# Thermodynamic Calculations and Diagrams for Geochemistry

## Documentation for package ‘CHNOSZ’ version 2.1.0

- 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 I L M N O P R S T U V W Z

CHNOSZ-package | Thermodynamic Calculations and Diagrams for Geochemistry

## -- A --

aasum | Amino Acid Compositions of Proteins
add.alpha | Functions to Create and Modify Plots
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.aa | Functions for Reading FASTA Files and Downloading from UniProt
count.elements | Parse Chemical Formulas
Cp_s_var | Regress Equations-of-State Parameters for Aqueous Species

## -- D --

demos | Run Examples from the Documentation
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 Examples from the Documentation
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)

## -- 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

## -- L --

label.figure | Functions to Create and Modify Plots
label.plot | Functions to Create and Modify Plots
lex | Functions to Make Legend Text
list2array | Functions to Work with Multidimensional Arrays
lNaCl | Functions to Make Legend Text
logB.to.OBIGT | Fit Thermodynamic Parameters to Formation Constants (log β)
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 | Functions to Create and Modify Plots

## -- N --

NaCl | Simple NaCl-Water Solution
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
pinfo | Summaries of Thermodynamic Properties of Proteins
protein.basis | Summaries of Thermodynamic Properties of Proteins
protein.equil | 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
read.fasta | Functions for Reading FASTA Files and Downloading from UniProt
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
seq2aa | Amino Acid Compositions of Proteins
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.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 | Functions to Create and Modify 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.fasta | Functions for Reading FASTA Files and Downloading from UniProt
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 | Functions to Create and Modify 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 | Functions to Create and Modify 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 | Functions to Create and Modify Plots