| Type: | Package |
| Title: | Easy Reference Generation for R Packages |
| Version: | 0.1.0 |
| Author: | Rasmus Rydbirk [aut, cre] |
| Maintainer: | Rasmus Rydbirk <rrydbirk@outlook.dk> |
| Description: | Generate citations and references for R packages from CRAN or Bioconductor. Supports RIS and BibTeX formats with automatic DOI retrieval from GitHub repositories and published papers. Includes command-line interface for batch processing. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| URL: | https://github.com/rrydbirk/easyRef |
| BugReports: | https://github.com/rrydbirk/easyRef/issues |
| Depends: | R (≥ 3.5.0) |
| Imports: | utils, xml2, rvest |
| Suggests: | BiocManager, stringr, testthat (≥ 3.0.0) |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-10-07 08:13:44 UTC; ucloud |
| Repository: | CRAN |
| Date/Publication: | 2025-10-10 19:30:02 UTC |
Extract authors from bibentry object
Description
Extract authors from bibentry object
Usage
authors_from_bibentry(be)
Arguments
be |
Bibentry object |
Value
Character vector of author names
Convert bibentry to BibTeX string
Description
Convert bibentry to BibTeX string
Usage
bibtex_from_bibentry(be, key_hint = NULL)
Arguments
be |
Bibentry object |
key_hint |
Optional key hint (not used currently) |
Value
BibTeX string or NULL if conversion fails
Get Bioconductor metadata for a package without installing it
Description
Get Bioconductor metadata for a package without installing it
Usage
bioc_meta_for(pkg)
Arguments
pkg |
Package name |
Value
List with package metadata or NULL if not found
Clean author names by removing bracketed content
Description
Clean author names by removing bracketed content
Usage
clean_author_name(x)
Arguments
x |
Author name string |
Value
Cleaned author name string
Collect package information and generate citations (internal)
Description
Collect package information and generate citations (internal)
Usage
collect_for_package_internal(pkg, database = "auto", verbose = FALSE)
Arguments
pkg |
Package name |
database |
Repository to search: "auto", "cran", or "bioconductor" |
verbose |
Logical. If TRUE, prints detailed information about each step |
Value
List with package information and formatted citations
Get CRAN metadata for a package without installing it
Description
Get CRAN metadata for a package without installing it
Usage
cran_meta_for(pkg)
Arguments
pkg |
Package name |
Value
List with package metadata or NULL if not found
Create BibTeX format citation for software
Description
Creates a properly formatted BibTeX citation entry for software packages.
Usage
createBibtex(
key,
title,
authors,
year,
url = NULL,
version = NULL,
filename = NULL,
overwrite = TRUE
)
Arguments
key |
BibTeX key for the entry |
title |
Software title |
authors |
Character vector of author names |
year |
Publication year |
url |
Software URL (optional) |
version |
Software version (optional) |
filename |
Output file path. If NULL, returns the BibTeX string without writing to file |
overwrite |
Allow overwriting existing files (default: TRUE) |
Value
Character string with BibTeX formatted citation, or writes to file if filename provided
Examples
createBibtex(
key = "ggplot2_2016",
title = "ggplot2: Create Elegant Data Visualisations",
authors = c("Wickham, Hadley"),
year = "2016",
url = "https://ggplot2.tidyverse.org",
filename = tempfile() # Omit filename
)
# Write to file
createBibtex(
key = "ggplot2_2016",
title = "ggplot2: Create Elegant Data Visualisations",
authors = c("Wickham, Hadley"),
year = "2016",
filename = tempfile() # Replace with e.g. "ggplot2.bib"
)
Create reference citation for Bioconductor packages
Description
Convenience function specifically for Bioconductor packages. Automatically detects Bioconductor packages and retrieves metadata from Bioconductor repositories.
Usage
createBiocRef(
pkg,
format = "ris",
filename = NULL,
overwrite = TRUE,
verbose = FALSE,
database = "auto"
)
Arguments
pkg |
Character vector of Bioconductor package names to process |
format |
Output format: "ris", "bib", "bibtex", or "both" (default: "ris") |
filename |
Output file path. If NULL, creates a default filename based on package name(s). If no file extension is provided, one will be added based on the format. |
overwrite |
Allow overwriting existing files (default: TRUE) |
verbose |
Logical. If TRUE, prints detailed information about each step (default: FALSE) |
database |
Repository to search: "auto" (default), "cran", or "bioconductor". For Bioconductor packages, "bioconductor" is recommended. |
Value
Invisible list of results with package information and formatted citations. Always writes to file.
Examples
# Generate citation for Bioconductor packages (requires BiocManager)
if (requireNamespace("BiocManager", quietly = TRUE)) {
result <- createBiocRef("Biobase", filename = tempfile())
# Generate citations for multiple Bioconductor packages
bioc_packages <- c("Biobase", "limma", "edgeR")
results <- createBiocRef(bioc_packages, format = "both", filename = tempfile()) # Omit filename
# Write Bioconductor package citations to file (extension added automatically)
createBiocRef("Biobase", filename = tempfile()) # Replace with e.g. "biobase_citation"
# Verbose output for Bioconductor packages (writes to default file)
createBiocRef("Biobase", verbose = TRUE, filename = tempfile()) # Omit filename = tempfile()
# Force search in Bioconductor repository
createBiocRef("Biobase", database = "bioconductor", verbose = TRUE,
filename = tempfile()) # Omit filename = tempfile()
}
Create reference citation for R packages
Description
This is the main function to collect information about R packages and generate citations in RIS or BibTeX format. Supports both CRAN and Bioconductor packages with automatic DOI retrieval from GitHub repositories and published papers.
Usage
createRef(
pkg,
format = "ris",
filename = NULL,
overwrite = TRUE,
verbose = FALSE,
database = "auto"
)
Arguments
pkg |
Character vector of package names to process |
format |
Output format: "ris", "bib", "bibtex", or "both" (default: "ris") |
filename |
Output file path. If NULL, creates a default filename based on package name(s). If no file extension is provided, one will be added based on the format. |
overwrite |
Allow overwriting existing files (default: TRUE) |
verbose |
Logical. If TRUE, prints detailed information about each step (default: FALSE) |
database |
Repository to search: "auto" (default), "cran", or "bioconductor". "auto" automatically detects the repository, "cran" searches only CRAN, "bioconductor" searches only Bioconductor. |
Value
Invisible list of results with package information and formatted citations. Always writes to file.
Examples
# Generate RIS citation for a CRAN package
result <- createRef("ggplot2", filename = tempfile()) # Omit filename
# Generate citation for a Bioconductor package (requires BiocManager)
if (requireNamespace("BiocManager", quietly = TRUE)) {
result <- createRef("Biobase", filename = tempfile())
}
# Generate both RIS and BibTeX for multiple packages
results <- createRef(c("ggplot2", "dplyr"), format = "both", filename = tempfile())
# Write to file (extension will be added automatically)
createRef("ggplot2", filename = tempfile()) # Replace with e.g. "ggplot2_citation"
# Verbose output showing each step (writes to default file)
createRef("ggplot2", verbose = TRUE, filename = tempfile()) # Omit filename
# Force search in specific repository
createRef("ggplot2", database = "cran", filename = tempfile()) # Omit filename
Create RIS format citation for software
Description
Creates a properly formatted RIS citation entry for software packages.
Usage
createRis(
title,
authors,
year,
url = NULL,
version = NULL,
doi = NULL,
notes = NULL,
publisher = "Comprehensive R Archive Network (CRAN)",
filename = NULL,
overwrite = TRUE
)
Arguments
title |
Software title |
authors |
Character vector of author names |
year |
Publication year |
url |
Software URL (optional) |
version |
Software version (optional) |
doi |
DOI (optional) |
notes |
Additional notes (optional) |
publisher |
Publisher name (default: "Comprehensive R Archive Network (CRAN)") |
filename |
Output file path. If NULL, returns the RIS string without writing to file |
overwrite |
Allow overwriting existing files (default: TRUE) |
Value
Character string with RIS formatted citation, or writes to file if filename provided
Examples
createRis(
title = "ggplot2: Create Elegant Data Visualisations",
authors = c("Wickham, Hadley"),
year = "2016",
url = "https://ggplot2.tidyverse.org",
filename = tempfile() # Omit filename
)
# Write to file
createRis(
title = "ggplot2: Create Elegant Data Visualisations",
authors = c("Wickham, Hadley"),
year = "2016",
filename = tempfile() # Replace with e.g. "ggplot2.ris"
)
Emit citation outputs in specified formats (internal)
Description
Emit citation outputs in specified formats (internal)
Usage
emit_outputs_internal(results, format, out, split, overwrite)
Arguments
results |
List of package citation results |
format |
Output format: "ris", "bib", "bibtex", or "both" |
out |
Output file path or directory |
split |
Write one file per package when multiple packages or format="both" |
overwrite |
Allow overwriting existing files |
Value
Invisible TRUE
Ensure directory exists
Description
Ensure directory exists
Usage
ensure_dir(path)
Arguments
path |
Directory path |
Extract DOI from reference sections in README content
Description
Extract DOI from reference sections in README content
Usage
extract_doi_from_reference_sections(readme_content)
Arguments
readme_content |
Character vector of README lines |
Value
DOI string or NULL if not found
Get author information from BioC package website
Description
Get author information from BioC package website
Usage
get_bioc_author_from_web(pkg)
Arguments
pkg |
Package name |
Value
Character string with author information or NULL if not available
Get author information from CRAN package website
Description
Get author information from CRAN package website
Usage
get_cran_author_from_web(pkg)
Arguments
pkg |
Package name |
Value
Character string with author information or NULL if not available
Get title information from CRAN package website
Description
Get title information from CRAN package website
Usage
get_cran_title_from_web(pkg)
Arguments
pkg |
Package name |
Value
Character string with title information or NULL if not available
Get DOI from GitHub repository
Description
Get DOI from GitHub repository
Usage
get_doi_from_github(repo)
Arguments
repo |
GitHub repository in format "owner/repo" |
Value
DOI string or NULL if not found
Get DOI from package citation or metadata
Description
Get DOI from package citation or metadata
Usage
get_doi_from_package(pkg)
Arguments
pkg |
Package name |
Value
DOI string or NULL if not found
Get GitHub repository information and DOI
Description
Get GitHub repository information and DOI
Usage
get_github_info(pkg, url = NULL)
Arguments
pkg |
Package name |
url |
Package URL (optional) |
Value
List with GitHub info and DOI or NULL if not found
Generate CRAN/Bioconductor DOI for a package
Description
Generate CRAN/Bioconductor DOI for a package
Usage
get_repository_doi(pkg, repository)
Arguments
pkg |
Package name |
repository |
Repository name ("CRAN" or "Bioconductor") |
Value
DOI string or NULL if not found
Check if a package is from Bioconductor
Description
Check if a package is from Bioconductor
Usage
is_bioc_package(pkg)
Arguments
pkg |
Package name |
Value
Logical indicating if package is from Bioconductor
Check if a package is installed
Description
Check if a package is installed
Usage
is_installed(pkg)
Arguments
pkg |
Package name to check |
Value
Logical indicating if package is installed
Generate RIS format citation for software (internal)
Description
Generate RIS format citation for software (internal)
Usage
make_ris_for_software_internal(
title,
authors,
year,
url = NULL,
version = NULL,
doi = NULL,
notes = NULL,
publisher = "Comprehensive R Archive Network (CRAN)"
)
Arguments
title |
Software title |
authors |
Character vector of author names |
year |
Publication year |
url |
Software URL (optional) |
version |
Software version (optional) |
doi |
DOI (optional) |
notes |
Additional notes (optional) |
publisher |
Publisher name (default: "Comprehensive R Archive Network (CRAN)") |
Value
Character string with RIS formatted citation
Normalize string for use as BibTeX key
Description
Normalize string for use as BibTeX key
Usage
normalize_key(x)
Arguments
x |
String to normalize |
Value
Normalized string
Check if a package exists on CRAN or Bioconductor repositories
Description
Check if a package exists on CRAN or Bioconductor repositories
Usage
package_exists_on_repos(pkg)
Arguments
pkg |
Package name |
Value
Logical indicating if package exists on any repository
Parse author text from DESCRIPTION file
Description
Parse author text from DESCRIPTION file
Usage
parse_author_text(x)
Arguments
x |
Author text string |
Value
Character vector of author names
Convert person object to string format
Description
Convert person object to string format
Usage
person_to_string(p)
Arguments
p |
Person object |
Value
Character string with formatted name
Sanitize text for RIS format (single-line)
Description
Sanitize text for RIS format (single-line)
Usage
ris_sanitize(x)
Arguments
x |
Text to sanitize |
Value
Sanitized text
Safely get element from list with default value
Description
Safely get element from list with default value
Usage
safely_get(x, name, default = NULL)
Arguments
x |
List or object to access |
name |
Name of element to get |
default |
Default value if element doesn't exist |
Value
Element value or default
Generate BibTeX format citation for software (internal)
Description
Generate BibTeX format citation for software (internal)
Usage
synthesize_bibtex_internal(
key,
title,
authors,
year,
url = NULL,
version = NULL,
doi = NULL
)
Arguments
key |
BibTeX key for the entry |
title |
Software title |
authors |
Character vector of author names |
year |
Publication year |
url |
Software URL (optional) |
version |
Software version (optional) |
doi |
DOI (optional) |
Value
Character string with BibTeX formatted citation
Try case-insensitive search for package name
Description
Try case-insensitive search for package name
Usage
try_case_insensitive_search(pkg, database, verbose = FALSE)
Arguments
pkg |
Package name to search for |
database |
Repository to search: "auto", "cran", or "bioconductor" |
verbose |
Logical. If TRUE, prints detailed information |
Value
List with origin and correct_name if found, NULL otherwise
Write text to file with overwrite control
Description
Write text to file with overwrite control
Usage
write_text(path, text, overwrite = FALSE)
Arguments
path |
File path |
text |
Text to write |
overwrite |
Whether to allow overwriting existing files |
Extract year from bibentry object
Description
Extract year from bibentry object
Usage
year_from_bibentry(be)
Arguments
be |
Bibentry object |
Value
Character string with year