zhuchcn/bookdown-for-manuscript

A template for manuscript writing using bookdown

This is an example of academic manuscript written based on R Markdown and bookdown (https://github.com/rstudio/bookdown).

The manuscript is published on the Metabolomics.

The HDL lipidome is widely remodeled by fast food versus Mediterranean diet in 4 days. Zhu, et al. Metabolomics August 2019

Title page

The index.Rmd defines the title page of the manuscript, including the title, authors, emails, addresses, and abbreviations. The bibliography in the yml header defines the reference file(s). The references must be stored in .bib file(s). The csl in the yaml header defines the citation stylesheets.

Chapters

Each chapter should be written as a separate Rmd file and labeled in the designated order. All Rmd files will be sourced and merged by bookdown.

Reference word document

In order to tell the bookdown to render it into word document, you need to specify it in the _output.yml file. The reference_doc.doc is a valid word document, in which the content is ignored and only the stylesheet is kept. Use the Styles Pane in Word to modify the stylesheet.

Equations Font

Unfortunately there is not way to specify the font in the equations in the word style pane, and by default the font of any equations will be Cambria Math. The script format_equations.py changes the font of all equations in the word document at once.

Reference

References are stored in one or more .bib file and needs to be specified in the yaml header of the index.Rmd. The references must be in valid BibTex format. The pubmed-bib is a command line tool that queries reference from PubMed and print out to the command line in a valid BibTex format.

The citation style is determined by a .csl file and needs to be specified also in the yaml header of the index.Rmd. The journal specific csl file can be downloaded from the Zotero Style Repository

Build

To build the book, either click the build button in RStudio, or run the build.sh script. The latter will also run the format_equation.py. However Windows users must figure something out. The rendered book can be found under the _book folder

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Please see the page "Get Started" at https://bookdown.org/ for how to compile this example.