Dataset Information

Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.

ABSTRACT:

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.

SUBMITTER: Holmes DT

PROVIDER: S-EPMC8662334 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.

Holmes Daniel T DT Mobini Mahdi M McCudden Christopher R CR

Journal of mass spectrometry and advances in the clinical lab 20210927

<h4>Introduction</h4>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.<h4>Objectives</h4>We describe the procedure for manuscript preparation us ...[more]

PMID: 34939050

Similar Datasets

Project description:BackgroundAlthough peer reviewers play a key role in the manuscript review process, their roles and tasks are poorly defined. Clarity around this issue is important as it may influence the quality of peer reviewer reports. This scoping review explored the roles and tasks of peer reviewers of biomedical journals.MethodsComprehensive literature searches were conducted in Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Educational Resources Information Center, EMBASE, MEDLINE, PsycINFO, Scopus and Web of Science from inception up to May 2017. There were no date and language restrictions. We also searched for grey literature. Studies with statements mentioning roles, tasks and competencies pertaining to the role of peer reviewers in biomedical journals were eligible for inclusion. Two reviewers independently performed study screening and selection. Relevant statements were extracted, collated and classified into themes.ResultsAfter screening 2763 citations and 600 full-text papers, 209 articles and 13 grey literature sources were included. A total of 1426 statements related to roles were extracted, resulting in 76 unique statements. These were grouped into 13 emergent themes: proficient experts in their field (3 items), dutiful/altruistic towards scientific community (7 items), familiar with journal (2 items), unbiased and ethical professionals (18 items), self-critical professionals (4 items), reliable professionals (7 items), skilled critics (15 items), respectful communicators (6 items), gatekeepers (2 items), educators (2 items), advocates for author/editor/reader (3 items) and advisors to editors (2 items). Roles that do not fall within the remit of peer reviewers were also identified (5 items). We also extracted 2026 statements related to peer reviewers' tasks, resulting in 73 unique statements. These were grouped under six themes: organisation and approach to reviewing (10 items), make general comments (10 items), assess and address content for each section of the manuscript (36 items), address ethical aspects (5 items), assess manuscript presentation (8 items) and provide recommendations (4 items).ConclusionsPeer reviewers are expected to perform a large number of roles and tasks for biomedical journals. These warrant further discussion and clarification in order not to overburden these key actors.

Dataset Information

Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.

Introduction

Objectives

Methods

Results

Conclusion

Publications

Reproducible manuscript preparation with RMarkdown application to JMSACL and other Elsevier Journals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets