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
Making a package CITATION file from BibTeX
4 messages · Achim Zeileis, Iñaki Ucar, Dr Gregory Jefferis
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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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
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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