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 |

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 |

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 |

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 |

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.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 |

find.tp | Chemical Activity Diagrams |

findit | Gridded Search to Optimize Objective Functions |

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 |

hkf | Equations of State |

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 |

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 |

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 |

nonideal | Activity coefficients of aqueous species |

nucleic.complement | Functions to Work with Sequence Data |

nucleic.formula | Functions to Work with Sequence Data |

OBIGT | Thermodynamic Database and System Settings |

objective | Objective Functions |

opt | Thermodynamic Database and System Settings |

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 |

qqr | Objective Functions |

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 |

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.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 |

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_s_var | Regress Equations-of-State Parameters for Aqueous Species |

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 |

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 |

ZC | Functions to Work with Chemical Formulas |

ZC.col | Functions to Create and Modify Plots |