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
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 >
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 <jefferis at mrc-lmb.cam.ac.uk> 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 I?aki
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