knitcitations is an R package designed to add dynamic citations to dynamic documents created with Yihui's knitr package.
Install directly from Github using Hadley's devtools package
You can also clone or download the repository and install with R CMD INSTALL. Once I'm through the early development phase a copy will be available on CRAN.
It is usually good to clear the bibliographic environment after loading the library, in case any citations are already stored there.
## Loading required package: bibtex
Cite an article by DOI and the full citation information is gathered automatically.
citep("10.1890/11-0011.1")
[1] “Abrams et. al. 2012”
Typically this is done with knitr's inline code syntax, creating a parenthetical citation in the text like this Abrams et. al. 2012. We display the command in code blocks only for documenting purposes here. citep provides a parenthetical citation; a in-text citation is generated with citet, such as this sentence cites Abrams et. al. (2012).
When the citation is called, a key in the format LastNameYear is automatically created for this citation, so we can now continue to cite this article without remembering the DOI, using the command:
citep("Abrams2012")
[1] “Abrams et. al. 2012”
Note that a custom key can also be given by naming the DOI, such as citep(c(AbramsEtAl="10.1890/11-0011.1")).
If we have a bibtex file, we can cite such articles by those keys as well. To demonstrate, let's first create a bibtex file with the citation information for some R packages, using the bibtex package utilities (a dependency of knitcitations):
write.bibtex(c(Yihui2013 = citation("knitr"), Boettiger2013 = citation("knitcitations"),
TempleLang2012 = citation("RCurl")))
bib <- read.bibtex("knitcitations.bib")
Now we can generate citations from bib
citep(bib[[2]])
## [1] "Halpern _et. al._ 2006"
citep(bib["Yihui2013"])
## [1] "Xie, 2013"
Generate the final bibliography in a knitr block using the chunk option results='asis' to display as text rather than code:
bibliography()
Abrams P, Ruokolainen L, Shuter B and McCann K (2012). “Harvesting
Creates Ecological Traps: Consequences of Invisible Mortality
Risks in Predator
Other formats can be given as options to bibliography, as described in the help documentation, ?bibliography. See the full tutorial for more about knitcitations.
Knitcitations can also return semantic RDFa markup around your citations. Simply select the “rdfa” in the bibliography option.
bibliography("rdfa")
Here's what the source HTML looks like (generated as R output by not setting results="asis" in the knitr block):
bibliography("rdfa")
## <div prefix="dc: http://purl.org/dc/terms/,
## bibo: http://purl.org/ontology/bibo/,
## foaf: http://xmlns.com/foaf/spec/,
## biro: http://purl.org/spar/biro/"
## property="http://purl.org/spar/biro/ReferenceList"> <ul class='bibliography'>
## <li> <span property="dc:title">Harvesting Creates Ecological Traps: Consequences of Invisible Mortality Risks in Predator<U+2013>Prey Metacommunities.</span> <span property="dc:creator"> <span property="foaf:givenName">Peter A.</span> <span property="foaf:familyName">Abrams</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Lasse</span> <span property="foaf:familyName">Ruokolainen</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Brian J.</span> <span property="foaf:familyName">Shuter</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Kevin S.</span> <span property="foaf:familyName">McCann</span>, </span> (<span property="dc:date">2012</span>) <span rel="http://purl.org/dc/terms/isPartOf"
## resource="[http://purl.org/dc/terms/journal]">
## <span property="http://purl.org/dc/terms/title"
## content=" Ecology ">
## </span>
## <span property="bibo:shortTitle"> Ecology </span>
## </span> <span property="bibo:volume">93</span> <a property="bibo:doi" href="http://dx.doi.org/10.1890/11-0011.1">10.1890/11-0011.1</a> </li>
## </ul>
## </div>
## <div prefix="dc: http://purl.org/dc/terms/,
## bibo: http://purl.org/ontology/bibo/,
## foaf: http://xmlns.com/foaf/spec/,
## biro: http://purl.org/spar/biro/"
## property="http://purl.org/spar/biro/ReferenceList"> <ul class='bibliography'>
## <li> <span property="dc:title">Accounting For Uncertainty in Marine Reserve Design.</span> <span property="dc:creator"> <span property="foaf:givenName">Benjamin</span> <span property="foaf:familyName">Halpern</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Helen</span> <span property="foaf:familyName">Regan</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Hugh</span> <span property="foaf:familyName">Possingham</span>, </span><span property="dc:creator"> <span property="foaf:givenName">Michael</span> <span property="foaf:familyName">McCarthy</span>, </span> (<span property="dc:date">2006</span>) <span rel="http://purl.org/dc/terms/isPartOf"
## resource="[http://purl.org/dc/terms/journal]">
## <span property="http://purl.org/dc/terms/title"
## content=" Ecology Letters ">
## </span>
## <span property="bibo:shortTitle"> Ecology Letters </span>
## </span> <span property="bibo:volume">9</span> <a property="bibo:doi" href="http://dx.doi.org/10.1111/j.1461-0248.2005.00827.x">10.1111/j.1461-0248.2005.00827.x</a> </li>
## </ul>
## </div>
## <div prefix="dc: http://purl.org/dc/terms/,
## bibo: http://purl.org/ontology/bibo/,
## foaf: http://xmlns.com/foaf/spec/,
## biro: http://purl.org/spar/biro/"
## property="http://purl.org/spar/biro/ReferenceList"> <ul class='bibliography'>
## <li> <span property="dc:title">knitr: A general-purpose package for dynamic report generation in R.</span> <span property="dc:creator"> <span property="foaf:givenName">Yihui</span> <span property="foaf:familyName">Xie</span>, </span> (<span property="dc:date">2013</span>) <span rel="http://purl.org/dc/terms/isPartOf"
## resource="[http://purl.org/dc/terms/journal]">
## <span property="http://purl.org/dc/terms/title"
## content=" ">
## </span>
## <span property="bibo:shortTitle"> </span>
## </span> <a property="bibo:doi" href="http://dx.doi.org/"></a> </li>
## </ul>
## </div>
Additional semantic markup can be added the the citations themselves, such as the reason for the citation. For instance, we can identify that we have used the method from