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Updated: Oct 9, 2025
Author Spotlight: Biological Standardization to Ensure Reproducibility and Harmonization in Research
Published on: August 4, 2023
Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals
Daniel T Holmes1,2, Mahdi Mobini1,3, Christopher R McCudden4,5,6
1St. Paul's Hospital, Department of Pathology and Laboratory Medicine, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada.
Introduction:
With the rising complexity of modern multimarker analytical techniques and notable scientific publication retractions required for erroneous statistical analysis, there is increasing awareness of the importance of research transparency and reproducibility. The development of mature open-source tools for literate programming in multiple langauge paradigms has made fully-reproducible authorship possible.
Objectives:
We describe the procedure for manuscript preparation using RMarkdown and the R statistical programming language with application to JMSACL or any other Elsevier journal.
Methods:
An instructional manuscript has been prepared in the RMarkdown markup language with stepwise directions on preparing sections, subsections, lists, tables, figures and reference management in an entirely reproducible format.
Results:
From RMarkdown code, a submission-ready PDF is generated and JMSACL-compatible LaTeX code is generated. These can be uploaded to the Editorial Manager.
Conclusion:
A completely reproducible manuscript preparation pipeline using the R and RMarkdown is described.
