CHNOSZ v1.3.2

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Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.

Functions in CHNOSZ

Name Description
eos Equations of State
eqdata Read data from an EQ6 output file
nonideal Activity Coefficients of Aqueous Species
objective Objective Functions
util.blast Functions to Work with BLAST Output Files
util.data Functions for Checking Thermodynamic Data
util.matrix Functions for Various Matrix Operations
util.misc Functions for Miscellaneous Tasks
EOSregress Regress Equations-of-State Parameters for Aqueous Species
IAPWS95 Properties of Water from IAPWS-95
palply Conditional Parallel Processing
basis Define Basis Species
protein Examples of Calculations for Proteins
berman Thermodynamic Properties of Minerals
NaCl Simple NaCl-Water Solution
equilibrate Equilibrium Chemical Activities of Species
examples Run Examples from the Documentation
add.obigt Functions to Work with the Thermodynamic Database
makeup Parse Chemical Formulas
mosaic Chemical Affinities with Changing Basis Species
util.expression Functions to Express Chemical Formulas and Properties
util.fasta Functions for Reading FASTA Files and Downloading from UniProt
util.seq Functions to Work with Sequence Data
util.test Functions for Writing Tests
water Properties of Water
buffer Calculating Buffered Chemical Activities
diagram Chemical Activity Diagrams
wjd Gibbs Energy Minimization by Steepest Descent
swap.basis Swap Basis Species
taxonomy Extract Data from NCBI Taxonomy Files
util.units Functions to Convert Units
util.water Functions for Properties of Water and Steam
add.protein Amino Acid Compositions of Proteins
affinity Chemical Affinities of Formation Reactions
CHNOSZ-package Thermodynamic Calculations and Diagrams for Geochemistry
extdata Extra Data
DEW Deep Earth Water (DEW) Model
findit Gridded Search to Optimize Objective Functions
info Search the Thermodynamic Database
protein.info Summaries of Thermodynamic Properties of Proteins
retrieve Retrieve Species by Element
species Species of Interest
ionize.aa Properties of Ionization of Proteins
revisit Plots and Optima of Objective Functions
subcrt Properties of Species and Reactions
util.plot Functions to Create and Modify Plots
solubility Equilibrium Chemical Activities of Species
util.protein Functions for Proteins (Other Calculations)
thermo Thermodynamic Database and System Settings
yeast Composition, Localization, and Abundances of Proteins in Yeast
util.array Functions to Work with Multidimensional Arrays
util.formula Functions to Work with Chemical Formulas
util.list Functions to Work with Lists
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Vignettes of CHNOSZ

Name
CHNOSZ.dia
CHNOSZ.png
anintro.Rmd
elementa.csl
eos-regress.Rmd
equilibrium.Rnw
equilibrium.lyx
hotspring.Rnw
hotspring.lyx
mklinks.sh
obigt.Rmd
obigt.bib
obigt.css
rubisco.svg
vig.bib
vig.css
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Details

Date 2019-04-20
Encoding UTF-8
License GPL (>= 2)
BuildResaveData no
VignetteBuilder knitr
URL http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/
NeedsCompilation yes
Packaged 2019-04-20 07:50:58 UTC; jedick
Repository CRAN
Date/Publication 2019-04-21 15:10:11 UTC

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