diff --git a/DESCRIPTION b/DESCRIPTION index 306532cd9..6da062436 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,7 +49,8 @@ Authors@R: c( person("Greg", "Macfarlane", role = c("ctb"), email = "gregmacfarlane@gmail.com", comment = c(github = "gregmacfarlane")), person("Matthias", "Templ", role = c("ctb"), email = "matthias.templ@gmail.com", comment = c(ORCID = "0000-0002-8638-5276", github = "matthias-da")), person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta")), - person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012")) + person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012")), + person("Gregory A.", "Pilgrim", role = c("ctb"), email = "gpilgrim2670@gmail.com", comment = c(github = "gpligrim2670", ORCID = "0000-0001-7831-442X")) ) Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions. diff --git a/NAMESPACE b/NAMESPACE index 47d0643d0..16d162faf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -22,6 +22,7 @@ export(ieee_article) export(ims_article) export(jasa_article) export(jedm_article) +export(jors_article) export(joss_article) export(journals) export(jss_article) diff --git a/NEWS.md b/NEWS.md index 3e7fd9a04..eb2e6f21d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,6 +6,8 @@ - Add `trb_article()` for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427). +- Add article template `jors_article()` for *Journal of Open Research Software* (JORS) (thanks, @gpilgrim2670, #397). + # rticles 0.21 ## NEW FEATURES diff --git a/R/article.R b/R/article.R index a1d61ee3f..9c2e5c054 100644 --- a/R/article.R +++ b/R/article.R @@ -244,6 +244,20 @@ jasa_article <- function( ) } +#' @section `jors_article`: Format for creating submissions to the +#' Journal of Open Research Software. Adapted from +#' +#' @export +#' @rdname article +jors_article <- function( + ..., keep_tex = TRUE, latex_engine = "xelatex", citation_package = "natbib" +) { + pdf_document_format( + "jors", keep_tex = keep_tex, latex_engine = latex_engine, + citation_package = citation_package, ... + ) +} + #' @section `lipics_article`: Format for creating submissions to #' LIPIcs - Leibniz International Proceedings Informatics - articles. #' Adapted from the official Instructions for Authors at diff --git a/README.Rmd b/README.Rmd index 2f2525d62..00b066545 100644 --- a/README.Rmd +++ b/README.Rmd @@ -62,7 +62,8 @@ Currently included templates and their contributors are the following: | [IEEE Transaction](http://www.ieee.org/publications_standards/publications/authors/author_templates.html) | [\@Emaasit](https://github.com/Emaasit), [\@espinielli](https://github.com/espinielli), [\@nathanweeks](https://github.com/nathanweeks), [\@DunLug](https://github.com/DunLug) | [\#97](https://github.com/rstudio/rticles/pull/97), [\#169](https://github.com/rstudio/rticles/pull/169), [\#227](https://github.com/rstudio/rticles/pull/227), [\#263](https://github.com/rstudio/rticles/pull/263), [\#264](https://github.com/rstudio/rticles/pull/264), [\#265](https://github.com/rstudio/rticles/pull/265) | `ieee_article()` | | [IMS: Institute of Mathematical Statistics](https://imstat.org/) [AoAS: Annals of Applied Statistics](https://imstat.org/journals-and-publications/annals-of-applied-statistics/) | [\@auzaheta](https://github.com/auzaheta)| [\#372](https://github.com/rstudio/rticles/pull/372) | `ims_article()`| | [JASA: Journal of the Acoustical Society of America](https://asa.scitation.org/journal/jas) | [\@stefanocoretta](https://github.com/stefanocoretta)| [\#364](https://github.com/rstudio/rticles/pull/364) | `jasa_article()` | -| [Journal of Educational Data Mining](https://jedm.educationaldatamining.org/index.php/JEDM/about/submissions) journal submissions | [\@jooyoungseo](https://github.com/jooyoungseo) | [#251](https://github.com/rstudio/rticles/pull/251) | `jedm_article()` | +| [Journal of Educational Data Mining](https://jedm.educationaldatamining.org/index.php/JEDM/about/submissions) journal submissions | [\@jooyoungseo](https://github.com/jooyoungseo) | [\#251](https://github.com/rstudio/rticles/pull/251) | `jedm_article()` | +| [JORS: Journal of Open Research Software](https://openresearchsoftware.metajnl.com/) | [@gpilgrim2670](https://github.com/gpilgrim2670) | [\#397](https://github.com/rstudio/rticles/pull/397) | `jors_article()` | | [JOSS: Journal of Open Source Software](https://joss.theoj.org/) [JOSE: Journal of Open Source Education](https://jose.theoj.org/)| [\@noamross](https://github.com/noamross)| [\#229](https://github.com/rstudio/rticles/pull/229) | `joss_article()` | | [JSS: Journal of Statistical Software](https://www.jstatsoft.org) ||| `jss_article()`| | [LIPIcs](https://www.dagstuhl.de/en/publications/lipics)| [\@nuest](https://github.com/nuest)| [\#288](https://github.com/rstudio/rticles/pull/288) | `lipics_article()` | diff --git a/README.md b/README.md index c5f94ce9e..5c1ce91b2 100644 --- a/README.md +++ b/README.md @@ -89,6 +89,7 @@ Currently included templates and their contributors are the following: | [IMS: Institute of Mathematical Statistics](https://imstat.org/) [AoAS: Annals of Applied Statistics](https://imstat.org/journals-and-publications/annals-of-applied-statistics/) | [@auzaheta](https://github.com/auzaheta) | [#372](https://github.com/rstudio/rticles/pull/372) | `ims_article()` | | [JASA: Journal of the Acoustical Society of America](https://asa.scitation.org/journal/jas) | [@stefanocoretta](https://github.com/stefanocoretta) | [#364](https://github.com/rstudio/rticles/pull/364) | `jasa_article()` | | [Journal of Educational Data Mining](https://jedm.educationaldatamining.org/index.php/JEDM/about/submissions) journal submissions | [@jooyoungseo](https://github.com/jooyoungseo) | [#251](https://github.com/rstudio/rticles/pull/251) | `jedm_article()` | +| [JORS: Journal of Open Research Software](https://openresearchsoftware.metajnl.com/) | [@gpilgrim2670](https://github.com/gpilgrim2670) | [#397](https://github.com/rstudio/rticles/pull/397) | `jors_article()` | | [JOSS: Journal of Open Source Software](https://joss.theoj.org/) [JOSE: Journal of Open Source Education](https://jose.theoj.org/) | [@noamross](https://github.com/noamross) | [#229](https://github.com/rstudio/rticles/pull/229) | `joss_article()` | | [JSS: Journal of Statistical Software](https://www.jstatsoft.org) | | | `jss_article()` | | [LIPIcs](https://www.dagstuhl.de/en/publications/lipics) | [@nuest](https://github.com/nuest) | [#288](https://github.com/rstudio/rticles/pull/288) | `lipics_article()` | diff --git a/inst/rmarkdown/templates/jors/resources/template.tex b/inst/rmarkdown/templates/jors/resources/template.tex new file mode 100644 index 000000000..a3590eed7 --- /dev/null +++ b/inst/rmarkdown/templates/jors/resources/template.tex @@ -0,0 +1,55 @@ +%% Journal of Open Research Software RMD Latex template -- Created by Greg Pilgrim based on a previous template by Stephen Bonner and John Brennan, Durham Universtiy, UK + +\documentclass{jors} + +%% Set the header information +\pagestyle{fancy} +\definecolor{mygray}{gray}{0.6} +\renewcommand\headrule{} +\rhead{\footnotesize 3} +\rhead{\textcolor{gray}{UP JORS software RMD paper template version 0.1}} +\setlength{\headheight}{14.5pt} +\fancyhead[L, C]{} % this prevents natbib from adding "References" to the L header after references section. Also blanks C header becuase nothing should be there. + +%% definitions +\def\tightlist{} + +% bibliography package - want a numbered in-text citation +\usepackage[numbers]{natbib} % bibliography package + +% Enable the 'Shaded' regions used in figures and code chunks +\usepackage{graphicx} +$if(highlighting-macros)$ +$highlighting-macros$ +$endif$ + +%% Body of article + +\begin{document} + +{\bf Software paper for submission to the Journal of Open Research Software} + +$body$ + +\vspace{2cm} + +\rule{\textwidth}{1pt} + +\bibliographystyle{jors} +\bibliography{$bibliography$} + + +\vspace{2cm} + +\rule{\textwidth}{1pt} + +{ \bf Copyright Notice} \\ +Authors who publish with this journal agree to the following terms: \\ + +Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a \href{http://creativecommons.org/licenses/by/3.0/}{Creative Commons Attribution License} that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. \\ + +Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. \\ + +By submitting this paper you agree to the terms of this Copyright Notice, which will apply to this submission if and when it is published by this journal + +\end{document} diff --git a/inst/rmarkdown/templates/jors/skeleton/jors.bst b/inst/rmarkdown/templates/jors/skeleton/jors.bst new file mode 100644 index 000000000..2a94bea02 --- /dev/null +++ b/inst/rmarkdown/templates/jors/skeleton/jors.bst @@ -0,0 +1,1552 @@ +%% +%% This is file `jors.bst', +%% generated with the docstrip utility. +%% +%% The original source files were: +%% +%% merlin.mbs (with options: `ay,nat,seq-no,nm-rv,jnrlst,keyxyr,blkyear,note-yr,atit-u,volp-sp,num-xser,jnm-x,bkpg-x,isbn,issn,doi,ppx,xedn,xand,nfss,') +%% ---------------------------------------- +%% *** Journal of Open Research Software (JORS) *** +%% +%% Copyright 1994-2011 Patrick W Daly + % =============================================================== + % IMPORTANT NOTICE: + % This bibliographic style (bst) file has been generated from one or + % more master bibliographic style (mbs) files, listed above. + % + % This generated file can be redistributed and/or modified under the terms + % of the LaTeX Project Public License Distributed from CTAN + % archives in directory macros/latex/base/lppl.txt; either + % version 1 of the License, or any later version. + % =============================================================== + % Name and version information of the main mbs file: + % \ProvidesFile{merlin.mbs}[2011/11/18 4.33 (PWD, AO, DPC)] + % For use with BibTeX version 0.99a or later + %------------------------------------------------------------------- + % This bibliography style file is intended for texts in ENGLISH + % This is an author-year citation style bibliography. As such, it is + % non-standard LaTeX, and requires a special package file to function properly. + % Such a package is natbib.sty by Patrick W. Daly + % The form of the \bibitem entries is + % \bibitem[Jones et al.(1990)]{key}... + % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}... + % The essential feature is that the label (the part in brackets) consists + % of the author names, as they should appear in the citation, with the year + % in parentheses following. There must be no space before the opening + % parenthesis! + % With natbib v5.3, a full list of authors may also follow the year. + % In natbib.sty, it is possible to define the type of enclosures that is + % really wanted (brackets or parentheses), but in either case, there must + % be parentheses in the label. + % The \cite command functions as follows: + % \citet{key} ==>> Jones et al. (1990) + % \citet*{key} ==>> Jones, Baker, and Smith (1990) + % \citep{key} ==>> (Jones et al., 1990) + % \citep*{key} ==>> (Jones, Baker, and Smith, 1990) + % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) + % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990) + % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., 1990, p. 32) + % \citeauthor{key} ==>> Jones et al. + % \citeauthor*{key} ==>> Jones, Baker, and Smith + % \citeyear{key} ==>> 1990 + %--------------------------------------------------------------------- + +ENTRY + { address + author + booktitle + chapter + doi + edition + editor + eid + howpublished + institution + isbn + issn + journal + key + month + note + number + organization + pages + publisher + school + series + title + type + volume + year + } + {} + { label extra.label sort.label short.list } +INTEGERS { output.state before.all mid.sentence after.sentence after.block } +FUNCTION {init.state.consts} +{ #0 'before.all := + #1 'mid.sentence := + #2 'after.sentence := + #3 'after.block := +} +STRINGS { s t} +FUNCTION {output.nonnull} +{ 's := + output.state mid.sentence = + { ", " * write$ } + { output.state after.block = + { add.period$ write$ + newline$ + "\newblock " write$ + } + { output.state before.all = + 'write$ + { add.period$ " " * write$ } + if$ + } + if$ + mid.sentence 'output.state := + } + if$ + s +} +FUNCTION {output} +{ duplicate$ empty$ + 'pop$ + 'output.nonnull + if$ +} +FUNCTION {output.check} +{ 't := + duplicate$ empty$ + { pop$ "empty " t * " in " * cite$ * warning$ } + 'output.nonnull + if$ +} +FUNCTION {fin.entry} +{ add.period$ + write$ + newline$ +} + +FUNCTION {new.block} +{ output.state before.all = + 'skip$ + { after.block 'output.state := } + if$ +} +FUNCTION {new.sentence} +{ output.state after.block = + 'skip$ + { output.state before.all = + 'skip$ + { after.sentence 'output.state := } + if$ + } + if$ +} +FUNCTION {add.blank} +{ " " * before.all 'output.state := +} + +FUNCTION {date.block} +{ + new.block +} + +FUNCTION {not} +{ { #0 } + { #1 } + if$ +} +FUNCTION {and} +{ 'skip$ + { pop$ #0 } + if$ +} +FUNCTION {or} +{ { pop$ #1 } + 'skip$ + if$ +} +STRINGS {z} + +FUNCTION {remove.dots} +{ 'z := + "" + { z empty$ not } + { z #1 #2 substring$ + duplicate$ "\." = + { z #3 global.max$ substring$ 'z := * } + { pop$ + z #1 #1 substring$ + z #2 global.max$ substring$ 'z := + duplicate$ "." = 'pop$ + { * } + if$ + } + if$ + } + while$ +} +FUNCTION {new.block.checkb} +{ empty$ + swap$ empty$ + and + 'skip$ + 'new.block + if$ +} +FUNCTION {field.or.null} +{ duplicate$ empty$ + { pop$ "" } + 'skip$ + if$ +} +FUNCTION {emphasize} +{ duplicate$ empty$ + { pop$ "" } + { "\emph{" swap$ * "}" * } + if$ +} +FUNCTION {tie.or.space.prefix} +{ duplicate$ text.length$ #3 < + { "~" } + { " " } + if$ + swap$ +} + +FUNCTION {capitalize} +{ "u" change.case$ "t" change.case$ } + +FUNCTION {space.word} +{ " " swap$ * " " * } + % Here are the language-specific definitions for explicit words. + % Each function has a name bbl.xxx where xxx is the English word. + % The language selected here is ENGLISH +FUNCTION {bbl.and} +{ "and"} + +FUNCTION {bbl.etal} +{ "et~al." } + +FUNCTION {bbl.editors} +{ "editors" } + +FUNCTION {bbl.editor} +{ "editor" } + +FUNCTION {bbl.edby} +{ "edited by" } + +FUNCTION {bbl.edition} +{ "edition" } + +FUNCTION {bbl.volume} +{ "volume" } + +FUNCTION {bbl.of} +{ "of" } + +FUNCTION {bbl.number} +{ "number" } + +FUNCTION {bbl.nr} +{ "no." } + +FUNCTION {bbl.in} +{ "in" } + +FUNCTION {bbl.pages} +{ "" } + +FUNCTION {bbl.page} +{ "" } + +FUNCTION {bbl.chapter} +{ "chapter" } + +FUNCTION {bbl.techrep} +{ "Technical Report" } + +FUNCTION {bbl.mthesis} +{ "Master's thesis" } + +FUNCTION {bbl.phdthesis} +{ "Ph.D. thesis" } + +MACRO {jan} {"January"} + +MACRO {feb} {"February"} + +MACRO {mar} {"March"} + +MACRO {apr} {"April"} + +MACRO {may} {"May"} + +MACRO {jun} {"June"} + +MACRO {jul} {"July"} + +MACRO {aug} {"August"} + +MACRO {sep} {"September"} + +MACRO {oct} {"October"} + +MACRO {nov} {"November"} + +MACRO {dec} {"December"} + +MACRO {acmcs} {"ACM Computing Surveys"} + +MACRO {acta} {"Acta Informatica"} + +MACRO {cacm} {"Communications of the ACM"} + +MACRO {ibmjrd} {"IBM Journal of Research and Development"} + +MACRO {ibmsj} {"IBM Systems Journal"} + +MACRO {ieeese} {"IEEE Transactions on Software Engineering"} + +MACRO {ieeetc} {"IEEE Transactions on Computers"} + +MACRO {ieeetcad} + {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} + +MACRO {ipl} {"Information Processing Letters"} + +MACRO {jacm} {"Journal of the ACM"} + +MACRO {jcss} {"Journal of Computer and System Sciences"} + +MACRO {scp} {"Science of Computer Programming"} + +MACRO {sicomp} {"SIAM Journal on Computing"} + +MACRO {tocs} {"ACM Transactions on Computer Systems"} + +MACRO {tods} {"ACM Transactions on Database Systems"} + +MACRO {tog} {"ACM Transactions on Graphics"} + +MACRO {toms} {"ACM Transactions on Mathematical Software"} + +MACRO {toois} {"ACM Transactions on Office Information Systems"} + +MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} + +MACRO {tcs} {"Theoretical Computer Science"} +FUNCTION {bibinfo.check} +{ swap$ + duplicate$ missing$ + { + pop$ pop$ + "" + } + { duplicate$ empty$ + { + swap$ pop$ + } + { swap$ + pop$ + } + if$ + } + if$ +} +FUNCTION {bibinfo.warn} +{ swap$ + duplicate$ missing$ + { + swap$ "missing " swap$ * " in " * cite$ * warning$ pop$ + "" + } + { duplicate$ empty$ + { + swap$ "empty " swap$ * " in " * cite$ * warning$ + } + { swap$ + pop$ + } + if$ + } + if$ +} +INTEGERS { nameptr namesleft numnames } + + +STRINGS { bibinfo} + +FUNCTION {format.names} +{ 'bibinfo := + duplicate$ empty$ 'skip$ { + 's := + "" 't := + #1 'nameptr := + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr + "{vv~}{ll}{ f{~}}{ jj}" + format.name$ + remove.dots + bibinfo bibinfo.check + 't := + nameptr #1 > + { + namesleft #1 > + { ", " * t * } + { + s nameptr "{ll}" format.name$ duplicate$ "others" = + { 't := } + { pop$ } + if$ + "," * + t "others" = + { + " " * bbl.etal * + } + { " " * t * } + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ + } if$ +} +FUNCTION {format.names.ed} +{ + 'bibinfo := + duplicate$ empty$ 'skip$ { + 's := + "" 't := + #1 'nameptr := + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr + "{f{~}~}{vv~}{ll}{ jj}" + format.name$ + remove.dots + bibinfo bibinfo.check + 't := + nameptr #1 > + { + namesleft #1 > + { ", " * t * } + { + s nameptr "{ll}" format.name$ duplicate$ "others" = + { 't := } + { pop$ } + if$ + "," * + t "others" = + { + + " " * bbl.etal * + } + { " " * t * } + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ + } if$ +} +FUNCTION {format.key} +{ empty$ + { key field.or.null } + { "" } + if$ +} + +FUNCTION {format.authors} +{ author "author" format.names +} +FUNCTION {get.bbl.editor} +{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ } + +FUNCTION {format.editors} +{ editor "editor" format.names duplicate$ empty$ 'skip$ + { + "," * + " " * + get.bbl.editor + * + } + if$ +} +FUNCTION {format.isbn} +{ isbn "isbn" bibinfo.check + duplicate$ empty$ 'skip$ + { + new.block + "ISBN " swap$ * + } + if$ +} + +FUNCTION {format.issn} +{ issn "issn" bibinfo.check + duplicate$ empty$ 'skip$ + { + new.block + "ISSN " swap$ * + } + if$ +} + +FUNCTION {format.doi} +{ doi empty$ + { "" } + { + new.block + "\doi{" doi * "}" * + } + if$ +} + +FUNCTION {format.note} +{ + note empty$ + { "" } + { note #1 #1 substring$ + duplicate$ "{" = + 'skip$ + { output.state mid.sentence = + { "l" } + { "u" } + if$ + change.case$ + } + if$ + note #2 global.max$ substring$ * "note" bibinfo.check + } + if$ +} + +FUNCTION {format.title} +{ title + "title" bibinfo.check +} +FUNCTION {format.full.names} +{'s := + "" 't := + #1 'nameptr := + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr + "{vv~}{ll}" format.name$ + 't := + nameptr #1 > + { + namesleft #1 > + { ", " * t * } + { + s nameptr "{ll}" format.name$ duplicate$ "others" = + { 't := } + { pop$ } + if$ + t "others" = + { + " " * bbl.etal * + } + { + numnames #2 > + { "," * } + 'skip$ + if$ + bbl.and + space.word * t * + } + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ +} + +FUNCTION {author.editor.key.full} +{ author empty$ + { editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.full.names } + if$ + } + { author format.full.names } + if$ +} + +FUNCTION {author.key.full} +{ author empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { author format.full.names } + if$ +} + +FUNCTION {editor.key.full} +{ editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.full.names } + if$ +} + +FUNCTION {make.full.names} +{ type$ "book" = + type$ "inbook" = + or + 'author.editor.key.full + { type$ "proceedings" = + 'editor.key.full + 'author.key.full + if$ + } + if$ +} + +FUNCTION {output.bibitem} +{ newline$ + "\bibitem[{" write$ + label write$ + ")" make.full.names duplicate$ short.list = + { pop$ } + { * } + if$ + "}]{" * write$ + cite$ write$ + "}" write$ + newline$ + "" + before.all 'output.state := +} + +FUNCTION {n.dashify} +{ + 't := + "" + { t empty$ not } + { t #1 #1 substring$ "-" = + { t #1 #2 substring$ "--" = not + { "--" * + t #2 global.max$ substring$ 't := + } + { { t #1 #1 substring$ "-" = } + { "-" * + t #2 global.max$ substring$ 't := + } + while$ + } + if$ + } + { t #1 #1 substring$ * + t #2 global.max$ substring$ 't := + } + if$ + } + while$ +} + +FUNCTION {word.in} +{ bbl.in capitalize + " " * } + +FUNCTION {format.date} +{ year "year" bibinfo.check duplicate$ empty$ + { + } + 'skip$ + if$ + extra.label * +} +FUNCTION {format.btitle} +{ title "title" bibinfo.check + duplicate$ empty$ 'skip$ + { + emphasize + } + if$ +} +FUNCTION {either.or.check} +{ empty$ + 'pop$ + { "can't use both " swap$ * " fields in " * cite$ * warning$ } + if$ +} +FUNCTION {format.bvolume} +{ volume empty$ + { "" } + { bbl.volume volume tie.or.space.prefix + "volume" bibinfo.check * * + series "series" bibinfo.check + duplicate$ empty$ 'pop$ + { swap$ bbl.of space.word * swap$ + emphasize * } + if$ + "volume and number" number either.or.check + } + if$ +} +FUNCTION {format.number.series} +{ volume empty$ + { number empty$ + { series field.or.null } + { series empty$ + { number "number" bibinfo.check } + { output.state mid.sentence = + { bbl.number } + { bbl.number capitalize } + if$ + number tie.or.space.prefix "number" bibinfo.check * * + bbl.in space.word * + series "series" bibinfo.check * + } + if$ + } + if$ + } + { "" } + if$ +} + +FUNCTION {format.edition} +{ edition duplicate$ empty$ 'skip$ + { + output.state mid.sentence = + { "l" } + { "t" } + if$ change.case$ + "edition" bibinfo.check + " " * bbl.edition * + } + if$ +} +INTEGERS { multiresult } +FUNCTION {multi.page.check} +{ 't := + #0 'multiresult := + { multiresult not + t empty$ not + and + } + { t #1 #1 substring$ + duplicate$ "-" = + swap$ duplicate$ "," = + swap$ "+" = + or or + { #1 'multiresult := } + { t #2 global.max$ substring$ 't := } + if$ + } + while$ + multiresult +} +FUNCTION {format.pages} +{ pages duplicate$ empty$ 'skip$ + { duplicate$ multi.page.check + { + n.dashify + } + { + } + if$ + "pages" bibinfo.check + } + if$ +} +FUNCTION {format.journal.pages} +{ pages duplicate$ empty$ 'pop$ + { swap$ duplicate$ empty$ + { pop$ pop$ format.pages } + { + ": " * + swap$ + n.dashify + "pages" bibinfo.check + * + } + if$ + } + if$ +} +FUNCTION {format.journal.eid} +{ eid "eid" bibinfo.check + duplicate$ empty$ 'pop$ + { swap$ duplicate$ empty$ 'skip$ + { + ": " * + } + if$ + swap$ * + } + if$ +} +FUNCTION {format.vol.num.pages} +{ volume field.or.null + duplicate$ empty$ 'skip$ + { + "volume" bibinfo.check + } + if$ + number "number" bibinfo.check duplicate$ empty$ 'skip$ + { + swap$ duplicate$ empty$ + { "there's a number but no volume in " cite$ * warning$ } + 'skip$ + if$ + swap$ + "(" swap$ * ")" * + } + if$ * + eid empty$ + { format.journal.pages } + { format.journal.eid } + if$ +} + +FUNCTION {format.chapter.pages} +{ chapter empty$ + 'format.pages + { type empty$ + { bbl.chapter } + { type "l" change.case$ + "type" bibinfo.check + } + if$ + chapter tie.or.space.prefix + "chapter" bibinfo.check + * * + pages empty$ + 'skip$ + { ", " * format.pages * } + if$ + } + if$ +} + +FUNCTION {format.booktitle} +{ + booktitle "booktitle" bibinfo.check + emphasize +} +FUNCTION {format.in.ed.booktitle} +{ format.booktitle duplicate$ empty$ 'skip$ + { + editor "editor" format.names.ed duplicate$ empty$ 'pop$ + { + "," * + " " * + get.bbl.editor + ", " * + * swap$ + * } + if$ + word.in swap$ * + } + if$ +} +FUNCTION {format.thesis.type} +{ type duplicate$ empty$ + 'pop$ + { swap$ pop$ + "t" change.case$ "type" bibinfo.check + } + if$ +} +FUNCTION {format.tr.number} +{ number "number" bibinfo.check + type duplicate$ empty$ + { pop$ bbl.techrep } + 'skip$ + if$ + "type" bibinfo.check + swap$ duplicate$ empty$ + { pop$ "t" change.case$ } + { tie.or.space.prefix * * } + if$ +} +FUNCTION {format.article.crossref} +{ + word.in + " \cite{" * crossref * "}" * +} +FUNCTION {format.book.crossref} +{ volume duplicate$ empty$ + { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ + pop$ word.in + } + { bbl.volume + capitalize + swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word * + } + if$ + " \cite{" * crossref * "}" * +} +FUNCTION {format.incoll.inproc.crossref} +{ + word.in + " \cite{" * crossref * "}" * +} +FUNCTION {format.org.or.pub} +{ 't := + "" + address empty$ t empty$ and + 'skip$ + { + t empty$ + { address "address" bibinfo.check * + } + { t * + address empty$ + 'skip$ + { ", " * address "address" bibinfo.check * } + if$ + } + if$ + } + if$ +} +FUNCTION {format.publisher.address} +{ publisher "publisher" bibinfo.warn format.org.or.pub +} + +FUNCTION {format.organization.address} +{ organization "organization" bibinfo.check format.org.or.pub +} + +FUNCTION {article} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.title "title" output.check + new.block + crossref missing$ + { + journal + "journal" bibinfo.check + emphasize + "journal" output.check + add.blank + format.vol.num.pages output + format.date "year" output.check + } + { format.article.crossref output.nonnull + format.pages output + } + if$ + format.issn output + format.doi output + new.block + % format.note output + fin.entry +} +FUNCTION {book} +{ output.bibitem + author empty$ + { format.editors "author and editor" output.check + editor format.key output + } + { format.authors output.nonnull + crossref missing$ + { "author and editor" editor either.or.check } + 'skip$ + if$ + } + if$ + new.block + format.btitle "title" output.check + crossref missing$ + { format.bvolume output + new.block + format.number.series output + new.sentence + format.publisher.address output + } + { + new.block + format.book.crossref output.nonnull + } + if$ + format.edition output + format.date "year" output.check + format.isbn output + format.doi output + new.block + % format.note output + fin.entry +} +FUNCTION {booklet} +{ output.bibitem + format.authors output + author format.key output + new.block + format.title "title" output.check + new.block + howpublished "howpublished" bibinfo.check output + address "address" bibinfo.check output + format.date "year" output.check + format.isbn output + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {inbook} +{ output.bibitem + author empty$ + { format.editors "author and editor" output.check + editor format.key output + } + { format.authors output.nonnull + crossref missing$ + { "author and editor" editor either.or.check } + 'skip$ + if$ + } + if$ + new.block + format.btitle "title" output.check + crossref missing$ + { + format.bvolume output + format.chapter.pages "chapter and pages" output.check + new.block + format.number.series output + new.sentence + format.publisher.address output + } + { + format.chapter.pages "chapter and pages" output.check + new.block + format.book.crossref output.nonnull + } + if$ + format.edition output + format.date "year" output.check + crossref missing$ + { format.isbn output } + 'skip$ + if$ + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {incollection} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.title "title" output.check + new.block + crossref missing$ + { format.in.ed.booktitle "booktitle" output.check + format.bvolume output + format.number.series output + format.chapter.pages output + new.sentence + format.publisher.address output + format.edition output + format.date "year" output.check + format.isbn output + } + { format.incoll.inproc.crossref output.nonnull + format.chapter.pages output + } + if$ + format.doi output + new.block + % format.note output + fin.entry +} +FUNCTION {inproceedings} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.title "title" output.check + new.block + crossref missing$ + { format.in.ed.booktitle "booktitle" output.check + format.bvolume output + format.number.series output + format.pages output + new.sentence + publisher empty$ + { format.organization.address output } + { organization "organization" bibinfo.check output + format.publisher.address output + } + if$ + format.date "year" output.check + format.isbn output + format.issn output + } + { format.incoll.inproc.crossref output.nonnull + format.pages output + } + if$ + format.doi output + new.block + % format.note output + fin.entry +} +FUNCTION {conference} { inproceedings } +FUNCTION {manual} +{ output.bibitem + format.authors output + author format.key output + new.block + format.btitle "title" output.check + organization address new.block.checkb + organization "organization" bibinfo.check output + address "address" bibinfo.check output + format.edition output + format.date "year" output.check + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {mastersthesis} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.btitle + "title" output.check + new.block + bbl.mthesis format.thesis.type output.nonnull + school "school" bibinfo.warn output + address "address" bibinfo.check output + format.date "year" output.check + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {misc} +{ output.bibitem + format.authors output + author format.key output + new.block + format.title output + new.block + howpublished "howpublished" bibinfo.check output + format.date "year" output.check + format.doi output + new.block + % format.note output + fin.entry +} +FUNCTION {phdthesis} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.btitle + "title" output.check + new.block + bbl.phdthesis format.thesis.type output.nonnull + school "school" bibinfo.warn output + address "address" bibinfo.check output + format.date "year" output.check + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {proceedings} +{ output.bibitem + format.editors output + editor format.key output + new.block + format.btitle "title" output.check + format.bvolume output + format.number.series output + new.sentence + publisher empty$ + { format.organization.address output } + { organization "organization" bibinfo.check output + format.publisher.address output + } + if$ + format.date "year" output.check + format.isbn output + format.issn output + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {techreport} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.title + "title" output.check + new.block + format.tr.number output.nonnull + institution "institution" bibinfo.warn output + address "address" bibinfo.check output + format.date "year" output.check + format.doi output + new.block + % format.note output + fin.entry +} + +FUNCTION {unpublished} +{ output.bibitem + format.authors "author" output.check + author format.key output + new.block + format.title "title" output.check + format.date "year" output.check + format.doi output + new.block + format.note "note" output.check + fin.entry +} + +FUNCTION {default.type} { misc } +READ +FUNCTION {sortify} +{ purify$ + "l" change.case$ +} +INTEGERS { len } +FUNCTION {chop.word} +{ 's := + 'len := + s #1 len substring$ = + { s len #1 + global.max$ substring$ } + 's + if$ +} +FUNCTION {format.lab.names} +{ 's := + "" 't := + s #1 "{vv~}{ll}" format.name$ + s num.names$ duplicate$ + #2 > + { pop$ + " " * bbl.etal * + } + { #2 < + 'skip$ + { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = + { + " " * bbl.etal * + } + { bbl.and space.word * s #2 "{vv~}{ll}" format.name$ + * } + if$ + } + if$ + } + if$ +} + +FUNCTION {author.key.label} +{ author empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { author format.lab.names } + if$ +} + +FUNCTION {author.editor.key.label} +{ author empty$ + { editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.lab.names } + if$ + } + { author format.lab.names } + if$ +} + +FUNCTION {editor.key.label} +{ editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.lab.names } + if$ +} + +FUNCTION {calc.short.authors} +{ type$ "book" = + type$ "inbook" = + or + 'author.editor.key.label + { type$ "proceedings" = + 'editor.key.label + 'author.key.label + if$ + } + if$ + 'short.list := +} + +FUNCTION {calc.label} +{ calc.short.authors + short.list + "(" + * + year duplicate$ empty$ + short.list key field.or.null = or + { pop$ "" } + 'skip$ + if$ + * + 'label := +} + +FUNCTION {sort.format.names} +{ 's := + #1 'nameptr := + "" + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr + "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" + format.name$ 't := + nameptr #1 > + { + " " * + namesleft #1 = t "others" = and + { "zzzzz" 't := } + 'skip$ + if$ + t sortify * + } + { t sortify * } + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ +} + +FUNCTION {sort.format.title} +{ 't := + "A " #2 + "An " #3 + "The " #4 t chop.word + chop.word + chop.word + sortify + #1 global.max$ substring$ +} +FUNCTION {author.sort} +{ author empty$ + { key empty$ + { "to sort, need author or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { author sort.format.names } + if$ +} +FUNCTION {author.editor.sort} +{ author empty$ + { editor empty$ + { key empty$ + { "to sort, need author, editor, or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { editor sort.format.names } + if$ + } + { author sort.format.names } + if$ +} +FUNCTION {editor.sort} +{ editor empty$ + { key empty$ + { "to sort, need editor or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { editor sort.format.names } + if$ +} +INTEGERS { seq.num } +FUNCTION {init.seq} +{ #0 'seq.num :=} +EXECUTE {init.seq} +FUNCTION {int.to.fix} +{ "000000000" swap$ int.to.str$ * + #-1 #10 substring$ +} +FUNCTION {presort} +{ calc.label + label sortify + " " + * + seq.num #1 + 'seq.num := + seq.num int.to.fix + 'sort.label := + sort.label + * + " " + * + title field.or.null + sort.format.title + * + #1 entry.max$ substring$ + 'sort.key$ := +} + +ITERATE {presort} +SORT +STRINGS { last.label next.extra } +INTEGERS { last.extra.num last.extra.num.extended last.extra.num.blank number.label } +FUNCTION {initialize.extra.label.stuff} +{ #0 int.to.chr$ 'last.label := + "" 'next.extra := + #0 'last.extra.num := + "a" chr.to.int$ #1 - 'last.extra.num.blank := + last.extra.num.blank 'last.extra.num.extended := + #0 'number.label := +} +FUNCTION {forward.pass} +{ last.label label = + { last.extra.num #1 + 'last.extra.num := + last.extra.num "z" chr.to.int$ > + { "a" chr.to.int$ 'last.extra.num := + last.extra.num.extended #1 + 'last.extra.num.extended := + } + 'skip$ + if$ + last.extra.num.extended last.extra.num.blank > + { last.extra.num.extended int.to.chr$ + last.extra.num int.to.chr$ + * 'extra.label := } + { last.extra.num int.to.chr$ 'extra.label := } + if$ + } + { "a" chr.to.int$ 'last.extra.num := + "" 'extra.label := + label 'last.label := + } + if$ + number.label #1 + 'number.label := +} +FUNCTION {reverse.pass} +{ next.extra "b" = + { "a" 'extra.label := } + 'skip$ + if$ + extra.label 'next.extra := + extra.label + duplicate$ empty$ + 'skip$ + { "{\natexlab{" swap$ * "}}" * } + if$ + 'extra.label := + label extra.label * 'label := +} +EXECUTE {initialize.extra.label.stuff} +ITERATE {forward.pass} +REVERSE {reverse.pass} +FUNCTION {bib.sort.order} +{ sort.label + " " + * + year field.or.null sortify + * + " " + * + title field.or.null + sort.format.title + * + #1 entry.max$ substring$ + 'sort.key$ := +} +ITERATE {bib.sort.order} +SORT +FUNCTION {begin.bib} +{ preamble$ empty$ + 'skip$ + { preamble$ write$ newline$ } + if$ + "\begin{thebibliography}{" number.label int.to.str$ * "}" * + write$ newline$ + "\providecommand{\natexlab}[1]{#1}" + write$ newline$ + "\expandafter\ifx\csname urlstyle\endcsname\relax" + write$ newline$ + " \providecommand{\doi}[1]{doi:\discretionary{}{}{}#1}\else" + write$ newline$ + " \providecommand{\doi}{doi:\discretionary{}{}{}\begingroup \urlstyle{rm}\Url}\fi" + write$ newline$ +} +EXECUTE {begin.bib} +EXECUTE {init.state.consts} +ITERATE {call.type$} +FUNCTION {end.bib} +{ newline$ + "\end{thebibliography}" write$ newline$ +} +EXECUTE {end.bib} +%% End of customized bst file +%% +%% End of file `jors.bst'. diff --git a/inst/rmarkdown/templates/jors/skeleton/jors.cls b/inst/rmarkdown/templates/jors/skeleton/jors.cls new file mode 100644 index 000000000..b45218b83 --- /dev/null +++ b/inst/rmarkdown/templates/jors/skeleton/jors.cls @@ -0,0 +1,63 @@ +%% Journal of Open Research Software Latex template -- Created By Stephen Bonner and John Brennan, Durham Universtiy, UK. + +\NeedsTeXFormat{LaTeX2e} +\ProvidesClass{jors}[2016/03/08 Journal Of Open Software Research] + +%% Article options +\DeclareOption{12pt}{ + \PassOptionsToClass{\CurrentOption}{article} +} + + +\DeclareOption{sansserif}{ + \PassOptionsToPackage{\CurrentOption}{paxcommands} +} +\DeclareOption{neverindent}{ + \PassOptionsToPackage{\CurrentOption}{paxcommands} +} + +%% Fallback +\DeclareOption*{ + \ClassWarning{jors}{Unknown option '\CurrentOption'} +} + + +\ExecuteOptions{12pt} + + +\ProcessOptions\relax + +\LoadClass[a4paper]{article} + +%% Load additional packages and commands. +\RequirePackage{xcolor} +\RequirePackage{sectsty} +\RequirePackage{enumitem} +\RequirePackage{hyperref} +\RequirePackage{fancyhdr} +\RequirePackage{titlesec} + +%% Additional TeX/LaTeX code... + +%% Remove the indentation +\newlength\tindent +\setlength{\tindent}{\parindent} +\setlength{\parindent}{0pt} +\renewcommand{\indent}{\hspace*{\tindent}} + +%% Remove the page numbers +\pagenumbering{gobble} + +%% Set the font too 13 for the titles +\sectionfont{\fontsize{13}{15}\selectfont} + +%% Set indentation for the lists +\setlist[description]{leftmargin=1cm,labelindent=1cm} + +%% Set spacing for the section headings +\titlespacing\section{0pt}{12pt plus 4pt minus 2pt}{0pt plus 2pt minus 2pt} + +%% Set margins +\usepackage[margin=1.2in,footskip=0.25in]{geometry} + +\endinput diff --git a/inst/rmarkdown/templates/jors/skeleton/jors.csl b/inst/rmarkdown/templates/jors/skeleton/jors.csl new file mode 100644 index 000000000..dedc216be --- /dev/null +++ b/inst/rmarkdown/templates/jors/skeleton/jors.csl @@ -0,0 +1,351 @@ + + diff --git a/inst/rmarkdown/templates/jors/skeleton/references.bib b/inst/rmarkdown/templates/jors/skeleton/references.bib new file mode 100644 index 000000000..3fe8cdebc --- /dev/null +++ b/inst/rmarkdown/templates/jors/skeleton/references.bib @@ -0,0 +1,16 @@ + +@article{piwowar2011, + title = {Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data}, + author = {{Piwowar}, {Heather A.}}, + year = {2011}, + month = {07}, + date = {2011-07-13}, + journal = {PLOS ONE}, + pages = {e18657}, + volume = {6}, + number = {7}, + doi = {10.1371/journal.pone.0018657}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018657}, + note = {Publisher: Public Library of Science}, + langid = {en} +} diff --git a/inst/rmarkdown/templates/jors/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/jors/skeleton/skeleton.Rmd new file mode 100644 index 000000000..730d8d49a --- /dev/null +++ b/inst/rmarkdown/templates/jors/skeleton/skeleton.Rmd @@ -0,0 +1,113 @@ +--- +# Journal of Open Research Software R Markdown template -- Created By Greg Pilgrim +bibliography: references.bib +output: rticles::jors_article +--- + + + + + +\section{Overview} + +\section*{Title} + + + +\section*{Paper Authors} + + + +\section*{Paper Author Roles and Affiliations} + + + +\section*{Abstract} + + +\section*{Keywords} + + + +\section*{Introduction} + + +\section*{Implementation and architecture} + + +\section*{Quality control} + + +\section{Availability} + +\section*{Operating system} + + + +\section*{Programming language} + + + +\section*{Additional system requirements} + + + +\section*{Dependencies} + + + +\section*{List of contributors} + + + +\section*{Software location:} + +**Archive** + +| **Name:** +| **Persistent identifier:** +| **Licence:** +| **Publisher:** +| **Version published:** +| **Date published:** + +**Code repository** + +| **Name:** +| **Persistent identifier:** +| **Licence:** +| **Date published:** + +**Emulation environment** + +| **Name:** +| **Persistent identifier:** +| **Licence:** +| **Date published:** + +\section*{Language} + + + +\section{Reuse potential} + + + +\section*{Acknowledgements} + + + +\section*{Funding statement} + + + +\section*{Competing interests} + + + + + + + diff --git a/inst/rmarkdown/templates/jors/template.yaml b/inst/rmarkdown/templates/jors/template.yaml new file mode 100644 index 000000000..5afc8fdab --- /dev/null +++ b/inst/rmarkdown/templates/jors/template.yaml @@ -0,0 +1,5 @@ +name: Journal of Open Research Software Article +description: > + Template for creating an article for submission to the Journal of Open Research Software +create_dir: FALSE + diff --git a/man/article.Rd b/man/article.Rd index c040c3844..923bec8f5 100644 --- a/man/article.Rd +++ b/man/article.Rd @@ -18,6 +18,7 @@ \alias{glossa_article} \alias{ims_article} \alias{jasa_article} +\alias{jors_article} \alias{lipics_article} \alias{jedm_article} \alias{mdpi_article} @@ -101,6 +102,13 @@ jasa_article( citation_package = "natbib" ) +jors_article( + ..., + keep_tex = TRUE, + latex_engine = "xelatex", + citation_package = "natbib" +) + lipics_article( ..., latex_engine = "xelatex", @@ -262,6 +270,12 @@ Journal of the Acoustical Society of America. Adapted from \url{https://acousticalsociety.org/preparing-latex-manuscripts/}. } +\section{\code{jors_article}}{ + Format for creating submissions to the +Journal of Open Research Software. Adapted from +\url{https://openresearchsoftware.metajnl.com/about/submissions/} +} + \section{\code{lipics_article}}{ Format for creating submissions to LIPIcs - Leibniz International Proceedings Informatics - articles. diff --git a/tests/testit/test-formats.R b/tests/testit/test-formats.R index 1313ce929..3d8789382 100644 --- a/tests/testit/test-formats.R +++ b/tests/testit/test-formats.R @@ -49,6 +49,7 @@ test_format("ieee") test_format("ims") test_format("ims", output_options = list(journal = "aap")) test_format("jasa") +test_format("jors") test_format("joss") test_format("joss", output_options = list(journal = "JOSE")) test_format("jss")