le-huynh / writing_journal_article_in_rmarkdown

Writing Journal Article with R Markdown

Writing Scientific Manuscript using Rmarkdown

This repository is a comprehensive yet simple example of a fully-fledged scientific project, encompassing every aspect from data to submission. It includes:

• Data/: Example dataset used in the project. The raw data serves as the source material but is not directly used for analysis; instead, the analysis relies on the processed data, derived from the raw data through code.
• Code/: Example scripts and code utilized to acquire processed data, create plot, and generate table.
• Results/: Visualizations, tables, and any output derived from the analysis code.
• Exploratory/: Additional materials for exploratory analysis or supplementary findings.
• Submission/: Contains a template manuscript encompassing thorough guidelines for creating the final manuscript, ensuring adherence to publication standards.
• Makefile: Automates the compilation process using GNU Make, streamlining the generation of the final manuscript.

Notes

• See /elsevier/manuscript.Rmd and /elsevier/manuscript.pdf for notes of Rmarkdown and LaTeX.
• Get the manuscript template at the R package lehuynh, template draft_elsevier.

Repo Overview

project
|- README.md		# the top level description of content (this doc)
|
|- elsevier/		# submission for Elsevier journals
| |- manuscript.Rmd	# executable Rmarkdown for this study
| |- manuscript.tex	# TeX version of *.Rmd file (for journal submission)
| |- manuscript.pdf	# PDF version of *.Rmd file
| |- manuscript.docx	# docx version of *.Rmd file
| |- my_header.tex	# LaTeX header file to format pdf version of manuscript
| |- bibliography.bib	# BibTeX formatted references
| |- XXXX.csl		# csl file to format references for journal XXX
| |- *.Rmd		# child documents
| +- other files	# optional files utilized for exporting the .Rmd file to the .pdf format (safe for deletion)
|
|- data			# raw and primary data, are not changed once created
| |- raw/		# raw data, will not be altered
| +- process/		# cleaned data, will not be altered once created
|
|- code/		# any programmatic code
|
|- results		# all output from workflows and analyses
| |- tables/		# text version of tables to be rendered with kable in R
| |- figures/		# graphs, likely designated for manuscript figures
| +- pictures/		# diagrams, images, and other non-graph graphics
|
|- exploratory/		# exploratory data analysis for study
| |- notebook/		# preliminary data analyses
| |- text/		# all information related to journal, meeting, outline, etc.
| |- springer/		# template for Springer journals, from `rticles` package
| +- scratch/		# temporary files that can be safely deleted or lost
|
+- Makefile		# executable Makefile for this study

Contribution

Contributions and improvements to this repository are welcome! If you have suggestions, additional templates, or enhancements, feel free to create pull requests or open issues.

Acknowledgements

This project is inspired by the new_project repository created by the Schloss lab and the rticles package.