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bibtex back in Imports and no longer used
conditionally in ReadBib() since it’s now back on
CRAN.ReadPDFs() (#95).useBytes is now FALSE in all
sub, grep, etc. calls in all package
functions.GetPubMedByID() with multiple book results
(#86).Cite,
Citep, etc. calls (#84)bibtex moved to Suggests in
DESCRIPTION due to it currently being orphaned on CRAN.
Work is underway by the ROpenSci team to rectify this. The package can
still be installed from GitHub. In the event that
bibtex is not installed, the functions
ReadBib(), GetBibEntryWithDOI(),
ReadCrossRef(), and ReadZotero() throw an
appropriate message asking the user to install bibtex and
invisibly return NULL.use.old.api is set to in , it will be ignored with a
warning.GetDOIs() had to be removed due to changes to the
CrossRef API. It will hopefully return in the next release.print method
for BibEntry objects is more robust against accented
characters being converted to incorrect ones when
bib.style = "authoryear". Additionally, for this style, a
period could be removed from the last initial in the first author’s
given name when first.inits = TRUE. This has been
corrected.GetDOIsReadCrossRef when use.old.api is
TRUE. Scores are sometimes not returned by the API call and
when this occurs the entries will now be added to the output
BibEntry object with a message indicating that no score was
available.max.names options is set to 1 (h/t
davidaknowles #56)ReadGS that was
occasionally causing errors from some scholar.ids (h/t Miao
Sun, #59)PrintBibliography for the case of
BibEntry objects with a single entry, an NA value could
appear next to the year in the output (#60)GetPubMedByID is better at extracting years and months
from the results returned by NCBI Entrez (h/t Dale Steele #52)as.data.framemethod for BibEntry
objects now correctly handles the case of a single entry with name list
fields containing multiple names (h/t Damon Bayer #51)+.BibEntry and merge.BibEntry gain an
argument ignore.case, which defaults to
BibOptions()$ignore.case (TRUE) so that case
is ignore when checking for duplicate fields (h/t Justin Calabrese
#47)BibOptions()$check.entries == "warn"
(h/t Justin Calabrese #48)ReadBibPrintBibliography gains parameters “start” and “end” to
allow for printing only a subset of all cited entries from a BibEntry
object (h/t Joseph Casillas #45, #46)GetDOIs to use httpsReadPDFsWriteBib
(h/t Stephane Plaisance)ReadBib won’t add an attribute “strings” if there are
none present in read bib file (h/t Stephane Plaisance)ReadCrossRef (h/t Ben Raymond)GetBibEntryWithDOI is now decoded
properlyBibEntry objectsBibOptions(style = 'yaml)c.BibEntry throws an error if not all objects are
bibentry objectsLaTeX macros added in package version
0.12.0 can only be used for R 3.3.z and higher; this corrects cause of
failed checks on R 3.2.zReadPubMed,
GetPubMedByID, etc. to use https as now required by NCBI
(h/t Dale Steele and Anthony Crane)ReadPubMed is updated to reflect that
the default number of entries returned (controlled by the argument
retmax) is 20 (h/t Dale Steele)LaTeX macros unknown to R are now defined as
macros in the package, and will be parsed using macros arg
in tools::parse_Rd (assuming
getRversion() >= "3.2.0" Note: corrected in 0.13.1 to be
getRversion() >= "3.3.0")LaTeX macro \textquotesingle in
author names (h/t Bill Denney)ReadCrossRef now uses the newer
CrossRef API and gains arguments filter and
offset to use with the new API; an additional argument
use.old.api is added if the user wishes to use the old API
(h/t Carl Boettiger)ReadCrossRef now parses the results returned by
CrossRef to create the BibEntry object when using the new
API; for the old API (and hence, older versions of the package) the
query only returns DOIs and ReadCrossRef would then use the
DOIs to request the corresponding BibTeX entries from CrossRef
(i.e. less HTTP requests when using the new API)tools::latexToUtf8 (PR#17138)
that is occasionally encountered when that function processes an unknown
macro (h/t Eric Bryant)BibOptions()$check.entries is not set to “error”
(default is “error”)ReadPDFs due to changed URL
(h/t Kurt Hornik)as.data.frame.BibEntry works for length one BibEntry
with multiple authors (h/t Dale Steele)httr::GET to fix ReadGStest-authors.R owing to changes
to person classReadCrossRef tests and error messageBibEntry are now properly parsed when specified as they
would be in BibTeX/BibLaTeX;
e.g. author = "Smith, Bob A. and Doe, Jane".BibEntry objects is now always
enforced to be uniqueas.data.frame.BibEntry is faster and now works if
duplicate keys are present; keys in (h/t Dale Steele)ReadCrossRef if downloaded BibTeX had leading
whitespace (h/t Carl Boettiger)useBytes = TRUE used for all calls to
grep, sub, etc. (h/t HI&RH Lord Ripley of
England)lubridate::new_intervalbibtex >= 0.4.0.9000 function
do_read_bib to avoid .External call and
R check note (request of HI&RH Lord Ripley of
England)ReadPDFsCite family of functions can now be
pandoc style, e.g. [@abibkey] by setting
BibOptions(cite.style = "pandoc") (h/t Dale Steele)ReadBib help page (h/t Dieter Menne)BibEntry objects by multiple fields when
no duplicatesopen.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’ fieldopen.BibEntry will message and not throw
error if entry cannot be openedReadPDFs when argument
use.metadata is FALSEReadPDFs when when reading one file
which is a JSTOR pdfBibOptions(sorting = "anyvt") and
BibOptions(sorting = "nyvt")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)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)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.GetPubMedByID (h/t Dale Steele)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).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)GetDOIs function (h/t Erich
Studerus)month = jun # "/" # jul,
month = "20~" # jan, month = "20==25~" # dec,
month = "10~" # jan # "/" # feb (request of Stephen
Eglen)ReadZotero for specifying a
groupID to query a group library instead of a user library (h/t Greg
Blomquist).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 presentGetDOIs which searches CrossRef for DOIs
for the citations stored in a BibEntry objectReadCrossRef fixed to account for change to CrossRef
API endpoint. (h/t Carl Boettiger)print.BibEntry with
BibOptions(style = "citation") now works properlyas.BibEntry will create entry key if given a
bibentry object with no key. Useful when citing packages
with citation.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)WriteBib that occasionally failed
checkReadGS when argument check.entries
is FALSE or “warn” (h/t Francisco Rodriguez Sanchez)names<-.BibEntryprint.BibEntry when entry has urldate field but
no url fieldbatch.mode = FALSE in
GetPubMedRelatedLookupPubMedID when index argument
specifiedopen.BibEntry now works properlytoBibtex.BibEntryWriteBib with biblatex
argumentThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.