Saturday, July 30, 2016

Practical LaTeX for the Health Sciences

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The purpose of this tutorial is to introduce health scientists, analysts, and writers to LaTeX for preparing scientific documents. LaTeX is a document preparation system for creating professionally typeset scientific documents.  LaTeX is freely available and widely used by data scientists, mathematicians, physicists, statisticians, engineers, demographers, and many other disciplines. Specifically, we will learn how to prepare a scientific article, report, and doctoral thesis. Additionally, we introduce selected software solutions that enhance the publication process.

The purpose of scientific writing is to communicate, persuade, educate, inform, or alert readers using content that is well-organized and clear.  Scientific and technical documents can be divided into the following components (in order of importance!):

  1. Content
  2. Structure
  3. Appearance

The document content is the main reason for writing anything: we want to effectively communicate, and perhaps persuade, our audience with our narrative and supporting tables and figures.  As writers, we want to spend our time and intellectual energy producing excellent content.  Next in importance is document structure: that is, how our document is organized for logic and flow: title, section headings, subheadings, bibliography, tables, figures, etc.  Good document structure optimizes the logic and flow of our content.  Last in importance is document appearance. We do not want to waste our time worrying about how the content will appear---this can be accomplished efficiently later if the document is well-structured to begin with.

Therefore, as we write, we should spend most of our time on content production, spend time on determining organization to optimize the order and flow of our content, and spend minimal time on formatting appearance.  All too often writers spend an extensive amount of time formatting the appearance of their document to give it a desired structure and appearance.  This is problematic for documents that are long or that require frequent updating.  Additionally, most writers are not trained in typography: the time wasted on formatting is much better spent on improving content.

Preparing scientific documents is not writing a fiction novel.  In many ways preparing a scientific document is easier.  First, the organization has an expected structure. For example, a scientific article generally has the following sections: introduction, methods, results, and discussion.  Second, scientific writing should be factual, concise, and clear.  And third, displays are generally limited to tables and figures.

Preparing scientific documents present the following challenges:

  • Organization is structured (introduction, methods, results,  etc.)
  • Document length may be long
  • Document may require periodic updating
  • Use of mathematical notation and equations
  • Management of references
  • Creation of bibliographies
  • Cross-references to equations, tables, and figures
  • Re-number equations, tables, and figures
  • Generation of table of contents, tables, and figures 

Because article manuscripts are relatively short (about 20 pages double-spaced), these issues are less problematic.  For a doctoral thesis (or long report), these issues are either addressed efficiently and save time, addressed incorrectly and waste someone's time (possibly an administrative assistant---or worse, the author---spending hours reformatting), or not addressed at all---resulting in a lower quality, less user-friendly document.

In general, document preparation systems can be classified as either visual design or logical design. Microsoft (MS) Word is a familiar example of a visual design system; it is also known as "what you see is what you get" (WYSIWYG).  What you see on the computer screen is almost identical to what you get when you print the document.  In MS Word, basic word processing is easy to learn, user-friendly, and convenient for local formatting.  Local formatting is achieved by highlighting a string a text and then formatting it: for example, italicizing, bolding, or changing font face, size or color.  A major limitation of visual design is that local formatting of appearance is so easy that it becomes (unintentionally) the formatting method of choice for structuring long documents.  Extensive local formatting of long documents become onerous and impractical; WYSIWYG comes to mean "what you see is what you got."

In contrast, logical design separates the process of content production from the processes of formatting structure and formatting appearance. LaTeX is a logical design system: it provides a "markup language" to mark up content to have structural and conceptual meaning.  This facilitates global formatting of structure and appearance using established typographical standards for scientific documents.  Once the content is marked up, the content is compiled into a professionally typeset document using well established formats for scientific publication.  The writer spends little time worrying about formatting structure and appearance, and more time on preparing high quality narrative content.  The best way to understand this is to experience it firsthand.
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Download full PDF article (first section above) 

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