CHNOSZ

Thermodynamic Calculations for Geobiochemistry

What is it?

The CHNOSZ package for R offers an integrated set of tools for thermodynamic calculations in geochemistry and compositional biology. Thermodynamic properties are taken from a database for minerals and inorganic and organic aqueous species including biomolecules, or from amino acid group additivity for proteins. High-temperature properties are calculated using the revised Helgeson-Kirkham-Flowers equations of state for aqueous species, and activity coefficients can be calculated for specified ionic strength. Functions are provided to define a system using basis species, automatically balance reactions, calculate the chemical affinities of formation reactions for selected species, calculate equilibrium activities, and plot the results on chemical activity diagrams.

canprot is a package that uses CHNOSZ for compositional and thermodynamic analysis of proteomic datasets.

An example

After Helgeson, 1970.

Getting started

Download R from the Comprehensive R Archive Network (CRAN). Launch an R session, then use these commands to install and load the package and run the examples from the documentation.

install.packages("CHNOSZ")
library(CHNOSZ)
data(thermo)
examples()

Download and documentation

Around the web

canprot package

Download canprot from Github or CRAN. The online manual and the vignettes from the package can be viewed here:

See the papers in PeerJ (2016, 2017) for more information.

About

CHNOSZ is free software made available under the GPL.

The maintainer of this package is Jeffrey Dick. Please contact me at j3ffdick@gmail.com.

To cite CHNOSZ in publications, use this reference: Dick, 2008. The thermodynamic database is made possible by the work of many different authors. If you publish results of calculations using any of these data, please cite the primary data sources! For a list of references, use the thermo.refs() function in the package, or access the table of references here.


Last updated: 2017-11-13