Thermodynamic Calculations and Diagrams for Geochemistry
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Documentation for package ‘CHNOSZ’ version 2.2.0
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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 --
| 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.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 |
| logK.to.OBIGT | Fit thermodynamic parameters to formation constants (log K) |
| 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 model |
| 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.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 |
| 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 |
| 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.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 |