Thermodynamic Calculations and Diagrams for Geochemistry
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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 |