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Questions tagged [pandoc-citeproc]

Pandoc filter and Haskell library for working with bibliographies. This is deprecated in favour of citeproc since 2020.

The pandoc-citeproc executable can be used as a filter with pandoc to resolve and format citations using a bibliography file and a CSL stylesheet. It can also be used (with --bib2yaml or --bib2json options) to convert a bibliography to a YAML format that can be put directly into a pandoc markdown document or to CSL JSON. Bibliographies can be in any of several formats, but bibtex and biblatex are the best supported. This is deprecated in favour of citeproc since 2020, and no additinal filter is required.

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Pandoc conversion to PDF not providing colored hyptertext links

Consider the following snippet of a PDF generated from pandoc by way of latex. Were you able to identify the hypertext links in there? Neither was I... It turns out that the second Kaplan Meier has a fully functional link to an external site. …
WestCoastProjects
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How to cite multiple papers in RMarkdown

How do I cite multiple papers in RMarkdown as I would do in LaTex with \cite{Bartel2004, Bartel2009a} I tried [@Bartel2004, @Bartel2009a] which renders to (D. P. Bartel 2004, David P. Bartel (2009)) which is not too bad, but the second brackets…
Gregor Sturm
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R Markdown: suppress parentheses in specific citations

I have an R Markdown document that includes some citations. I am using the default citation style, which usually works well for me. But I have some sentences that lie within parentheses, and in these sentences, I want to cite works without adding a…
user697473
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pandoc citations in revealjs from markdown

I use pandoc to generate Reveal.js slides from a Markdown file. All the citations are dumped in in the last slide, so I finish the .md file with the title # References, which is fitting. However, all references are in the same slide, and they would…
Trylks
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How to move superscript citation numbers inside of punctuation in Markdown file?

I am using Rmarkdown to write a paper with citations. When I use Nature's CSL (or any superscript numeric style) and render with Pandoc and pandoc-citeproc, the in line citations are outside of the punctuation. How can I move them inside the…
Daijiang Li
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Show all used references when using compact numeric citation style

I'm rendering html from markdown using bookdown, and using a compact numeric citation style so that e.g., 1, 2, 3 is shown as 1-3. I'd like references to be shown at the bottom of each page (link-citations: yes), but only the first and last…
jbaums
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knitr/Rmarkdown/pandoc : How to set bibliography paths globally in .Rmd files

[FYI: This question is related to rmarkdown: how to use multiple bibliographies for a document In LaTeX documemnts or even in Rmarkdown .Rnw, I can simply use something like \bibliography{graphics, statistics, timeref} to have BibTeX search for the…
user101089
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pandoc does not produce bibliography when biblio file is in YAML-metadata only

I assume that inserting a reference to a BibTex bibliography in a YAML-metadata is sufficient for the references to be produced. This is like pandoc does not print references when .bib file is in YAML, which was perhaps misunderstood and which has…
user855443
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Can I specify multiple bibliography (BibTeX) files in Pandoc Metadata?

Often, scientific journal websites and other sources offer downloadable *.bib files for referring to individual articles. If I use these, I like to keep them as they are instead of merging them into a single file. On the command line, several files…
das-g
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Building a self-contained binary executable in Haskell with the dependency pandoc-citeproc

I'm trying to compile a self-contained executable for a CLI tool written in Haskell. I followed this example to automatically build the executables for different operating systems with Github Actions using Cabal v3.2 and ghc v8.10.3. This seems to…
nevrome
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How to use --citeproc instead of pandoc-citeproc in RStudio when bibliography is used in an RMarkdown document?

I get the following error when trying to render a RMarkdown document in RStudio with bibliography specified in the YAML as bibliography: references.bib: [WARNING] Deprecated: pandoc-citeproc filter. Use --citeproc instead. Error running filter…
ForEverNewbie
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Pandoc conversion from LaTeX+BibLaTeX to Markdown

This should be relatively simple but I can't find a clear answer about how to do it. I am using the command: pandoc -s myfile.tex -o outfile.md --bibliography mybib.bib But outfile.md does not end up having any bibliography. What is going on?
Joshua Meyers
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Organizing references by year in Pandoc when generating HTML

I am relatively new with Pandoc and I am trying to generate an HTML file with my publications to put up on my website. I'd like to have the publication list numbered and organized by year first, with the most recent first and the oldest last. I can…
TomCho
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How can I use a URL for the bibliography YAML element in an RMarkdown document?

Goal: I am able to use a URL to specify the csl for my document within my YAML front matter, and I'd like to be able to do the same for the bibliography element. Question: Is this possible? Motivation: Using URLs for these elements, as opposed to…
mikoontz
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Bibtex authors appearing as dashed lines in references when using bookdown and pandoc

I'm generating a reference section using Rmarkdown, bookdown and pandoc. I have a reference section with 6 entries. One of the entries does not have the author list, and instead appears as: ———. 2004. “Multimodel Inference.” Sociological Methods &…
Michael Barton
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