Maintainer: Jeffrey M. Dick <j3ffdick@gmail.com>

Description: This package includes functions and data sets to support chemical thermodynamic
modeling in biochemistry and low-temperature geochemistry. The features include calculation
of the standard molal thermodynamic properties and chemical affinities of reactions involving
minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline
and gaseous species; amino acid group additivity for the standard molal thermodynamic
properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers
equations of state for aqueous species; construction of equilibrium activity diagrams as a
function of temperature, pressure, and chemical activities or fugacities of basis species.

Suggests: limSolve, parallel, testthat, knitr
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.

Imports: grDevices, graphics, stats, utils

Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
Imports: grDevices, graphics, stats, utils, colorspace
Description: An integrated set of tools for thermodynamic calculations in compositional
biology and geochemistry. 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. Functions are
provided to define a system using basis species, automatically balance reactions,
calculate the chemical affinities of reactions for selected species, and plot the results
on potential diagrams or equilibrium activity diagrams. Experimental features are
available to calculate activity coefficients for aqueous species or for multidimensional
optimization of thermodynamic variables using an objective function.