[R-pkgs] New package: CHNOSZ

Jeffrey Dick jmdick at asu.edu
Sat Apr 25 01:33:22 CEST 2009

Dear R users,

A new package, CHNOSZ (version 0.8), is available on CRAN.

CHNOSZ is a package for thermodynamic calculations and analysis. 
Functions are available for calculating the standard Gibbs energies and 
other thermodynamic properties, and chemical affinities, of reactions 
between species contained in the thermodynamic database. The database 
includes standard thermodynamic properties and equations of state 
parameters for a variety of minerals and inorganic and organic aqueous 
species. The relative abundances of species in equilibrium can be drawn 
on activity diagrams as a function of temperature, pressure and/or 
chemical activities of basis species.

The documentation includes many examples taken from the literature, as 
well as calculations of the metastability relationships in systems of 
proteins. The protein examples were developed to explore the chemical 
features of thermophilic adaptation, subcellular localization, proteomic 
stress response, and microbial diversity. Calculation of the standard 
Gibbs energies of proteins is based on a published group additivity 
algorithm and is further supported in this package by the inclusion of 
data files for the amino acid compositions of selected proteins and of 
proteins in yeast and E. coli.

A paper describing some applications of the package can be found in 
Geochemical Transactions:


The project website highlights many of the example calculations. There 
is also an Rpad script available for download that presents basic 
functionality of the program in a browser interface. The website is 
located at:


This release offers major enhancements over previous versions available 
on the project website. Chemical affinities of formation reactions can 
be calculated as a function of more than two variables, parallel 
processing of some computations is optionally carried out using the 
mclapply function of the multicore package, amino acid compositions of 
proteins can be read from FASTA files, protein stress response and 
richness calculations were added to the examples, and a mass transfer 
algorithm for reaction path modeling has been introduced.

Feedback about the package is appreciated.


Jeff Dick

Jeffrey M. Dick
NSF Postdoctoral Fellow
School of Earth and Space Exploration
Arizona State University
Tempe, AZ 85287-1404

More information about the R-packages mailing list