Package 'fairpub' reference manual

Title:	How Fair Are You When You Publish/Cite Scientific Works?
Description:	Provides a user-friendly way to compute the non-profit and academic friendly ratio of the bibliographic reference list before submitting a manuscript for peer review.
Authors:	Nicolas Casajus [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-5537-5294>)
Maintainer:	Nicolas Casajus <[email protected]>
License:	GPL (>= 2)
Version:	1.0.0
Built:	2026-05-31 09:55:39 UTC
Source:	https://github.com/FRBCesab/fairpub

Clean a DOI vector

Description

This helper cleans DOIs (Digital Object Identifier) by removing prefix (⁠doi:⁠, ⁠https://doi.org/⁠ and ⁠http://dx.doi.org/⁠) and using lower case.

Usage

fp_clean_doi(doi = NULL)
fp_clean_doi(doi = NULL)

Arguments

doi

a character vector with Digital Object Identifiers (DOI).

Value

A character of DOI without prefix and in lower case.

Examples

dois <- c(
  "10.1098/rsos.160384",
  "10.1098/RSOS.160384",
  "doi: 10.1098/rsos.160384",
  "http://dx.doi.org/10.1098/rsos.160384",
  "https://doi.org/10.1098/rsos.160384",
  "HTTPS://DOI.ORG/10.1098/RSOS.160384",
  NA
)

fp_clean_doi(dois)
dois <- c(
  "10.1098/rsos.160384",
  "10.1098/RSOS.160384",
  "doi: 10.1098/rsos.160384",
  "http://dx.doi.org/10.1098/rsos.160384",
  "https://doi.org/10.1098/rsos.160384",
  "HTTPS://DOI.ORG/10.1098/RSOS.160384",
  NA
)

fp_clean_doi(dois)

Non profit & academic friendly ratio of citations

Description

Scientific journals operate over a broad spectrum of publishing strategies, from strictly for-profit, to non-profit, and in-between business models (e.g. for-profit but academic friendly journals).

From a list of references, this function computes three citation ratios: the proportion of non-profit citations, the proportion of for-profit and academic friendly citations, and the proportion of for-profit and non-academic friendly citations (Beck et al. 2026).

It uses the OpenAlex bibliographic database (https://openalex.org) to retrieve journal names from article DOI and the DAFNEE database (https://dafnee.isem-evolution.fr/) to get the business model and the academic friendly status of journals.

Usage

fp_compute_citation_ratio(doi = NULL)
fp_compute_citation_ratio(doi = NULL)

Arguments

doi

a character vector of Digital Object Identifiers (DOI). Can contain NA (book, book chapter, etc.).

Value

A list of two elements:

summary, a data.frame with two columns (metric and value) reporting the following statistics:
- number of total references (length of doi argument)
- number of references with DOI
- number of deduplicated references
- number of references found in the OpenAlex database
- number of references whose journal is indexed in the DAFNEE database
- number of non-profit and academic friendly references
- number of for-profit and academic friendly references
- number of for-profit and non academic friendly references
ratios, a vector of three ratios:
- non-profit and academic friendly ratio
- for-profit and academic friendly ratio
- for-profit and non academic friendly ratio

References

Beck M et al. (2026) Citation self-awareness for a fairer academic publishing landscape. BioScience. DOI: doi:10.1093/biosci/biag028

Examples

# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

# Path to the BibTeX provided by <fairpub> ----
filename <- system.file(
  file.path("extdata", "references.bib"),
  package = "fairpub"
)

# Extract DOI from BibTeX ----
doi_list <- fp_extract_doi(file = filename)

# Print DOI ----
head(doi_list)

## Not run: 
# Compute citation ratio ----
fp_compute_citation_ratio(doi_list)
#> $summary
#>                                            metric value
#> 1                                Total references    38
#> 2                             References with DOI    33
#> 3                         Deduplicated references    33
#> 4                    References found in OpenAlex    33
#> 5                      References found in DAFNEE    11
#> 6     Non-profit and academic friendly references     9
#> 7     For-profit and academic friendly references     2
#> 8 For-profit and non-academic friendly references     0
#>
#> $ratios
#>     Non-profit and academic friendly     For-profit and academic friendly
#>                                 0.82                                 0.18
#> For-profit and non-academic friendly
#>                                 0.00

## End(Not run)
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

# Path to the BibTeX provided by <fairpub> ----
filename <- system.file(
  file.path("extdata", "references.bib"),
  package = "fairpub"
)

# Extract DOI from BibTeX ----
doi_list <- fp_extract_doi(file = filename)

# Print DOI ----
head(doi_list)

## Not run: 
# Compute citation ratio ----
fp_compute_citation_ratio(doi_list)
#> $summary
#>                                            metric value
#> 1                                Total references    38
#> 2                             References with DOI    33
#> 3                         Deduplicated references    33
#> 4                    References found in OpenAlex    33
#> 5                      References found in DAFNEE    11
#> 6     Non-profit and academic friendly references     9
#> 7     For-profit and academic friendly references     2
#> 8 For-profit and non-academic friendly references     0
#>
#> $ratios
#>     Non-profit and academic friendly     For-profit and academic friendly
#>                                 0.82                                 0.18
#> For-profit and non-academic friendly
#>                                 0.00

## End(Not run)

Extract DOI from a BibTeX file or a string

Description

This function detects and extracts DOI from bibliographic records. User can provides either a character vector (argument x) or the path to a BibTex file (argument file).

Usage

fp_extract_doi(x = NULL, file = NULL)
fp_extract_doi(x = NULL, file = NULL)

Arguments

x

a character vector. A string containing bibliographic records.

file

a character of length 1. The path to the BibTeX file to open.

Value

A character vector with extracted DOI. Some values can be NA in case of books, chapters, etc. or if references are malformed in the BibTeX.

Examples

# Argument 'x' (one DOI per element) ----
string <- c(
  "Beck M (2026) Citation self-awareness... 10.1093/biosci/biag028.",
  "Galtier N (2026) Time to publish... DOI: 10.32942/X24933",
  "Doe J (9999) Title... http://dx.doi.org/10.1162/qss(c)_00305",
  "Receveur A (2024) David vs Goliath... https://doi.org/10.1111/ele.14395",
  "Smith J (9999) This is a fake article."
)

## Extract DOI from a vector ----
fp_extract_doi(x = string)

# Argument 'x' (many DOI per element) ----
string <- paste(string, collapse = "\n")
cat(string)

## Extract DOI from a vector ----
fp_extract_doi(x = string)

# Argument 'file' ----

## Path to the BibTeX provided by <fairpub> ----
filename <- system.file(
  file.path("extdata", "references.bib"),
  package = "fairpub"
)

## Extract DOI from BibTeX ----
fp_extract_doi(file = filename)
# Argument 'x' (one DOI per element) ----
string <- c(
  "Beck M (2026) Citation self-awareness... 10.1093/biosci/biag028.",
  "Galtier N (2026) Time to publish... DOI: 10.32942/X24933",
  "Doe J (9999) Title... http://dx.doi.org/10.1162/qss(c)_00305",
  "Receveur A (2024) David vs Goliath... https://doi.org/10.1111/ele.14395",
  "Smith J (9999) This is a fake article."
)

## Extract DOI from a vector ----
fp_extract_doi(x = string)

# Argument 'x' (many DOI per element) ----
string <- paste(string, collapse = "\n")
cat(string)

## Extract DOI from a vector ----
fp_extract_doi(x = string)

# Argument 'file' ----

## Path to the BibTeX provided by <fairpub> ----
filename <- system.file(
  file.path("extdata", "references.bib"),
  package = "fairpub"
)

## Extract DOI from BibTeX ----
fp_extract_doi(file = filename)

Get the fairness status of an article

Description

By querying the OpenAlex bibliographic database (https://openalex.org) and the DAFNEE database (https://dafnee.isem-evolution.fr/), this function returns the business model and the academic friendly status of an article (more precisely the fairness status of the journal).

Usage

fp_get_article_fairness(doi = NULL)
fp_get_article_fairness(doi = NULL)

Arguments

doi

a character of length 1. The Digital Object Identifiers (DOI) of the article.

Value

A data.frame with two columns: journal, the journal name, and fairness, the fairness status with the following possible values:

Non-profit and academic friendly
For-profit and academic friendly
For-profit and non academic friendly
Record not found in OpenAlex
Record not found in DAFNEE database

Examples

# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

## Not run: 
# Fairness status ----
fp_get_article_fairness(doi = "10.1126/science.162.3859.1243")
#>   journal                           fairness
#> 1 Science   Non-profit and academic friendly

fp_get_article_fairness(doi = "10.1111/j.1461-0248.2005.00792.x")
#>           journal                         fairness
#> 1 Ecology Letters For-profit and academic friendly

fp_get_article_fairness(doi = "10.1038/35002501")
#>   journal                               fairness
#> 1  Nature   For-profit and non-academic friendly

# Article not found in OA ----
fp_get_article_fairness(doi = "10.xxxx/xxxx")
#>   journal                       fairness
#> 1      NA   Record not found in OpenAlex

# Journal not found in the DAFNEE database ----
fp_get_article_fairness(doi = "10.21105/joss.05753")
#>                               journal                            fairness
#> 1 The Journal of Open Source Software Record not found in DAFNEE database

## End(Not run)
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

## Not run: 
# Fairness status ----
fp_get_article_fairness(doi = "10.1126/science.162.3859.1243")
#>   journal                           fairness
#> 1 Science   Non-profit and academic friendly

fp_get_article_fairness(doi = "10.1111/j.1461-0248.2005.00792.x")
#>           journal                         fairness
#> 1 Ecology Letters For-profit and academic friendly

fp_get_article_fairness(doi = "10.1038/35002501")
#>   journal                               fairness
#> 1  Nature   For-profit and non-academic friendly

# Article not found in OA ----
fp_get_article_fairness(doi = "10.xxxx/xxxx")
#>   journal                       fairness
#> 1      NA   Record not found in OpenAlex

# Journal not found in the DAFNEE database ----
fp_get_article_fairness(doi = "10.21105/joss.05753")
#>                               journal                            fairness
#> 1 The Journal of Open Source Software Record not found in DAFNEE database

## End(Not run)

Get the fairness status of a journal

Description

Usage

fp_get_journal_fairness(journal = NULL)
fp_get_journal_fairness(journal = NULL)

Arguments

journal

a character of length 1. The name of the journal. Do not use journal abbreviation.

Value

A data.frame with two columns: journal, the journal name, and fairness, the fairness status with the following possible values:

Non-profit and academic friendly
For-profit and academic friendly
For-profit and non academic friendly
Record not found in OpenAlex
Record not found in DAFNEE database

Examples

# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

## Not run: 
# Fairness status ----
fp_get_journal_fairness("Science")
#>   journal                           fairness
#> 1 Science   Non-profit and academic friendly

# Fuzzy search ----
fp_get_journal_fairness("Science of Nature")
#> No exact match found!
#> The fuzzy search returns these three best candidates:
#>   'The Science of Nature'
#>   'Science Advances'
#>   'People and Nature'

fp_get_journal_fairness("The Science of Nature")
#>                 journal                               fairness
#> 1 The Science of Nature   For-profit and non-academic friendly

## End(Not run)
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

## Not run: 
# Fairness status ----
fp_get_journal_fairness("Science")
#>   journal                           fairness
#> 1 Science   Non-profit and academic friendly

# Fuzzy search ----
fp_get_journal_fairness("Science of Nature")
#> No exact match found!
#> The fuzzy search returns these three best candidates:
#>   'The Science of Nature'
#>   'Science Advances'
#>   'People and Nature'

fp_get_journal_fairness("The Science of Nature")
#>                 journal                               fairness
#> 1 The Science of Nature   For-profit and non-academic friendly

## End(Not run)

Get OpenAlex author ID

Description

Queries the OpenAlex bibliographic database (https://openalex.org) to retrieve an author's identifier.

Usage

fp_get_openalex_author_id(author = NULL, n = 10)
fp_get_openalex_author_id(author = NULL, n = 10)

Arguments

author

a character vector of length 1. Name of the author.

n

an integer of length 1. Number of results to return (between 1 and 200, default is 10).

Value

A data frame with the following columns:

id: OpenAlex author ID
display_name: Author name in OpenAlex
orcid: ORCID identifier
works_count: Number of publications

Examples

## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

fp_get_openalex_author_id("Nicolas Casajus")
#>            id    display_name               orcid works_count
#> 1 A5004806463 Nicolas Casajus 0000-0002-5537-5294         102

fp_get_openalex_author_id("Nicolas Mouquet")
#>            id    display_name               orcid works_count
#> 1 A5001034207 Nicolas Mouquet 0000-0003-1840-6984         210

## End(Not run)
## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

fp_get_openalex_author_id("Nicolas Casajus")
#>            id    display_name               orcid works_count
#> 1 A5004806463 Nicolas Casajus 0000-0002-5537-5294         102

fp_get_openalex_author_id("Nicolas Mouquet")
#>            id    display_name               orcid works_count
#> 1 A5001034207 Nicolas Mouquet 0000-0003-1840-6984         210

## End(Not run)

Get and filter an author's works from OpenAlex

Description

Queries the OpenAlex bibliographic database (https://openalex.org) to retrieve works associated with an OpenAlex author identifier. Optionally filters publication types and incomplete records.

Usage

fp_get_openalex_author_works(
  author_id = NULL,
  select = c("article", "review", "letter"),
  drop_na = TRUE
)
fp_get_openalex_author_works(
  author_id = NULL,
  select = c("article", "review", "letter"),
  drop_na = TRUE
)

Arguments

author_id

a character of length 1. OpenAlex author ID. This identifier can be retrieved with fp_get_openalex_author_id().

select

a character vector of work types to retain. Use fp_list_openalex_work_types() to list valid work types. Defaults to c("article", "review", "letter"). Set to NULL to keep all work types.

drop_na

a logical. If TRUE (default), works with missing DOI or missing source information are removed.

Details

This function is a wrapper around the OpenAlex API using the openalexR package. Results are automatically standardized and cleaned for downstream bibliometric analyses.

Some repositories and preprint servers (e.g. Zenodo, HAL, bioRxiv, figshare) may be excluded depending on the selected work types.

Value

A data frame containing one row per work with the following columns:

id: OpenAlex work identifier
authors: Work (first) author
title: Work title
publication_year: Year of publication
source_display_name: Journal or source name
source_id: OpenAlex source identifier
doi: Digital Object Identifier
cited_by_count: Citation count in OpenAlex
type: OpenAlex work type

Examples

## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

fp_get_openalex_author_works("A5004806463")
#>          id                    authors                               title
#> 1 W7143431770  Brunno F. Oliveira et al.     Species range shifts often...
#> 2 W7153879999         Miriam Beck et al.    Citation self-awareness for...
#> 3 W4406766122 Érica Rievrs Borges et al.         Road‐river intersectio...
#> 4 W4415048605   Jonathan Bonfanti et al. Geographic, taxonomic and metr...
#> 5 W4411408576      Matthew McLean et al.       Conserving the beauty of...
#> 6 W4415113473     Nicolas Casajus et al.           forcis: An R package...
#>   publication_year                             source_display_name
#> 1             2026 Proceedings of the National Academy of Sciences
#> 2             2026                                      BioScience
#> 3             2025                      Applied Vegetation Science
#> 4             2025                                 Ecology Letters
#> 5             2025 Proceedings of the National Academy of Sciences
#> 6             2025             The Journal of Open Source Software
#>     source_id                     doi cited_by_count    type
#> 1  S125754415 10.1073/pnas.2515903123              1 article
#> 2  S121830084  10.1093/biosci/biag028              0 article
#> 3  S179963793      10.1111/avsc.70011              0 article
#> 4   S80967739       10.1111/ele.70220              1  review
#> 5  S125754415 10.1073/pnas.2415931122              1 article
#> 6 S4210214273     10.21105/joss.09217              0 article

## End(Not run)
## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

fp_get_openalex_author_works("A5004806463")
#>          id                    authors                               title
#> 1 W7143431770  Brunno F. Oliveira et al.     Species range shifts often...
#> 2 W7153879999         Miriam Beck et al.    Citation self-awareness for...
#> 3 W4406766122 Érica Rievrs Borges et al.         Road‐river intersectio...
#> 4 W4415048605   Jonathan Bonfanti et al. Geographic, taxonomic and metr...
#> 5 W4411408576      Matthew McLean et al.       Conserving the beauty of...
#> 6 W4415113473     Nicolas Casajus et al.           forcis: An R package...
#>   publication_year                             source_display_name
#> 1             2026 Proceedings of the National Academy of Sciences
#> 2             2026                                      BioScience
#> 3             2025                      Applied Vegetation Science
#> 4             2025                                 Ecology Letters
#> 5             2025 Proceedings of the National Academy of Sciences
#> 6             2025             The Journal of Open Source Software
#>     source_id                     doi cited_by_count    type
#> 1  S125754415 10.1073/pnas.2515903123              1 article
#> 2  S121830084  10.1093/biosci/biag028              0 article
#> 3  S179963793      10.1111/avsc.70011              0 article
#> 4   S80967739       10.1111/ele.70220              1  review
#> 5  S125754415 10.1073/pnas.2415931122              1 article
#> 6 S4210214273     10.21105/joss.09217              0 article

## End(Not run)

Get OpenAlex publication DOI

Description

Queries the OpenAlex bibliographic database (https://openalex.org) to retrieve metadata about publications matching a given title, including their DOI.

Usage

fp_get_openalex_doi(title = NULL, n = 10)
fp_get_openalex_doi(title = NULL, n = 10)

Arguments

title

a character vector of length 1. The title of the publication.

n

an integer of length 1. Number of results to return (between 1 and 200, default is 10).

Value

A data frame with the following columns:

display_name: Title of the publication
publication_year: Year of publication
source_display_name: Journal or source name
doi: Digital Object Identifier (DOI)

Examples

## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

# Search for an full title ----
fp_get_openalex_doi(
  "Citation self-awareness for a fairer academic publishing landscape"
)
#>                                       display_name publication_year
#> 1 Citation self-awareness for a fairer academic...             2026
#>   source_display_name                    doi
#> 1          BioScience 10.1093/biosci/biag028

# Search for a partial title ----
fp_get_openalex_doi("Citation fairer academic landscape")
#>                                       display_name publication_year
#> 1     Strategic citations for a fairer academic...             2025
#> 2 Citation self-awareness for a fairer academic...             2026
#>                       source_display_name                       doi
#> 1 bioRxiv (Cold Spring Harbor Laboratory) 10.1101/2025.08.06.668908
#> 2                              BioScience    10.1093/biosci/biag028

## End(Not run)
## Not run: 
# Be polite and send your email to OpenAlex API ----
options(openalexR.mailto = '[email protected]')

# Search for an full title ----
fp_get_openalex_doi(
  "Citation self-awareness for a fairer academic publishing landscape"
)
#>                                       display_name publication_year
#> 1 Citation self-awareness for a fairer academic...             2026
#>   source_display_name                    doi
#> 1          BioScience 10.1093/biosci/biag028

# Search for a partial title ----
fp_get_openalex_doi("Citation fairer academic landscape")
#>                                       display_name publication_year
#> 1     Strategic citations for a fairer academic...             2025
#> 2 Citation self-awareness for a fairer academic...             2026
#>                       source_display_name                       doi
#> 1 bioRxiv (Cold Spring Harbor Laboratory) 10.1101/2025.08.06.668908
#> 2                              BioScience    10.1093/biosci/biag028

## End(Not run)

Identify duplicate works based on title similarity

Description

Groups potentially duplicate bibliographic records by computing pairwise string distances between work titles and clustering similar items.

Usage

fp_identify_duplicate_works(
  data = NULL,
  string_dist = "lv",
  hclust_method = "single",
  threshold = 0.2
)
fp_identify_duplicate_works(
  data = NULL,
  string_dist = "lv",
  hclust_method = "single",
  threshold = 0.2
)

Arguments

data

a data.frame containing at least a title column.

string_dist

a character string specifying the distance metric used by stringdist::stringdistmatrix(). Defaults to "lv" (Levenshtein distance).

hclust_method

a character string specifying the hierarchical clustering method used by stats::hclust(). Defaults to "single".

threshold

a numeric value controlling cluster separation. Lower values produce more fine-grained clusters (stricter matching), while higher values merge more records into the same group.

Details

Title similarity is computed after basic text normalization (lowercasing, punctuation removal, whitespace trimming). Distances are calculated using stringdist::stringdistmatrix() and normalized by title length before hierarchical clustering.

This function does not remove duplicates but assigns a cluster identifier that can be used for downstream deduplication or grouping.

Value

The input data.frame with an additional column:

ref_id: Integer cluster identifier grouping similar titles.

Examples

## Not run: 
df <- data.frame(
  title = c(
    "Deep Learning for NLP",
    "Deep learning for natural language processing",
    "Quantum Computing Basics"
  )
)

fp_identify_duplicate_works(df)

## End(Not run)
## Not run: 
df <- data.frame(
  title = c(
    "Deep Learning for NLP",
    "Deep learning for natural language processing",
    "Quantum Computing Basics"
  )
)

fp_identify_duplicate_works(df)

## End(Not run)

List DAFNEE journals

Description

The DAFNEE database (Database of Academia‑Friendly Journals in Ecology and Evolution, https://dafnee.isem-evolution.fr/) provides the business model and the academic friendly status of several journals in the field of Ecology and Evolution.

The fairpub package provides a selection of 287 DAFNEE journals and this function returns information about these journals.

Usage

fp_list_dafnee_journals()
fp_list_dafnee_journals()

Value

A data.frame with three columns:

journal, the name of the journal
business_model, the business model of the journal (non-profit or for-profit)
academic_friendly, the academic friendly status of the journal (yes or no)

Examples

# List DAFNEE journals in fairpub ----
journals <- fp_list_dafnee_journals()

# Number of journals ----
nrow(journals)

# Preview of the outputs ----
head(journals)
# List DAFNEE journals in fairpub ----
journals <- fp_list_dafnee_journals()

# Number of journals ----
nrow(journals)

# Preview of the outputs ----
head(journals)

List valid OpenAlex work types

Description

Returns the set of work types recognized by the OpenAlex database and used for filtering bibliographic records.

Usage

fp_list_openalex_work_types()
fp_list_openalex_work_types()

Details

These work types correspond to the classification system used by OpenAlex to describe scholarly outputs. They can be used to filter results in functions such as fp_get_openalex_author_works().

Value

a character vector of valid OpenAlex work types.

Examples

fp_list_openalex_work_types()
fp_list_openalex_work_types()

Package 'fairpub'

Help Index

Clean a DOI vector

Description

Usage

Arguments

Value

Examples

Non profit & academic friendly ratio of citations

Description

Usage

Arguments

Value

References

Examples

Extract DOI from a BibTeX file or a string

Description

Usage

Arguments

Value

Examples

Get the fairness status of an article

Description

Usage

Arguments

Value

Examples

Get the fairness status of a journal

Description

Usage

Arguments

Value

Examples

Get OpenAlex author ID

Description

Usage

Arguments

Value

Examples

Get and filter an author's works from OpenAlex

Description

Usage

Arguments

Details

Value

Examples

Get OpenAlex publication DOI

Description

Usage

Arguments

Value

Examples

Identify duplicate works based on title similarity

Description

Usage

Arguments

Details

Value

Examples

List DAFNEE journals

Description

Usage

Value

Examples

List valid OpenAlex work types

Description

Usage

Details

Value

Examples