Thermodynamic Calculations and Diagrams for Geochemistry


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Documentation for package ‘CHNOSZ’ version 1.4.1

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

CHNOSZ-package Thermodynamic Calculations and Diagrams for Geochemistry

-- 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
AkDi Equations of State
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
cgl Equations of State
check.OBIGT Functions for Checking Thermodynamic Data
checkEOS Functions for Checking Thermodynamic Data
checkGHS 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
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
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
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.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)

-- 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
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
logact Objective Functions
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
maxdiff Functions for Writing Tests
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
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

-- 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.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
rebalance Combine Diagrams for Multi-Metal Systems
reset Thermodynamic Database and System Settings
retrieve Retrieve Species by Element
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

-- 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
solubility Equilibrium Chemical Activities of Species
spearman Objective Functions
species Species of Interest
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 --

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.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.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
WP02.auxiliary Functions for Properties of Water and Steam
write.blast Functions to Work with BLAST Output Files

-- Z --

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