from list to data frame
#'
#' The function converts a list of keywords obtained using \code{oa_request} or
#' \code{oa_fetch(output = "list")} into a data frame/tibble. More on keyword at
#' <https://help.openalex.org/hc/en-us/articles/24736201130391-Keywords>.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#'
#' @examples
#' \dontrun{
#'
#' x <- oa_fetch(
#' entity = "keywords",
#' options = list(sample = 5),
#' output = "list"
#' )
#'
#' df <- oa2df(x, entity = "keywords")
#'
#' df
#' }
#'
#' @export
keywords2df <- function(data, verbose = TRUE) {
tibble::as_tibble(subs_na(data, "rbind_df")[[1]])
}
#' Convert OpenAlex collection of funders' records from list format to data frame
#'
#' It converts bibliographic collection of funders' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of funders' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get funders located in Canada with more than 100,000 citations
#'
#' res <- oa_request(
#' "https://api.openalex.org/funders?filter=country_code:ca,cited_by_count:>100000"
#' )
#'
#' df <- oa2df(res, entity = "funders")
#'
#' df
#' }
#'
#' @export
funders2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
funder_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"flat", "alternate_titles",
"identical", "country_code",
"identical", "description",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "grants_count",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"flat", "ids",
"rbind_df", "counts_by_year",
"rbind_df", "roles",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- funder_process[funder_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
list_df[[i]] <- sim_fields
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of sources' records from list format to data frame
#'
#' It converts bibliographic collection of sources' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of sources' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get sources from Nature
#'
#' res <- oa_request(
#' "https://api.openalex.org/sources?search=nature"
#' )
#'
#' df <- oa2df(res, entity = "sources")
#'
#' df
#' }
#'
#' @export
sources2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
source_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "issn_l",
"flat", "issn",
"identical", "display_name",
"identical", "host_organization",
"identical", "host_organization_name",
"flat", "host_organization_lineage",
"identical", "relevance_score",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"identical", "is_oa",
"identical", "is_in_doaj",
"identical", "is_indexed_in_scopus",
"flat", "ids",
"identical", "homepage_url",
"rbind_df", "apc_prices",
"identical", "apc_usd",
"identical", "country_code",
"flat", "societies",
"flat", "alternate_titles",
"identical", "abbreviated_title",
"identical", "type",
"rbind_df", "counts_by_year",
"identical", "works_api_url",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- source_process[source_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, topics)
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of publishers' records from list format to data frame
#'
#' It converts bibliographic collection of publishers' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of publishers' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get publishers located in Canada with more than 100,000 citations
#'
#' res <- oa_request(
#' "https://api.openalex.org/publishers?filter=country_codes:ca"
#' )
#'
#' df <- oa2df(res, entity = "publishers")
#'
#' df
#' }
#'
#' @export
publishers2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
publisher_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"flat", "alternate_titles",
"identical", "hierarchy_level",
"flat", "parent_publisher",
"flat", "lineage",
"identical", "country_codes",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"flat", "ids",
"rbind_df", "counts_by_year",
"rbind_df", "roles",
"identical", "sources_api_url",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- publisher_process[publisher_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
list_df[[i]] <- sim_fields
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of topics' records from list format to data frame
#'
#' It converts collection of topics' records gathered from the OpenAlex database.
#' The function converts a list of topics' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#'
#' res <- oa_query(
#' entity = "topics",
#' display_name.search = "electrodynamics",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "topics")
#'
#' df
#' }
#'
#' @export
topics2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
topic_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "description",
"flat", "ids",
"identical", "relevance_score",
"identical", "works_count",
"identical", "cited_by_count",
"identical", "updated_date",
"identical", "created_date",
"rbind_df", "siblings",
"flat", "keywords"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- topic_process[topic_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
domains <- unlist(item[c("subfield", "field", "domain")], recursive = FALSE)
domains <- as.data.frame(do.call(cbind, domains))
names(domains) <- gsub("\\.", "_", names(domains))
list_df[[i]] <- c(sim_fields, domains)
}
col_order <- c(
"id", "display_name", "description", "keywords", "ids",
"subfield_id", "subfield_display_name", "field_id", "field_display_name",
"domain_id", "domain_display_name", "siblings", "relevance_score",
"works_count", "cited_by_count", "updated_date", "created_date"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Flatten snowball result
#'
#' @param data List result from `oa_snowball`.
#' @param verbose Logical. If TRUE, print information on wrangling process.
#'
#' @return Tibble/data.frame of works with additional columns:
#' append `citing`, `backward_count`, `cited_by`, `forward_count`, `connection`,
#' and `connection_count.` For each work/row, these counts are WITHIN one
#' data search, and so `forward_count` <= `cited_by_count`.
#'
#' Consider the universe of all works linked to a set of starting works, (`oa_input = TRUE`)
#' for each work/row i:
#' - citing: works in the universe that i cites
#' - backward_count: number of works in the universe that i cites
#' - cited_by: works that i is cited by
#' - forward_count: number of works in the universe that i is cited by
#' - connection: works in the universe linked to i
#' - connection_count: number of works in the universe linked to i (degree of i)
#'
#' @export
#'
#' @examples
#' \dontrun{
#' flat_snow <- snowball2df(oa_snowball(
#' identifier = "W1516819724",
#' verbose = TRUE
#' ))
#'
#' flat_snow[, c("id", "connection", "connection_count")]
#' }
snowball2df <- function(data, verbose = FALSE) {
nodes <- data$nodes
ids <- nodes$id[nodes$oa_input]
edges_df <- data$edges
citing <- do.call(rbind.data.frame, by(
edges_df, list(edges_df$from),
function(x) {
list(
id = unique(x$from),
citing = paste(x$to, collapse = ";"),
backward_count = nrow(x)
)
}
))
cited_by <- do.call(rbind.data.frame, by(
edges_df, list(edges_df$to),
function(x) {
list(
id = unique(x$to),
cited_by = paste(x$from, collapse = ";"),
forward_count = nrow(x)
)
}
))
if (verbose) message("Appending new columns...")
nodes_augmented <- merge(
merge(nodes, citing, all.x = TRUE),
cited_by,
all.x = TRUE
)
nodes_augmented$connection <- apply(
nodes_augmented[, c("citing", "cited_by")], 1,
function(x) paste(x[!is.na(x)], collapse = ";")
)
nodes_augmented[is.na(nodes_augmented$backward_count), "backward_count"] <- 0
nodes_augmented[is.na(nodes_augmented$forward_count), "forward_count"] <- 0
nodes_augmented$connection_count <-
nodes_augmented$backward_count + nodes_augmented$forward_count
tibble::as_tibble(nodes_augmented)
}
massimoaria/openalexR documentation built on June 9, 2025, 7:44 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions snowball2df topics2df publishers2df sources2df funders2df keywords2df concepts2df institutions2df authors2df works2df oa2df
Documented in authors2df concepts2df funders2df institutions2df keywords2df oa2df publishers2df snowball2df sources2df topics2df works2df
#' Convert OpenAlex collection from list to data frame
#'
#' It converts bibliographic collections gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a collection of records about works, authors, institutions, venues or keywords obtained using \code{oa_request} into a data frame/tibble.
#'
#' @param data List. Output of \code{oa_request}.
#' @param entity Character. Scholarly entity of the search.
#' The argument can be one of
#' c("works", "authors", "institutions", "keywords", "funders", "sources", "publishers", "topics").
#' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
#' Ignored if entity is different from "works". Defaults to TRUE.
#' @param verbose Logical.
#' If TRUE, print information about the dataframe conversion process.
#' Defaults to TRUE.
#'
#' @inheritParams oa_query
#' @inheritParams oa_request
#' @return A tibble/dataframe result of the original OpenAlex result list.
#'
#' @examples
#' \dontrun{
#'
#' # Query to search all works citing the article:
#' # Aria, M., & Cuccurullo, C. (2017). bibliometrix:
#' # An R-tool for comprehensive science mapping analysis.
#' # Journal of informetrics, 11(4), 959-975.
#'
#' # published in 2021.
#' # The paper is associated to the OpenAlex id W2755950973.
#'
#' # Results have to be sorted by relevance score in a descending order.
#'
#' query <- oa_query(
#' entity = "works",
#' cites = "W2755950973",
#' from_publication_date = "2021-01-01",
#' to_publication_date = "2021-04-30"
#' )
#'
#' res <- oa_request(
#' query_url = query,
#' count_only = FALSE,
#' verbose = FALSE
#' )
#'
#' oa2df(res, entity = "works")
#' }
#'
#' @export
oa2df <- function(data, entity, options = NULL, count_only = FALSE, group_by = NULL, abstract = TRUE, verbose = TRUE) {
if (rlang::is_interactive()) {
rlang::warn(
"Note: `oa_fetch` and `oa2df` now return new names for some columns in openalexR v2.0.0.
See NEWS.md for the list of changes.
Call `get_coverage()` to view the all updated columns and their original names in OpenAlex.",
.frequency = "regularly",
.frequency_id = "oa2df_column_change"
)
}
if (length(data) == 0) {
return(NULL)
}
if (!is.null(group_by)) {
return(do.call(rbind.data.frame, data))
}
if (count_only && length(data) < 8) { # assuming less than 8 fields in output$meta
return(unlist(data))
}
if (entity != "snowball") {
ch <- ifelse(is.null(options$select), "id", options$select[[1]])
if (!is.null(data[[ch]])) {
data <- list(data)
}
}
switch(entity,
works = works2df(data, abstract, verbose),
authors = authors2df(data, verbose),
institutions = institutions2df(data, verbose),
concepts = concepts2df(data, verbose),
keywords = keywords2df(data, verbose),
funders = funders2df(data, verbose),
sources = sources2df(data, verbose),
publishers = publishers2df(data, verbose),
topics = topics2df(data, verbose),
snowball = snowball2df(data)
)
}
#' Convert OpenAlex collection of works from list format to data frame
#'
#' It converts bibliographic collection of works gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of works obtained using \code{oa_request} into a data frame/tibble.
#'
#' @param abstract Logical. If TRUE, the function returns also the abstract of each item.
#' Defaults to TRUE.
#' @param pb Progress bar object. If verbose, computed from `oa_progress`.
#' NULL otherwise.
#' @inheritParams oa2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#' @importFrom stats setNames
#'
#' @examples
#' \dontrun{
#'
#' # Query to search all works citing the article:
#' # Aria, M., & Cuccurullo, C. (2017). bibliometrix:
#' # An R-tool for comprehensive science mapping analysis.
#' # Journal of informetrics, 11(4), 959-975.
#'
#' # published in 2021.
#' # The paper is associated to the OpenAlex id W2755950973.
#'
#' # Results have to be sorted by relevance score in a descending order.
#'
#' query <- oa_query(
#' identifier = NULL,
#' entity = "works",
#' cites = "W2755950973",
#' from_publication_date = "2021-01-01",
#' to_publication_date = "2021-12-31",
#' search = NULL,
#' endpoint = "https://api.openalex.org"
#' )
#'
#' res <- oa_request(
#' query_url = query,
#' count_only = FALSE,
#' verbose = FALSE
#' )
#'
#' df <- oa2df(res, entity = "works")
#'
#' df
#' }
#'
#' @export
#'
works2df <- function(data, abstract = TRUE, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
col_order <- c(
"id", "title", "display_name", "authorships", "abstract", "doi",
"publication_date", "publication_year", "relevance_score", "fwci",
"cited_by_count", "counts_by_year", "cited_by_api_url", "ids", "type",
"is_oa", "is_oa_anywhere", "oa_status", "oa_url",
"any_repository_has_fulltext", "source_display_name", "source_id", "issn_l",
"host_organization", "host_organization_name",
"landing_page_url", "pdf_url", "license", "version", "referenced_works",
"referenced_works_count", "related_works", "concepts", "topics", "keywords",
"is_paratext", "is_retracted", "language", "grants", "apc",
"first_page", "last_page", "volume", "issue"
)
works_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "title",
"identical", "publication_date",
"identical", "doi",
"identical", "type",
"identical", "cited_by_count",
"identical", "publication_year",
"identical", "cited_by_api_url",
"identical", "is_paratext",
"identical", "is_retracted",
"identical", "relevance_score",
"identical", "language",
"identical", "fwci",
"identical", "referenced_works_count",
"flat", "grants",
"flat", "referenced_works",
"flat", "related_works",
"rbind_df", "keywords",
"rbind_df", "counts_by_year",
"rbind_df", "concepts",
"flat", "apc_list",
"flat", "apc_paid",
"flat", "ids"
)
so_cols <- c(
source_id = "id",
source_display_name = "display_name",
issn_l = "issn_l",
host_organization = "host_organization",
host_organization_name = "host_organization_name"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
paper <- data[[i]]
fields <- works_process[works_process$field %in% names(paper), ]
sim_fields <- mapply(
function(x, y) subs_na(paper[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
if (!is.null(sim_fields$publication_date)) {
sim_fields$publication_date <- as.Date(sim_fields$publication_date)
}
authorships <- process_paper_authors(paper$authorships)
ab <- abstract_build(paper$abstract_inverted_index, abstract)
paper_biblio <- replace_w_na(paper$biblio)
open_access <- replace_w_na(paper$open_access)
if (length(open_access) > 0) {
names(open_access)[[1]] <- "is_oa_anywhere"
}
so_info <- paper$primary_location
venue <- so_info[names(so_info) != "source"]
source <- so_info$source
if (!is.null(source)){
source <- setNames(source[so_cols], names(so_cols))
}
# Process APC
apc <- NULL
if (any(lengths(paper[c("apc_list", "apc_paid")]) > 0)) {
apc_fields <- list(
value = NA_real_, currency = NA_character_,
value_usd = NA_real_, provenance = NA_character_
)
apc_list <- paper$apc_list[lengths(paper$apc_list) != 0]
apc_paid <- paper$apc_paid[lengths(paper$apc_paid) != 0]
apc <- list(rbind.data.frame(
c(type = "list", utils::modifyList(apc_fields, as.list(apc_list))),
c(type = "paid", utils::modifyList(apc_fields, as.list(apc_paid)))
))
}
topics <- process_topics(paper, "score")
out_ls <- c(sim_fields, venue, source, open_access, paper_biblio,
list(authorships = authorships, abstract = ab, apc = apc), topics)
out_ls[sapply(out_ls, is.null)] <- NULL
list_df[[i]] <- out_ls
}
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of authors' records from list format to data frame
#'
#' It converts bibliographic collection of authors' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of authors' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all authors affiliated to the University of Naples Federico II
#' # which have authored at least 100 publications:
#'
#' # University of Naples Federico II is associated to the OpenAlex id I71267560.
#'
#'
#' res <- oa_fetch(
#' entity = "authors",
#' last_known_institutions.id = "I71267560",
#' works_count = ">700",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "authors")
#'
#' df
#' }
#'
#' @export
authors2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
n <- length(data)
list_df <- vector(mode = "list", length = n)
author_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "works_count",
"identical", "display_name",
"identical", "orcid",
"identical", "works_api_url",
"identical", "cited_by_count",
"identical", "relevance_score",
"flat", "display_name_alternatives",
"rbind_df", "counts_by_year",
"flat", "ids"
)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- author_process[author_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
# current affiliations
if (!is.null(item$last_known_institutions)) {
l_inst <- item$last_known_institutions
affs <- list(last_known_institutions = process_affil(l_inst))
} else {
affs <- NULL
}
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, affs, item$summary_stats, topics)
}
col_order <- c(
"id", "display_name", "display_name_alternatives", "relevance_score",
"ids", "orcid", "works_count", "cited_by_count", "counts_by_year",
"2yr_mean_citedness", "h_index", "i10_index",
"last_known_institutions", "topics", "works_api_url"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of institutions' records from list format to data frame
#'
#' It converts bibliographic collection of institutions' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of institutions' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#' res <- oa_fetch(
#' entity = "institutions",
#' country_code = "it",
#' type = "education",
#' output = "list"
#' )
#'
#' oa2df(res, entity = "institutions")
#' }
#'
#' @export
institutions2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
n <- length(data)
list_df <- vector(mode = "list", length = n)
institution_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "ror",
"identical", "works_api_url",
"identical", "type",
"identical", "works_count",
"identical", "display_name",
"identical", "country_code",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "cited_by_count",
"identical", "updated_date",
"identical", "created_date",
"identical", "relevance_score",
"flat", "summary_stats",
"flat", "display_name_alternatives",
"flat", "display_name_acronyms",
"row_df", "geo",
"rbind_df", "counts_by_year",
"rbind_df", "associated_institutions",
"flat", "ids"
)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- institution_process[institution_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
interna <- NULL
if (!is.null(item$international)) {
interna <- list(
international_display_name = subs_na(
item$international$display_name,
type = "flat"
)
)
}
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, interna, topics)
}
col_order <- c(
"id", "display_name", "display_name_alternatives", "display_name_acronyms",
"international_display_name", "ror", "ids", "country_code", "geo", "type",
"homepage_url", "image_url", "image_thumbnail_url",
"associated_institutions", "relevance_score", "works_count",
"cited_by_count", "counts_by_year", "summary_stats",
"works_api_url", "topics", "updated_date", "created_date"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert OpenAlex collection of concepts' records from list format to data frame
#'
#' It converts bibliographic collection of concepts' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of concepts' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#'
#' res <- oa_query(
#' entity = "concepts",
#' display_name.search = "electrodynamics",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "concepts")
#'
#' df
#' }
#'
#' @export
concepts2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
concept_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "wikidata",
"identical", "level",
"identical", "description",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "works_count",
"identical", "cited_by_count",
"identical", "works_api_url",
"identical", "relevance_score",
"rbind_df", "counts_by_year",
"rbind_df", "ancestors",
"rbind_df", "related_concepts",
"flat", "ids"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- concept_process[concept_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
intern_fields <- NULL
if (!is.null(item$international)) {
intern_fields <- lapply(
item$international[c("display_name", "description")],
subs_na,
type = "flat"
)
names(intern_fields) <- paste(names(intern_fields), "international", sep = "_")
}
list_df[[i]] <- c(sim_fields, intern_fields)
}
col_order <- c(
"id", "display_name", "display_name_international", "description",
"description_international", "wikidata", "level", "ids",
"image_url", "image_thumbnail_url", "ancestors",
"related_concepts", "relevance_score", "works_count",
"cited_by_count", "counts_by_year",
"works_api_url"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Convert keywords from list to data frame
#'
#' The function converts a list of keywords obtained using \code{oa_request} or
#' \code{oa_fetch(output = "list")} into a data frame/tibble. More on keyword at
#' <https://help.openalex.org/hc/en-us/articles/24736201130391-Keywords>.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#'
#' @examples
#' \dontrun{
#'
#' x <- oa_fetch(
#' entity = "keywords",
#' options = list(sample = 5),
#' output = "list"
#' )
#'
#' df <- oa2df(x, entity = "keywords")
#'
#' df
#' }
#'
#' @export
keywords2df <- function(data, verbose = TRUE) {
tibble::as_tibble(subs_na(data, "rbind_df")[[1]])
}
#' Convert OpenAlex collection of funders' records from list format to data frame
#'
#' It converts bibliographic collection of funders' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of funders' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get funders located in Canada with more than 100,000 citations
#'
#' res <- oa_request(
#' "https://api.openalex.org/funders?filter=country_code:ca,cited_by_count:>100000"
#' )
#'
#' df <- oa2df(res, entity = "funders")
#'
#' df
#' }
#'
#' @export
funders2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
funder_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"flat", "alternate_titles",
"identical", "country_code",
"identical", "description",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "grants_count",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"flat", "ids",
"rbind_df", "counts_by_year",
"rbind_df", "roles",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- funder_process[funder_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
list_df[[i]] <- sim_fields
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of sources' records from list format to data frame
#'
#' It converts bibliographic collection of sources' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of sources' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get sources from Nature
#'
#' res <- oa_request(
#' "https://api.openalex.org/sources?search=nature"
#' )
#'
#' df <- oa2df(res, entity = "sources")
#'
#' df
#' }
#'
#' @export
sources2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
source_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "issn_l",
"flat", "issn",
"identical", "display_name",
"identical", "host_organization",
"identical", "host_organization_name",
"flat", "host_organization_lineage",
"identical", "relevance_score",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"identical", "is_oa",
"identical", "is_in_doaj",
"identical", "is_indexed_in_scopus",
"flat", "ids",
"identical", "homepage_url",
"rbind_df", "apc_prices",
"identical", "apc_usd",
"identical", "country_code",
"flat", "societies",
"flat", "alternate_titles",
"identical", "abbreviated_title",
"identical", "type",
"rbind_df", "counts_by_year",
"identical", "works_api_url",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- source_process[source_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
topics <- process_topics(item, "count")
list_df[[i]] <- c(sim_fields, topics)
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of publishers' records from list format to data frame
#'
#' It converts bibliographic collection of publishers' records gathered from OpenAlex database \href{https://openalex.org/}{https://openalex.org/} into data frame.
#' The function converts a list of publishers' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Get publishers located in Canada with more than 100,000 citations
#'
#' res <- oa_request(
#' "https://api.openalex.org/publishers?filter=country_codes:ca"
#' )
#'
#' df <- oa2df(res, entity = "publishers")
#'
#' df
#' }
#'
#' @export
publishers2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
publisher_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"flat", "alternate_titles",
"identical", "hierarchy_level",
"flat", "parent_publisher",
"flat", "lineage",
"identical", "country_codes",
"identical", "homepage_url",
"identical", "image_url",
"identical", "image_thumbnail_url",
"identical", "works_count",
"identical", "cited_by_count",
"flat", "summary_stats",
"flat", "ids",
"rbind_df", "counts_by_year",
"rbind_df", "roles",
"identical", "sources_api_url",
"identical", "updated_date",
"identical", "created_date"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- publisher_process[publisher_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
list_df[[i]] <- sim_fields
}
out_df <- rbind_oa_ls(list_df)
out_df
}
#' Convert OpenAlex collection of topics' records from list format to data frame
#'
#' It converts collection of topics' records gathered from the OpenAlex database.
#' The function converts a list of topics' records obtained using \code{oa_request} into a data frame/tibble.
#'
#' @inheritParams works2df
#'
#' @return a data.frame.
#'
#' For more extensive information about OpenAlex API, please visit: <https://docs.openalex.org>
#'
#'
#' @examples
#' \dontrun{
#'
#' # Query to search information about all Italian educational institutions
#'
#'
#' res <- oa_query(
#' entity = "topics",
#' display_name.search = "electrodynamics",
#' output = "list"
#' )
#'
#' df <- oa2df(res, entity = "topics")
#'
#' df
#' }
#'
#' @export
topics2df <- function(data, verbose = TRUE,
pb = if (verbose) oa_progress(length(data)) else NULL) {
topic_process <- tibble::tribble(
~type, ~field,
"identical", "id",
"identical", "display_name",
"identical", "description",
"flat", "ids",
"identical", "relevance_score",
"identical", "works_count",
"identical", "cited_by_count",
"identical", "updated_date",
"identical", "created_date",
"rbind_df", "siblings",
"flat", "keywords"
)
n <- length(data)
list_df <- vector(mode = "list", length = n)
for (i in seq.int(n)) {
if (verbose) pb$tick()
item <- data[[i]]
fields <- topic_process[topic_process$field %in% names(item), ]
sim_fields <- mapply(
function(x, y) subs_na(item[[x]], type = y),
fields$field,
fields$type,
SIMPLIFY = FALSE
)
domains <- unlist(item[c("subfield", "field", "domain")], recursive = FALSE)
domains <- as.data.frame(do.call(cbind, domains))
names(domains) <- gsub("\\.", "_", names(domains))
list_df[[i]] <- c(sim_fields, domains)
}
col_order <- c(
"id", "display_name", "description", "keywords", "ids",
"subfield_id", "subfield_display_name", "field_id", "field_display_name",
"domain_id", "domain_display_name", "siblings", "relevance_score",
"works_count", "cited_by_count", "updated_date", "created_date"
)
out_df <- rbind_oa_ls(list_df)
out_df[, intersect(col_order, names(out_df))]
}
#' Flatten snowball result
#'
#' @param data List result from `oa_snowball`.
#' @param verbose Logical. If TRUE, print information on wrangling process.
#'
#' @return Tibble/data.frame of works with additional columns:
#' append `citing`, `backward_count`, `cited_by`, `forward_count`, `connection`,
#' and `connection_count.` For each work/row, these counts are WITHIN one
#' data search, and so `forward_count` <= `cited_by_count`.
#'
#' Consider the universe of all works linked to a set of starting works, (`oa_input = TRUE`)
#' for each work/row i:
#' - citing: works in the universe that i cites
#' - backward_count: number of works in the universe that i cites
#' - cited_by: works that i is cited by
#' - forward_count: number of works in the universe that i is cited by
#' - connection: works in the universe linked to i
#' - connection_count: number of works in the universe linked to i (degree of i)
#'
#' @export
#'
#' @examples
#' \dontrun{
#' flat_snow <- snowball2df(oa_snowball(
#' identifier = "W1516819724",
#' verbose = TRUE
#' ))
#'
#' flat_snow[, c("id", "connection", "connection_count")]
#' }
snowball2df <- function(data, verbose = FALSE) {
nodes <- data$nodes
ids <- nodes$id[nodes$oa_input]
edges_df <- data$edges
citing <- do.call(rbind.data.frame, by(
edges_df, list(edges_df$from),
function(x) {
list(
id = unique(x$from),
citing = paste(x$to, collapse = ";"),
backward_count = nrow(x)
)
}
))
cited_by <- do.call(rbind.data.frame, by(
edges_df, list(edges_df$to),
function(x) {
list(
id = unique(x$to),
cited_by = paste(x$from, collapse = ";"),
forward_count = nrow(x)
)
}
))
if (verbose) message("Appending new columns...")
nodes_augmented <- merge(
merge(nodes, citing, all.x = TRUE),
cited_by,
all.x = TRUE
)
nodes_augmented$connection <- apply(
nodes_augmented[, c("citing", "cited_by")], 1,
function(x) paste(x[!is.na(x)], collapse = ";")
)
nodes_augmented[is.na(nodes_augmented$backward_count), "backward_count"] <- 0
nodes_augmented[is.na(nodes_augmented$forward_count), "forward_count"] <- 0
nodes_augmented$connection_count <-
nodes_augmented$backward_count + nodes_augmented$forward_count
tibble::as_tibble(nodes_augmented)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.