Add nucleotide acid research template

[tcgriffith]

I'll work on the NAR template. this issue serves as a record.

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[tcgriffith]

Basically working. Some issues:

• The skeleton is quite bulky as I copied&pasted the original draft from nar-sample.tex.

• The bibliography is a bit strange without using natbib in pandoc(nar-sample.tex doesn't use natbib) but I can't get the non-natbib bibliography to work at the moment:

  • NAR.cls from https://github.com/dcjones/quip-paper/blob/master/NAR.cls
  • nar.bst from https://github.com/dcjones/quip-paper/blob/master/nar.bst
    Now the bibliography and style are consistent with the nar-sample.

• longtable(pandoc's default) doesn't work in this template because nar is 2-column, similar to Add a PNAS template #72. So I provided a table example using knitr::kable(format="latex")

• Figures are fine. and I figured out the fig.env="figure*" trick. for two-column figure.

• I noticed that the syntax for cross-reference from bookdown::pdf_document2() is different from the default rmarkdown::pdf_document()

[tcgriffith]

hyperlinks likehttps://github.com/sokrypton/GREMLIN_CPP in rmd will be translated into\url{https://github.com/sokrypton/GREMLIN_CPP} and failed to compile
investigating.

[tcgriffith]

bibliography seems broken.I can use latexmk -pdf xxx.tex to generate the correct bibliography, but the knit button won't generate the desired bib.

[tcgriffith]

Seems that \usepackage{hyperref} is not included in the original nar.cls. This package is required for \url{} to which pandoc convert all links.

[tcgriffith]

List items will report an undefined control sequence error.
add the following command seems to fix the issue.
\def\tightlist{}

source
https://tex.stackexchange.com/questions/257418/error-tightlist-converting-md-file-into-pdf-using-pandoc/408474

[tcgriffith]

Strange behaviour on natbib:

if there's \label{xxx} in the rmd, the natbib bibliography will appear in the final pdf as expected.

deleting \label{xxx}, all references are gone and report undefined references:

Package natbib Warning: There were undefined citations.

But the generated test.tex can be correctly compiled with bibliography with
latexmk -pdf test.tex

So the issue is narrowed down to how rmarkdown calls the latex engine AFTER the .tex file is generated.

MRE:

devtools::install_github("tcgriffith/rticles", ref="nar_dev")
rmarkdown::render("./test.Rmd")

test.Rmd,
delete \label{aaa} will remove bibliography

---
title: Template for preparing your research report submission to NAR using RMarkdown
bibliography: NAR-sample.bib
output: rticles::nar_article
---

# Introduction
\label{aaa} 
[@NovikovaSizinglongnoncoding2012]

NAR-sample.bib

@Article{NovikovaSizinglongnoncoding2012,
  title = {Sizing up Long Non-Coding {{RNAs}}: {{Do lncRNAs}} Have Secondary and Tertiary Structure?},
  volume = {2},
  issn = {1949-0992},
  shorttitle = {Sizing up Long Non-Coding {{RNAs}}},
  number = {6},
  journal = {BioArchitecture},
  doi = {10.4161/bioa.22592},
  author = {Irina V. Novikova and Scott P. Hennelly and Karissa Y. Sanbonmatsu},
  month = {nov},
  year = {2012},
  keywords = {cancer,epigenetics,RNA structure,hormone receptor,HOTAIR,lincRNA,lncRNA,long noncoding RNA,MALAT,non-coding,RNA,secondary structure,structural biology},
  pages = {189-199},
  file = {/home/tc/.mozilla/firefox/wh762y60.default/zotero/storage/H9MYM9JS/Novikova et al. - 2012 - Sizing up long non-coding RNAs Do lncRNAs have se.pdf;/home/tc/.mozilla/firefox/wh762y60.default/zotero/storage/EVMVWMGZ/bioa.html},
  pmid = {23267412},
}

[cderv]

This is still open. The first PR has been close because it needs a rework. It can be used as base for a new one.
If anyone is willing to help @tcgriffith on this one, feel free to join ! Thanks.