From ec4862ab8d47440c5a73bee32fdb0d642159fb88 Mon Sep 17 00:00:00 2001 From: Chris Sobczak Date: Tue, 5 May 2026 12:42:45 -0700 Subject: Create basic templates and utility scripts --- lit-review-template.qmd | 52 +++++++++++++++++++++++++++++++++++++++++++++++++ lit-review-template.rmd | 46 +++++++++++++++++++++++++++++++++++++++++++ references.bib | 2 ++ scripts/doi2bib | 5 +++++ scripts/qmd2pdf | 2 ++ scripts/rmd2pdf | 2 ++ 6 files changed, 109 insertions(+) create mode 100644 lit-review-template.qmd create mode 100644 lit-review-template.rmd create mode 100644 references.bib create mode 100755 scripts/doi2bib create mode 100755 scripts/qmd2pdf create mode 100755 scripts/rmd2pdf diff --git a/lit-review-template.qmd b/lit-review-template.qmd new file mode 100644 index 0000000..3329a3d --- /dev/null +++ b/lit-review-template.qmd @@ -0,0 +1,52 @@ +--- +title: "TEMPLATE_FIELD" +author: "TEMPLATE_FIELD" +date: now +date-format: "DD MMMM YYYY - HH:mm" +format: + pdf: + toc: false + number-sections: true + fig-caption: yes + highlight-style: "zenburn" + include-in-header: + - text: | + \usepackage{etoolbox} + + \AtEndPreamble{\hypersetup{colorlinks=true,linkcolor=blue,urlcolor=blue,citecolor=red}} + extra-dependencies: + - float + - multicol + +bibliography: references.bib +link-citations: true +editor-options: + markdown: + wrap: 72 +--- + +\tableofcontents +\newpage + + +# Topic one + +## Paper one [@Shin_2014] + +## Paper two [@Suhre_2011] + +# Topic two + +\newpage + + +# Online resources + +\newpage + + +# Glossary + +\newpage + +# References diff --git a/lit-review-template.rmd b/lit-review-template.rmd new file mode 100644 index 0000000..3ad65f3 --- /dev/null +++ b/lit-review-template.rmd @@ -0,0 +1,46 @@ +--- +title: "TEMPLATE_FIELD" +author: "TEMPLATE_FIELD" +date: "`r format(Sys.time(), '%d %B %Y - %H:%M')`" +output: + pdf_document: + toc: false + number_sections: true + fig_caption: yes + highlight: "zenburn" + extra_dependencies: ['float','multicol'] +bibliography: references.bib +link-citations: true +header-includes: + - \usepackage{etoolbox} + - \AtEndPreamble{\hypersetup{colorlinks=true,linkcolor=blue,urlcolor=blue,citecolor=red}} +editor_options: + markdown: + wrap: 72 +--- + +\tableofcontents +\newpage + + +# Topic one + +## Paper one [@Shin_2014] + +## Paper two [@Suhre_2011] + +# Topic two + +\newpage + + +# Online resources + +\newpage + + +# Glossary + +\newpage + +# References diff --git a/references.bib b/references.bib new file mode 100644 index 0000000..268585f --- /dev/null +++ b/references.bib @@ -0,0 +1,2 @@ +@article{Shin_2014, title={An atlas of genetic influences on human blood metabolites}, volume={46}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.2982}, DOI={10.1038/ng.2982}, number={6}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={ and Shin, So-Youn and Fauman, Eric B and Petersen, Ann-Kristin and Krumsiek, Jan and Santos, Rita and Huang, Jie and Arnold, Matthias and Erte, Idil and Forgetta, Vincenzo and Yang, Tsun-Po and Walter, Klaudia and Menni, Cristina and Chen, Lu and Vasquez, Louella and Valdes, Ana M and Hyde, Craig L and Wang, Vicky and Ziemek, Daniel and Roberts, Phoebe and Xi, Li and Grundberg, Elin and Waldenberger, Melanie and Richards, J Brent and Mohney, Robert P and Milburn, Michael V and John, Sally L and Trimmer, Jeff and Theis, Fabian J and Overington, John P and Suhre, Karsten and Brosnan, M Julia and Gieger, Christian and Kastenmüller, Gabi and Spector, Tim D and Soranzo, Nicole}, year={2014}, month=May, pages={543–550} } +@article{Suhre_2011, title={Human metabolic individuality in biomedical and pharmaceutical research}, volume={477}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature10354}, DOI={10.1038/nature10354}, number={7362}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={ and Suhre, Karsten and Shin, So-Youn and Petersen, Ann-Kristin and Mohney, Robert P. and Meredith, David and Wägele, Brigitte and Altmaier, Elisabeth and Deloukas, Panos and Erdmann, Jeanette and Grundberg, Elin and Hammond, Christopher J. and de Angelis, Martin Hrabé and Kastenmüller, Gabi and Köttgen, Anna and Kronenberg, Florian and Mangino, Massimo and Meisinger, Christa and Meitinger, Thomas and Mewes, Hans-Werner and Milburn, Michael V. and Prehn, Cornelia and Raffler, Johannes and Ried, Janina S. and Römisch-Margl, Werner and Samani, Nilesh J. and Small, Kerrin S. and -Erich Wichmann, H. and Zhai, Guangju and Illig, Thomas and Spector, Tim D. and Adamski, Jerzy and Soranzo, Nicole and Gieger, Christian}, year={2011}, month=Aug, pages={54–60} } diff --git a/scripts/doi2bib b/scripts/doi2bib new file mode 100755 index 0000000..358c728 --- /dev/null +++ b/scripts/doi2bib @@ -0,0 +1,5 @@ +#!/bin/sh +case "$1" in + *"doi.org"*) curl -LH "Accept: application/x-bibtex" $1;; + *) curl -LH "Accept: application/x-bibtex" "https://doi.org/$1";; +esac diff --git a/scripts/qmd2pdf b/scripts/qmd2pdf new file mode 100755 index 0000000..4442b34 --- /dev/null +++ b/scripts/qmd2pdf @@ -0,0 +1,2 @@ +#!/bin/sh +quarto render "$1" diff --git a/scripts/rmd2pdf b/scripts/rmd2pdf new file mode 100755 index 0000000..3c7a287 --- /dev/null +++ b/scripts/rmd2pdf @@ -0,0 +1,2 @@ +#!/bin/sh +Rscript -e "rmarkdown::render('$1')" -- cgit v1.2.3