An introduction to CHNOSZ

This document will orient you to the basic functionality of CHNOSZ, a package for the R software environ-ment. R is a powerful language and also very fun to use. Don’t worry if you’re new to it; just plow through the examples below and you’ll start to get the hang of it. If you want a more structured approach to learning the language, there are some excellent guides in the Manuals section of the R Project page. The package was developed since 2006 to support a research project on the thermodynamic proper-ties of proteins. Since that time, the functions in the package have expanded to include calculation of the thermodynamic properties of reactions, and especially the construction of equilibrium chemical activity di-agrams for both inorganic and organic systems. The development of the package since 2009 has focused on the calculation of the equilibrium chemical activities of large numbers of proteins with applications to interpretation of metagenomic data and protein abundances in a variety of settings. The database and functions are flexible in their use, allowing one to model the relative stabilities of pro-teins, minerals or aqueous species using very similar commands. Examples below are intended to demon-strate basic usage to new users. 1.1 Outline of workflow CHNOSZ is made up of a set of functions and supporting datasets. The major components of the packag