Making a package CITATION file from BibTeX

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Making a package CITATION file from BibTeX

Dr Gregory Jefferis
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 ...).

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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Re: Making a package CITATION file from BibTeX

Achim Zeileis-4
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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: Making a package CITATION file from BibTeX

Iñaki Ucar
In reply to this post by Dr Gregory Jefferis
I believe r-package-devel is the proper list for this. Now in CC.

On Thu, 30 May 2019 at 00:16, Dr Gregory Jefferis
<[hidden email]> 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 ...).
>
> 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.

There's a specific section in the manual about this (1.9 CITATION
files), and lots of examples out there. Here's one:

https://github.com/r-simmer/simmer/blob/master/inst/CITATION

Iñaki

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Re: Making a package CITATION file from BibTeX

Dr Gregory Jefferis
In reply to this post by Achim Zeileis-4
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
>>
>> ______________________________________________
>> [hidden email] 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

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