# Thermodynamic Calculations for Geobiochemistry

## Documentation for package ‘CHNOSZ’ version 1.1.3

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

CHNOSZ-package | Thermodynamic Calculations for Geobiochemistry

## -- A --

aasum | Amino Acid Compositions of Proteins
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
Bdot | Activity coefficients of aqueous species
berman | Thermodynamic Properties of Minerals
buffer | Calculating Buffered Chemical Activities
buffers | Thermodynamic Database and System Settings

## -- 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
cgl | Equations of State
check.obigt | Functions for Checking Thermodynamic Data
checkEOS | Functions for Checking Thermodynamic Data
checkGHS | Functions for Checking Thermodynamic Data
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
CV | Objective Functions
CVRMSD | Objective Functions

## -- D --

DDGmix | Objective Functions
def2gi | Functions to Work with BLAST Output Files
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
DGinf | Objective Functions
DGmix | Objective Functions
DGtr | Objective Functions
diagram | Chemical Activity Diagrams
dimSums | Functions to Work with Multidimensional Arrays
dPdTtr | Functions for Miscellaneous Tasks

## -- E --

E.units | Functions to Convert Units
element | Thermodynamic Database and System Settings
element.mu | Swap Basis Species
element.potentials | Gibbs Energy Minimization by Steepest Descent
entropy | Functions to Work with Chemical Formulas
eos | Equations of State
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
eqdata | Read data from an EQ6 output file
equil.boltzmann | Equilibrium Chemical Activities of Species
equil.potentials | Gibbs Energy Minimization by Steepest Descent
equil.reaction | Equilibrium Chemical Activities of Species
equilibrate | Equilibrium Chemical Activities of Species
examples | Run Examples from the Documentation
expect_maxdiff | Functions for Writing Tests
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
findit | Gridded Search to Optimize Objective Functions

## -- 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)
groups | Thermodynamic Database and System Settings
guess | Gibbs Energy Minimization by Steepest Descent

## -- H --

hkf | Equations of State

## -- I --

i2A | Functions to Work with Chemical Formulas
IAPWS95 | Properties of Water from IAPWS-95
ibasis | Swap Basis Species
id.blast | Functions to Work with BLAST Output Files
info | Search the Thermodynamic Database
invertible.combs | Functions for Various Matrix Operations
ionize.aa | Properties of Ionization of Proteins
is.near.equil | Gibbs Energy Minimization by Steepest Descent

## -- L --

label.figure | Functions to Create and Modify Plots
label.plot | Functions to Create and Modify Plots
list2array | Functions to Work with Multidimensional Arrays
logact | Objective Functions

## -- M --

makeup | Parse Chemical Formulas
mass | Functions to Work with Chemical Formulas
maxdiff | Functions for Writing Tests
mod.buffer | Calculating Buffered Chemical Activities
mod.obigt | Functions to Work with the Thermodynamic Database
mosaic | Chemical Affinities with Changing Basis Species
MP90.cp | Functions for Proteins (Other Calculations)
mtitle | Functions to Create and Modify Plots

## -- N --

nonideal | Activity coefficients of aqueous species
nucleic.complement | Functions to Work with Sequence Data
nucleic.formula | Functions to Work with Sequence Data

## -- O --

OBIGT | Thermodynamic Database and System Settings
objective | Objective Functions
opt | Thermodynamic Database and System Settings

## -- P --

P.units | Functions to Convert Units
palply | Conditional Parallel Processing
parent | Extract Data from NCBI Taxonomy Files
pearson | Objective Functions
pinfo | Summaries of Thermodynamic Properties of Proteins
plot_findit | Gridded Search to Optimize Objective Functions
protein | Examples of Calculations for 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

## -- Q --

qqr | Objective Functions

## -- R --

ratlab | Functions to Express Chemical Formulas and Properties
read.blast | Functions to Work with BLAST Output Files
read.fasta | Functions for Reading FASTA Files and Downloading from UniProt
refs | Thermodynamic Database and System Settings
revisit | Plots and Optima of Objective Functions
RH2obigt | Functions for Checking Thermodynamic Data
rho.IAPWS95 | Functions for Properties of Water and Steam
richness | Plots and Optima of Objective Functions
RMSD | Objective Functions
run.guess | Gibbs Energy Minimization by Steepest Descent
run.wjd | Gibbs Energy Minimization by Steepest Descent

## -- S --

sciname | Extract Data from NCBI Taxonomy Files
SD | Objective Functions
seq2aa | Amino Acid Compositions of Proteins
shannon | Objective Functions
slice | Functions to Work with Multidimensional Arrays
slice.affinity | Functions to Work with Multidimensional Arrays
spearman | Objective Functions
species | Species of Interest
strip | Chemical Activity Diagrams
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.plot.new | Functions to Create and Modify Plots
thermo.refs | Functions for Checking Thermodynamic Data
today | Functions to Work with the Thermodynamic Database
Ttr | Functions for Miscellaneous Tasks

## -- U --

uniprot.aa | Functions for Reading FASTA Files and Downloading from UniProt
unitize | Functions for Miscellaneous Tasks
usrfig | Functions to Create and Modify Plots
util.array | Functions to Work with Multidimensional Arrays
util.blast | Functions to Work with BLAST Output Files
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.list | Functions to Work with Lists
util.matrix | Functions for Various Matrix Operations
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.test | Functions for Writing Tests
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
wjd | Gibbs Energy Minimization by Steepest Descent
WP02.auxiliary | Functions for Properties of Water and Steam
write.blast | Functions to Work with BLAST Output Files

## -- Y --

yeast | Composition, Localization, and Abundances of Proteins in Yeast
yeast.aa | Composition, Localization, and Abundances of Proteins in Yeast
yeastgfp | Composition, Localization, and Abundances of Proteins in Yeast

## -- Z --

ZC | Functions to Work with Chemical Formulas
ZC.col | Functions to Create and Modify Plots