RefManageR

RefManageR provides tools for importing and working with bibliographic references. It greatly enhances the bibentry class by providing a class BibEntry which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX .bib files can be read into R and converted to BibEntry objects. Interfaces to NCBI's Entrez, CrossRef, and Zotero are provided for importing references and references can be created from locally stored PDFs using Poppler. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with RMarkdown or RHTML.

Please see the vignette.

NEWS

Changes in Version 0.8.63 (2014-04-18)

NEW FEATURES

• Use bibtex >= 0.4.9000 function do_read_bib to avoid .External call and R check note (request of HI&RH Lord Ripley of England)
• Improve parsing of dates in ReadPDFs
• Citations using Cite family of functions can now be pandoc style, e.g. [@abibkey] by setting BibOptions(cite.style = "pandoc") (h/t Dale Steele)
• Added note about locales when parsing string 'month' fields to ReadBib help page (h/t Dieter Menne)

BUG FIXES

• Fixed merging BibEntry objects by multiple fields when no duplicates
• open.BibEntry fixed to not use partial matching of field names; e.g. an error would occur if the specified entry had a 'urldate' field, but no 'url' field
• open.BibEntry will message and not throw error if entry cannot be opened
• Fixes for ReadPDFs when argument use.metadata is FALSE
• Fix for ReadPDFs when when reading one file which is a JSTOR pdf
• Fix for sorting by volume (BibOptions(sorting = "anyvt") and BibOptions(sorting = "nyvt")
• Fix for sorting by label (BibOptions()sorting equal to "anyvt" or "anyt")
• GetBibEntryWithDOI.R will not stop if an error occurs downloading any of the DOIs (e.g., if one entry in the doi vector has a typo and the rest are valid)

Changes in Version 0.8.52 (2014-01-26)

NEW FEATURES

• GetPubMedByID: Now returns some additional fields including 'month' and 'issn' for articles; will print a warning if PubMed does not return the complete list of authors; will use the name of a collective if one is available and the individual authors are missing (h/t Dale Steele)

BUG FIXES

• ReadBib: If a name list field in an entry cannot be parsed in the bib file, the entry will be ignored, but the rest of the file will still be processed and returned. In the past, this caused an error and no output would be returned.
• 'Book' entries will now be parsed correctly by GetPubMedByID (h/t Dale Steele)
• Fix error/warning messages when entry is missing required fields (introduced in Version 0.8.45)
• Name lists containing a comma in braces will now be parsed correctly, e.g. "Buchalter, Louis and {Murder, Inc.} and Anastasia, Albert"

Changes in Version 0.8.45 (2014-12-29)

BUG FIXES

• ReadCrossRef now correctly handles the small number of cases where BibTeX information cannot be obtained for a particular DOI, which resulted in 'stack imbalance' warnings and no results being returned (h/t Norman L Guinasso Jr).
• ReadGS fixed to account for changes to Google "API" (h/t Norman L Guinasso Jr).
• Improved parsing for BibTeX format names ending with a '}' (h/t Henrik Bengtsson).
• Printing references with style = "html" would not always add an opening tag when bib.style = "numeric" or bib.style = "alphabetic" (h/t Henrik Bengtsson).
• format.BibEntry would ignore the .style argument if called directly by the user. Note, this function should normally not need to be called directly. (h/t Henrik Bengtsson)

Changes in Version 0.8.40 (2014-10-28)

NEW FEATURES

• Improved formatting of citation given to CrossRef for increased chances of finding matches with GetDOIs function (h/t Erich Studerus)
• Additional parsing of 'month' field to accomodate days and ranges of days and months. Example bib entries that will be parsed correctly include month = jun # "/" # jul, month = "20~" # jan, month = "20--25~" # dec, month = "10~" # jan # "/" # feb (request of Stephen Eglen)
• Added argument 'group' to ReadZotero for specifying a groupID to query a group library instead of a user library (h/t Greg Blomquist).

BUG FIXES

• DOI's hyperlinks in Markdown format are now correct (h/t Stephen Eglen)
• print.BibEntry with BibOptions(style = "Biblatex") fixed (h/t Artem Klevtsov)
• unlist.BibEntry and RelistBibEntry now retains @strings and mheader and mfooter attributes (see ?BibEntry) if they are present

Changes in Version 0.8.34 (2014-08-18)

NEW FEATURES

• Added function GetDOIs which searches CrossRef for DOIs for the citations stored in a BibEntry object

BUG FIXES

• ReadCrossRef fixed to account for change to CrossRef API endpoint. (h/t Carl Boettiger)
• Abstracts returned by NCBI Entrez can be multiple parts. This is now handled correctly and the complete abstract will be returned in the 'abstract' field. (h/t Erich Studerus)
• DOI's were too naively extracted from NCBI Entrez results, resulting in some entries having 'doi' fields with length greater than one. Now fixed. (h/t Erich Studerus)

Changes in Version 0.8.32 (2014-08-14)

NEW FEATURES

• Functions for interacting with NCBI Entrez return abstract of each article (request of Erich Studerus)

BUG FIXES

• print.BibEntry with BibOptions(style = "citation") now works properly
• Examples calling web resources should no longer upset the check farm (h/t HI&RH Lord Ripley of England)

Changes in Version 0.8.3 (2013-07-30)

NEW FEATURES

• as.BibEntry will create entry key if given a bibentry object with no key. Useful when citing packages with citation.
• PrintBibliography and Cite functions (Cite, Citet, etc.) accept bibentry objects in addition to BibEntry objects.
• $<-.BibEntry will now accept a single person object, so that a single author in a multi-author entry may be updated. An example may be found at help("$<-.BibEntry"). (h/t Carl Boettiger)

BUG FIXES

• validated html
• changed example for WriteBib that occasionally failed check

Changes in Version 0.8.2 (2013-06-01)

BUG FIXES

• Cite functions work if a specified entry has no key. Note that keys should always be provided for all entries as they are required for all entries in a BibLaTeX bib file (h/t Carl Boettiger)
• Entries returned by Crossref that have entry type 'Data' which is not supported by default in BibLaTeX are converted to type 'Online' (h/t Carl Boettiger)
• Fix for ReadGS when argument check.entries is FALSE or "warn" (h/t Francisco Rodriguez Sanchez)
• Family names from Scholar in all caps are handled correctly in ReadGS

NEW FEATURES

• Functions for interacting with PubMed return language of each article (h/t Dale Steele)
• Added CITATION file
• Updated License to explicitly include GPL-2 and GPL-3

Changes in Version 0.8.1 (2013-03-09)

BUG FIXES

• Fix for names<-.BibEntry
• Fix for print.BibEntry when entry has urldate field but no url field
• Corrections for some documentation typos
• Fix pmidrelated field when batch.mode = FALSE in GetPubMedRelated
• Fix for LookupPubMedID when index argument specified
• open.BibEntry now works properly
• Fix for converting thesis entries in toBibtex.BibEntry
• Fix for WriteBib with biblatex argument

NEW FEATURES

• Added Vignettes including user manual and Rmd citation examples
• Added NEWS
• Added HTML output of Rmd and RHTML citation examples to doc/