![]() ![]() As control of MS Word formatting is somewhat more challenging from RMarkdown, some manual intervention may be required after knitting depending on the author and journal preferences. Although many journals do not accept LaTeX as a submission format, it is fairly easy to use the bookdown package and to select MS Word as the output format. This workflow is suitable for any Elsevier journal with only minor modifications from what we have shown in this example for JMSACL. We have outlined the process for preparing a manuscript reproducibly using RMarkdown and RStudio. With these tools, a dataframe can be rendered as a table easily, as in the following example code chunk. While there are a number of ways to render a table into an RMarkdown document, to our mind the simplest means is to prepare a dataframe of results and to use the kable() function from the knitr package with the kableExtra package to permit many of the complex table structures available natively in LaTeX. ndka: Nucleoside diphosphate kinase A concentration (nkda in μg/L). s100b: S100 calcium-binding protein B concentration (s100b in μg/L) and 7. wfns: The World Federation of Neurological Surgeons score (1–5) 6. gos6: the Glasgow Coma Outcome Score (1–6) 2. examining blood biomarkers in patients suffering subarachnoid hemmorhage. įor the purposes of illustration we will use a biomedical dataset available in the pROC package taken from a 2010 study by Turck et al. LaTeX (stylized as ) is a versatile and powerful type setting system used for publishing. The result is LaTeX source code that can be submitted and/or compiled to PDF. In this article, we will review all aspects of reproducible manuscript preparation for JMSACL using the R programming language and the rmarkdown and knitr packages to generate all calculated/rendered aspects of a manuscript, including headers, sections, figures, tables, captions, inline numerical results (including p-values and confidence intervals), references, and reference formatting. While there are a number of approaches to reproducible document preparation, , perhaps the most mature of these is the use of the R knitr package and RMarkdown document format inside of the RStudio open-source development environment for the R programming language. The use of reproducible research tools has become more common because of the large and complex data sets on which modern clinical research is performed and in response to conspicuous examples of serious inferential error, which would have been more easily detected (or perhaps avoided entirely) were the research performed reproducibly to begin with. PDF, Microsoft (MS) Word or HTML) complete with statistics and figures. When the program or code is executed, it produces a human readable document to which we are accustomed (e.g. These terms refer to a document that is itself a script or program that directly pulls in the raw data for the study and reveals the entire statistical methodology in the code. A concrete way to address statistical transparency is the so-called “executable document” or “literate programming”. ![]() One aspect of research reproducibility is statistical transparency, which primarily falls into the category of methods reproducibility, but encompasses some aspects of results and inferential reproducibility. Reproducibility in research has different components, which have been previously defined as i) methods reproducibility: protocols, measurement procedures, reagents, data processing and analysis ii) results reproducibility: the ability for an independent study to obtain similar results in similar experimental conditions, iii) inferential reproducibility: the ability of another researcher to draw the same conclusions from the original data or a similar data set. The problem of poor reproducibility of biomedical research has been attributed to a number of factors: study design, preanalytical handling, reagent lot variation, suboptimal analytical reproducibility, researcher bias, incorrect use of statistical methodologies, and unexpected artifacts of software-even when working-as-designed. There is increasing attention paid to the concept of reproducible research in the biological and medical sciences. ![]()
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