limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
grDevices, graphics, stats, utils, colorspace
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.

c(
person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0687-5890")),
person("R Core Team", role = "ctb",
comment = "code derived from R's pmax()")
)
Jeffrey Dick [aut, cre] (0000-0002-0687-5890),
R Core Team [ctb] (code derived from R's pmax())
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.

Thermodynamic Calculations and Diagrams for Geochemistry
Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>),
R Core Team [ctb] (code derived from R's pmax())
limSolve, testthat, knitr, rmarkdown, tufte
An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ
also has unique capabilities for comparing the compositional and thermodynamic
properties of different proteins.