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scirep: dynamic and reproducible scientific reports

Giulio Stancari
Fermilab
August 2015

The project scirep provides a template for writing scientific, engineering, and mathematical reports that are reproducible and dynamic. It can be used for internal notes, memos, journal articles, theses, etc.

It is based on existing and well-developed free open-source multi-platform tools:

  • LaTeX as typesetting language and glue for logic and narrative
  • R for scripting, statistics, data analysis, numerical calculations, and visualization
  • Sage for symbolic and numerical mathematics, numerical computations, and plotting
  • knitr for R and LaTeX integration
  • SageTeX for integrating Sage and LaTeX

This project is simply an example on how to use and integrate these tools to write a high-quality document that can be written, maintained and updated on any computer platform. It assumes that the user has a working installation of the tools.

The repository contains a minimal example and the instructions to assemble it in a Unix-like environment (but it can be adapted to other platforms as well):

  • minimal.Rnw and minimal.R are the source files
  • the Makefile contains the compilation instructions to obtain the final report minimal.pdf