Reproducible Science with \LaTeX

This paper proposes a procedure to execute external source codes from a \LaTeX\space document and include the calculation outputs in the resulting Portable Document Format (pdf) file automatically. It integrates programming tools into the \LaTeX\space writing tool to facilitate the production of reproducible research. In our proposed approach to a \LaTeX-based scientific notebook the user can easily invoke any programming language or a command-line program when compiling the \LaTeX\space document, while using their favorite \LaTeX\space editor in the writing process. The required \LaTeX\space setup, a new \proglang{Python} package, and the defined preamble are discussed in detail, and working examples using \proglang{R}, \proglang{Julia}, and \proglang{MatLab} to reproduce existing research are provided to illustrate the proposed procedure. We also demonstrate how to include system setting information in a paper by invoking shell scripts when compiling the document.