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
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--
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
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