yes. now i have hunted around a little bit but do not find the following utility: convert a BibTex text file to a citEntry structure suitable for including in CITATION. we can import bibtex using the bibtex package, coerce to bibentry, but not clear how to convert to citEntry. utils::bibentry is supposedly the current interface, citEntry is "older". This is not a showstopper, and it is clear that bibtex data may not always be susceptible to the intended conversion, but I want to avoid needless manual data entry. pointers would be appreciated.
On Fri, May 30, 2014 at 9:55 AM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > I was just about to say that this should be a nice carrot for authors to > start improving their citations... > > > On Fri, May 30, 2014 at 6:27 AM, Vincent Carey <st...@channing.harvard.edu > > wrote: > >> Very nice. We'll give it a couple of weeks and then announce more >> broadly? I'll start improving >> my package citations shortly. >> >> >> On Fri, May 30, 2014 at 9:11 AM, Martin Morgan <mtmor...@fhcrc.org> >> wrote: >> >>> On 04/25/2014 01:46 PM, Martin Morgan wrote: >>> >>>> On 04/24/2014 01:51 PM, Michael Lawrence wrote: >>>> >>>>> Agreed. Would be nice if the build system could detect changes to >>>>> CITATION >>>>> and update the web page accordingly. Must already happen for >>>>> DESCRIPTION. >>>>> >>>> >>>> This will be implemented (over the next several weeks). >>>> >>> >>> Dan has implemented this, see e.g., >>> >>> 1. http://bioconductor.org/packages/release/bioc/html/ >>> GenomicRanges.html >>> 2. http://bioconductor.org/packages/release/bioc/html/limma.html >>> 3. http://bioconductor.org/packages/release/bioc/html/ >>> GenomeInfoDb.html >>> >>> The citations are derived from a CITATION file if it exists (examples 1 >>> and 2) or auto-generated from the DESCRIPTION file (example 3), using the >>> equivalent of print(citation("GenomicRanges"), style="html") with some >>> post-processing to work around bugs in print.bibentry related to parsing >>> strings with embedded escape sequences '%' (example 1). print.bibentry >>> prints the citation, but not for instance citHeader (in example 2). >>> >>> Martin >>> >>> >>> >>>> Martin >>>> >>>> >>>>> >>>>> On Thu, Apr 24, 2014 at 1:44 PM, Vincent Carey >>>>> <st...@channing.harvard.edu>wrote: >>>>> >>>>> +1. this will be a good motivation for maintainers to get the >>>>>> CITATION >>>>>> entry right. >>>>>> >>>>>> >>>>>> On Thu, Apr 24, 2014 at 3:39 PM, Wolfgang Huber <whu...@embl.de> >>>>>> wrote: >>>>>> >>>>>> I wonder whether the software that makes the package landing pages >>>>>>> (e.g.: >>>>>>> http://bioconductor.org/packages/release/bioc/html/minfi.html ) >>>>>>> could be >>>>>>> tweaked to display the actual citation suggested in a package >>>>>>> CITATION >>>>>>> >>>>>> file. >>>>>> >>>>>>> >>>>>>> Right now, it says 'To cite this package in a publication, start R >>>>>>> and >>>>>>> enter: citation("minfi")'. Which is already a good start, but >>>>>>> requires >>>>>>> >>>>>> the >>>>>> >>>>>>> reader to have an R session available, install the package, and type >>>>>>> >>>>>> these >>>>>> >>>>>>> words. Things that could be easily automated, and where there is no >>>>>>> >>>>>> obvious >>>>>> >>>>>>> benefit from having the user do these computations, as their result >>>>>>> is >>>>>>> anyway predictable. >>>>>>> >>>>>>> What do you think? >>>>>>> >>>>>>> Kind regards >>>>>>> Wolfgang >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioc-devel@r-project.org mailing list >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>>> >>>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>> >>>>>> >>>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>>> >>>> >>> >>> -- >>> Computational Biology / Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >>> >> >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
