# Thermodynamic Calculations and Diagrams for Geochemistry

## Documentation for package ‘CHNOSZ’ version 2.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P R S T U V W Z

CHNOSZ-package | Thermodynamic calculations and diagrams for geochemistry

## -- A --

add.OBIGT | Functions to Work with the Thermodynamic Database
add.protein | Amino acid compositions of proteins
affinity | Chemical affinities of formation reactions
allparents | Extract data from NCBI taxonomy files
aminoacids | Functions to work with sequence data
as.chemical.formula | Functions to work with chemical formulas
axis.label | Functions to express chemical formulas and properties

## -- B --

basis | Define basis species
basis.elements | Swap basis species
basis.logact | Swap basis species
Berman | Thermodynamic properties of minerals
bgamma | Activity coefficients of aqueous species
buffer | Calculating buffered chemical activities

## -- C --

calculateDensity | Deep Earth Water (DEW) model
calculateEpsilon | Deep Earth Water (DEW) model
calculateGibbsOfWater | Deep Earth Water (DEW) model
calculateQ | Deep Earth Water (DEW) model
check.EOS | Functions for checking thermodynamic data
check.GHS | Functions for checking thermodynamic data
check.OBIGT | Functions for checking thermodynamic data
CHNOSZ | Thermodynamic database and system settings
convert | Functions to convert units
count.elements | Parse chemical formulas
Cp_s_var | Regress equations-of-state parameters for aqueous species

## -- D --

demos | Run package examples and demos
describe.basis | Functions to express chemical formulas and properties
describe.property | Functions to express chemical formulas and properties
describe.reaction | Functions to express chemical formulas and properties
DEW | Deep Earth Water (DEW) model
diagram | Chemical activity diagrams
dimSums | Functions to work with multidimensional arrays
dPdTtr | Functions for miscellaneous tasks
dumpdata | Functions for checking thermodynamic data

## -- E --

E.units | Functions to convert units
element.mu | Swap basis species
entropy | Functions to work with chemical formulas
EOScalc | Regress equations-of-state parameters for aqueous species
EOScoeffs | Regress equations-of-state parameters for aqueous species
EOSlab | Regress equations-of-state parameters for aqueous species
EOSplot | Regress equations-of-state parameters for aqueous species
EOSregress | Regress equations-of-state parameters for aqueous species
EOSvar | Regress equations-of-state parameters for aqueous species
equil.boltzmann | Equilibrium chemical activities of species
equil.reaction | Equilibrium chemical activities of species
equilibrate | Equilibrium chemical activities of species
examples | Run package examples and demos
expr.property | Functions to express chemical formulas and properties
expr.species | Functions to express chemical formulas and properties
expr.units | Functions to express chemical formulas and properties
extdata | Extra data

## -- F --

find.tp | Chemical activity diagrams

## -- G --

getnames | Extract data from NCBI taxonomy files
getnodes | Extract data from NCBI taxonomy files
getrank | Extract data from NCBI taxonomy files
GHS | Functions to work with chemical formulas
GHS_Tr | Functions for miscellaneous tasks
group.formulas | Functions for proteins (other calculations)

## -- H --

hyphen.in.pdf | Utility functions for plots

## -- I --

i2A | Functions to work with chemical formulas
IAPWS95 | Properties of water from IAPWS-95
ibasis | Swap basis species
info | Search the thermodynamic database
ionize.aa | Properties of ionization of proteins

## -- J --

JANAF.to.OBIGT | Import thermodynamic data from NIST-JANAF tables

## -- L --

label.figure | Utility functions for plots
label.plot | Utility functions for plots
list2array | Functions to work with multidimensional arrays
lNaCl | Functions to make legend text
logK.to.OBIGT | Fit thermodynamic parameters to formation constants (log K)
lP | Functions to make legend text
lS | Functions to make legend text
lT | Functions to make legend text
lTP | Functions to make legend text

## -- M --

makeup | Parse chemical formulas
mash | Combine diagrams for multi-metal systems
mass | Functions to work with chemical formulas
mix | Combine diagrams for multi-metal systems
mod.buffer | Calculating buffered chemical activities
mod.OBIGT | Functions to Work with the Thermodynamic Database
moles | Equilibrium chemical activities of species
mosaic | Chemical affinities with changing basis species
MP90.cp | Functions for proteins (other calculations)
mtitle | Utility functions for plots

## -- N --

NaCl | Simple NaCl-water solution model
nonideal | Activity coefficients of aqueous species

## -- O --

OBIGT | Thermodynamic database and system settings

## -- P --

P.units | Functions to convert units
palply | Conditional parallel processing
parent | Extract data from NCBI taxonomy files
phospho.plot | Calculate affinity of phosphorylation reactions with pH-dependent speciation
phosphorylate | Calculate affinity of phosphorylation reactions with pH-dependent speciation
pinfo | Summaries of thermodynamic properties of proteins
protein.basis | Summaries of thermodynamic properties of proteins
protein.formula | Summaries of thermodynamic properties of proteins
protein.info | Summaries of thermodynamic properties of proteins
protein.length | Summaries of thermodynamic properties of proteins
protein.OBIGT | Summaries of thermodynamic properties of proteins

## -- R --

rank.affinity | Average ranks of chemical affinities
ratlab | Functions to express chemical formulas and properties
rebalance | Combine diagrams for multi-metal systems
reset | Thermodynamic database and system settings
retrieve | Retrieve species by element
RH2OBIGT | Functions for checking thermodynamic data
rho.IAPWS95 | Functions for properties of water and steam

## -- S --

sciname | Extract data from NCBI taxonomy files
slice | Functions to work with multidimensional arrays
slice.affinity | Functions to work with multidimensional arrays
solubility | Equilibrium chemical activities of species
species | Species of interest
stack_mosaic | Stacked mosaic diagram
subcrt | Properties of species and reactions
swap.basis | Swap basis species
syslab | Functions to express chemical formulas and properties

## -- T --

T.units | Functions to convert units
taxonomy | Extract data from NCBI taxonomy files
thermo | Thermodynamic database and system settings
thermo.axis | Functions to create and modify plots
thermo.plot | Functions to create and modify plots
thermo.plot.new | Functions to create and modify plots
thermo.refs | Functions for checking thermodynamic data
Ttr | Functions for miscellaneous tasks

## -- U --

unitize | Functions for miscellaneous tasks
usrfig | Utility functions for plots
util.array | Functions to work with multidimensional arrays
util.data | Functions for checking thermodynamic data
util.expression | Functions to express chemical formulas and properties
util.formula | Functions to work with chemical formulas
util.legend | Functions to make legend text
util.list | Functions to work with lists
util.misc | Functions for miscellaneous tasks
util.plot | Utility functions for plots
util.protein | Functions for proteins (other calculations)
util.seq | Functions to work with sequence data
util.units | Functions to convert units
util.water | Functions for properties of water and steam

## -- V --

V_s_var | Regress equations-of-state parameters for aqueous species

## -- W --

water | Properties of water
water.AW90 | Functions for properties of water and steam
water.DEW | Properties of water
water.IAPWS95 | Properties of water
water.lines | Utility functions for plots
water.SUPCRT92 | Properties of water
which.pmax | Functions to work with lists
WP02.auxiliary | Functions for properties of water and steam

## -- Z --

ZC | Functions to work with chemical formulas
ZC.col | Utility functions for plots