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Tracking coverage of OA entities #211

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merged 26 commits into from
Nov 18, 2024
Merged

Tracking coverage of OA entities #211

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b8a0378
coverage for works first draft
yjunechoe Feb 26, 2024
f28cf5c
consult oa_entities()
yjunechoe Feb 26, 2024
755bf5b
document
yjunechoe Feb 26, 2024
59c702e
add get_coverage to pkgdown
yjunechoe Feb 26, 2024
4a445be
test for field coverage
yjunechoe Feb 27, 2024
1dc2d53
document coverage of authors
yjunechoe Feb 27, 2024
fbfd66b
deprecating oa2bibliometrix
trangdata Nov 13, 2024
d9f2804
update tests
trangdata Nov 13, 2024
dfd0ba9
refactor
trangdata Nov 13, 2024
9dc6637
update news
trangdata Nov 13, 2024
2cea19e
update docs
trangdata Nov 13, 2024
bf9bc71
minor edit
trangdata Nov 13, 2024
a358002
internal functions
trangdata Nov 13, 2024
c3ba411
organize, add fwci
trangdata Nov 13, 2024
1481f2d
Merge branch 'main' into all-institutions
trangdata Nov 13, 2024
3b15193
Merge branch 'refine' into works-coverage
trangdata Nov 13, 2024
6bd3a36
add keywords, refine column names
trangdata Nov 14, 2024
3bf0638
oa2df_coverage
trangdata Nov 14, 2024
304575d
mans
trangdata Nov 14, 2024
eb0e01e
refine
trangdata Nov 14, 2024
37a14be
tibble vignette
trangdata Nov 15, 2024
133c793
add warnings
trangdata Nov 15, 2024
f77e77c
minor edit
trangdata Nov 15, 2024
2bb285c
add back host_organization and host_organization_name
trangdata Nov 15, 2024
2240671
update readme
trangdata Nov 15, 2024
c300f3f
update news
trangdata Nov 15, 2024
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -3,6 +3,7 @@
export(authors2df)
export(concepts2df)
export(funders2df)
export(get_coverage)
export(institutions2df)
export(oa2bibliometrix)
export(oa2df)
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112 changes: 112 additions & 0 deletions R/openalexR-coverage.R
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@@ -0,0 +1,112 @@
#' Get coverage of OpenAlex fields in openalexR
#'
#' @param entity The OA entity to inspect field coverage for. Returns
#' information for all fields if `NULL` (default).
#'
#' @return Data frame of field coverage information
#' @export
#'
#' @seealso oa_entities()
#' @examples
#' oa_entities()
#' head(get_coverage(entity = "works"))
get_coverage <- function(entity = NULL) {
if (!is.null(entity)) {
entity <- match.arg(entity, oa_entities())
oa2df_coverage[[entity]]
} else {
oa2df_coverage
}
}

#' @keywords internal
oa2df_coverage <- list()

oa2df_coverage$works <- tibble::tribble(
~original, ~covered_by, ~comments,
"abstract_inverted_index", "ab", "reconstructed from inverted index",
"apc_list", NA, NA,
"apc_paid", NA, NA,
"authorships", "author", NA,
"best_oa_location", NA, NA,
"biblio", "volume", NA,
"biblio", "issue", NA,
"biblio", "first_page", NA,
"biblio", "last_page", NA,
"cited_by_api_url", "cited_by_api_url", NA,
"cited_by_count", "cited_by_count", NA,
"cited_by_percentile_year", NA, NA,
"concepts", "concepts", NA,
"corresponding_author_ids", NA, "reconstructable from `author$is_corresponding`",
"corresponding_institution_ids", NA, "reconstructable from `author$is_corresponding`",
"countries_distinct_count", NA, "reconstructable from `author$institution_country_code`",
"counts_by_year", "counts_by_year", NA,
"created_date", NA, NA,
"display_name", "display_name", NA,
"doi", "doi", NA,
"fulltext_origin", NA, NA,
"grants", "grants", NA,
"has_fulltext", "any_repository_has_fulltext", NA,
"id", "id", NA,
"ids", "ids", NA,
"indexed_in", NA, NA,
"institutions_distinct_count", NA, "reconstructable from `author$institution_id`",
"is_paratext", "is_paratext", NA,
"is_retracted", "is_retracted", NA,
"keywords", NA, NA,
"language", "language", NA,
"locations", NA, NA,
"locations_count", NA, NA,
"mesh", NA, NA,
"ngrams_url", NA, "see `oa_ngrams()`",
"open_access", "is_oa_anywhere", "see PR #135",
"open_access", "oa_status", NA,
"open_access", "oa_url", NA,
"primary_location", "is_oa", NA,
"primary_location", "so", NA,
"primary_location", "so_id", NA,
"primary_location", "host_organization", NA,
"primary_location", "issn_l", NA,
"primary_location", "url", NA,
"primary_location", "pdf_url", NA,
"primary_location", "license", NA,
"primary_location", "version", NA,
"primary_topic", NA, NA,
"publication_date", "publication_date", NA,
"publication_year", "publication_year", NA,
"referenced_works", "referenced_works", NA,
"referenced_works_count", NA, "reconstructable from `referenced_works`",
"related_works", "related_works", NA,
"sustainable_development_goals", NA, NA,
"title", "display_name", NA,
"topics", NA, NA,
"type", "type", NA,
"type_crossref", NA, NA,
"updated_date", NA, NA
)

oa2df_coverage$authors <- tibble::tribble(
~original, ~covered_by, ~comments,
"id", "id", NA,
"orcid", "orcid", NA,
"display_name", "display_name", NA,
"display_name_alternatives", "display_name_alternatives", NA,
"works_count", "works_count", NA,
"cited_by_count", "cited_by_count", NA,
"summary_stats", NA, NA,
"ids", "ids", NA,
"affiliations", "affiliation_display_name", NA,
"affiliations", "affiliation_id", NA,
"affiliations", "affiliation_ror", NA,
"affiliations", "affiliation_country_code", NA,
"affiliations", "affiliation_type", NA,
"affiliations", "affiliation_lineage", NA,
"affiliations", "affiliations_other", NA,
"last_known_institution", NA, "first entry in `affiliation_id`",
"last_known_institutions", NA, "`affiliation_id` + `affiliations_other`",
"x_concepts", "x_concepts", NA,
"counts_by_year", "counts_by_year", NA,
"works_api_url", "works_api_url", NA,
"updated_date", NA, NA,
"created_date", NA, NA
)
1 change: 1 addition & 0 deletions _pkgdown.yml
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Expand Up @@ -34,4 +34,5 @@ reference:
- countrycode
- concept_abbrev
- oa_entities
- get_coverage
- oa2bibliometrix
25 changes: 25 additions & 0 deletions man/get_coverage.Rd
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16 changes: 16 additions & 0 deletions tests/testthat/test-coverage.R
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test_that("field coverage information is up to date", {
skip_on_cran()
cols <- lapply(get_coverage(), function(x) {
covered_by <- x$covered_by[!is.na(x$covered_by)]
# Additional fields from the parent Search entity
c(covered_by, "relevance_score")
})

# Works
w <- oa_fetch("works", options = list(sample = 1))
expect_true(all(colnames(w) %in% cols$works))

# Authors
a <- oa_fetch("authors", options = list(sample = 1))
expect_true(all(colnames(a) %in% cols$authors))
})
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