From je||er|@ @end|ng |rom mrc-|mb@c@m@@c@uk  Thu May 30 02:31:30 2019
From: je||er|@ @end|ng |rom mrc-|mb@c@m@@c@uk (Dr Gregory Jefferis)
Date: Thu, 30 May 2019 01:31:30 +0100
Subject: [Rd] Making a package CITATION file from BibTeX
In-Reply-To: <alpine.DEB.2.21.1905300038070.6310@paninaro>
References: <D3161B69-D245-47A3-BBC0-030CA767EFC9@mrc-lmb.cam.ac.uk>
 <alpine.DEB.2.21.1905300038070.6310@paninaro>
Message-ID: <59AB7C12-A77C-450A-B71F-FAA3F149A3CC@mrc-lmb.cam.ac.uk>

Dear Achim,

Thank you so much for taking the time to write out a perfect response to 
my question. I hope it will soon be available for others to google!

@Inaki: Thank you. You are quite right. I intended to write to 
r-package-devel. Achim's reply is still copied below for users of that 
list.

All the best,

Greg.

On 29 May 2019, at 23:46, Achim Zeileis wrote:

> On Thu, 30 May 2019, Dr Gregory Jefferis wrote:
>
>> Dear Colleagues,
>>
>> I would like to provide a CITATION file for my package nat.nblast 
>> [1].
>>
>> I have the correct citation in BibTeX format [2]. How can I convert 
>> this BibTeX to the format needed by R for a package CITATION file (I 
>> have a lot of other packages needing citations ...).
>
> (1) You can use read.bib() from the "bibtex" package to read the .bib 
> file containing the relevant reference.
>
> (2) This gives you a "bibentry" object that can be turned into the R 
> code generating it with format(..., style = "R") from the basic 
> "utils" package.
>
> (3) Then you can writeLines() this R code on the console or 
> writeLines(..., "CITATION") to a CITATION file.
>
> (4) Optionally you can also include a $header in your bibentry with a 
> short introductory sentence. Or if you have multiple references to go 
> into the same CITATION you might want to include a $header for each 
> and an $mheader for everything.
>
> A worked example is included below. Background information is given 
> in: https://doi.org/10.32614/RJ-2012-009
>
> Let's assume that your BibTeX entry [2] is the first entry in a file 
> called "my.bib". Then you can do:
>
> ## read first item from BibTeX as "bibentry" object
> b <- bibtex::read.bib("my.bib")[[1]]
>
> ## delete the bib key and add a header for the citation
> b$key <- NULL
> b$header <- "To cite nat.nblast in publications use:"
>
> ## turn the "bibentry" into the R code generating it
> b <- format(b, style = "R")
>
> ## write the R code to the console
> writeLines(b)
>
> bibentry(bibtype = "Article",
>          header = "To cite nat.nblast in publications use:",
>          author = c(person(given = "Marta",
>                            family = "Costa"),
>                     person(given = c("James", "D"),
>                            family = "Manton"),
>                     person(given = c("Aaron", "D"),
>                            family = "Ostrovsky"),
>                     person(given = "Steffen",
>                            family = "Prohaska"),
>                     person(given = c("Gregory", "S", "X", "E"),
>                            family = "Jefferis")),
>          doi = "10.1016/j.neuron.2016.06.012",
>          journal = "Neuron",
>          month = "Jul",
>          number = "2",
>          pages = "293-311",
>          title = "NBLAST: Rapid, Sensitive Comparison of Neuronal 
> Structure and Construction of Neuron Family Databases",
>          volume = "91",
>          year = "2016")
>
>
>> I think what I need is the opposite of RefManageR::toBiblatex [3]. 
>> This seems like it should be a common need, so I feel sure I must be 
>> missing something, but I can't seem to google up any hints.
>>
>> With many thanks,
>>
>> Greg Jefferis.
>>
>> [1] http://github.com/jefferislab/nat.nblast 
>> https://cran.r-project.org/package=nat.nblast
>> [2]
>>
>> @article{Costa:2016aa,
>> 	Author = {Costa, Marta and Manton, James D and Ostrovsky, Aaron D 
>> and Prohaska, Steffen and Jefferis, Gregory S X E},
>> 	Doi = {10.1016/j.neuron.2016.06.012},
>> 	Journal = {Neuron},
>> 	Month = {Jul},
>> 	Number = {2},
>> 	Pages = {293-311},
>> 	Title = {NBLAST: Rapid, Sensitive Comparison of Neuronal Structure 
>> and Construction of Neuron Family Databases},
>> 	Volume = {91},
>> 	Year = {2016}}
>>
>> [3] https://rdrr.io/github/ropensci/RefManageR/man/toBiblatex.html
>>
>>
>> --
>> Gregory Jefferis
>> Division of Neurobiology
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue
>> Cambridge Biomedical Campus
>> Cambridge, CB2 OQH, UK
>>
>> http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
>> http://jefferislab.org
>> http://www.zoo.cam.ac.uk/departments/connectomics
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>


--
Gregory Jefferis, PhD                   Tel: +44 1223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/departments/connectomics



[Rd] Making a package CITATION file from BibTeX
Dr Gregory Jefferis