Chemical Thermodynamics and Activity Diagrams


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Documentation for package ‘CHNOSZ’ version 0.9-2

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

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CHNOSZ-package Chemical Thermodynamics and Activity Diagrams

-- A --

abundance.new Calculate and Plot Relative Abundances of Species
abundance.old Calculate and Plot Relative Abundances of Species
add.obigt Functions to Modify the Thermodynamic Database
add.protein Functions to Modify the Thermodynamic Database
affinity Chemical Affinities of Formation Reactions
allparents Extract Data from NCBI Taxonomy Files
aminoacids Functions to Work with Sequence Data
apc Mass Transfer Calculations
axis.label Functions to Create and Modify Plots

-- B --

basis Basis Species
basis.comp Miscellaneous Utility Functions
buffer Chemical Potential Buffers

-- C --

c2s Functions to Manipulate Character Objects
can.be.numeric Functions to Manipulate Character Objects
cgl Equations of State
change Functions to Modify the Thermodynamic Database
check Search the Thermodynamic Database
CHNOSZ Chemical Thermodynamics and Activity Diagrams
convert Functions to Convert Units
count.taxa Functions to Work with BLAST Output Files

-- D --

danger Functions to Modify the Thermodynamic Database
describe Miscellaneous Utility Functions
diagram Calculate and Plot Relative Abundances of Species
dimSums Functions to Work with Multidimensional Arrays
dPdTtr Miscellaneous Utility Functions
draw.diversity Diversity Calculations for Chemical Species
draw.transfer Mass Transfer Calculations

-- E --

ECO Thermodynamic Properties and Compositional Data
element Functions to Work with Chemical Formulas
energy Chemical Affinities of Formation Reactions
energy.args Chemical Affinities of Formation Reactions
envert Functions to Convert Units
eos.args Functions for Processing Argument Lists
eqdata Read data from an EQ6 output file
examples Run examples from the documentation
expand.formula Functions to Work with Chemical Formulas
extremes Diversity Calculations for Chemical Species

-- F --

feldspar Mass Transfer Calculations

-- G --

get.protein Proteins from Model Organisms
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
grep.file Functions for Accessing FASTA Files
groups Thermodynamic Properties and Compositional Data

-- H --

hkf Equations of State

-- I --

info Search the Thermodynamic Database
ionize Ionization Properties of Proteins
is.fasta Functions for Accessing FASTA Files

-- L --

label.plot Functions to Create and Modify Plots
list2array Functions to Work with Multidimensional Arrays
longex Run examples from the documentation
lsub Functions to Work with Lists
lsum Functions to Work with Lists

-- M --

makeup Chemical Formulas and Compositions
mod.buffer Chemical Potential Buffers
mod.obigt Functions to Modify the Thermodynamic Database
MP90.cp Miscellaneous Utility Functions
mtitle Functions to Create and Modify Plots
mylapply Functions to Work with Lists

-- N --

nonideal Miscellaneous Utility Functions
nucleicacids Functions to Work with Sequence Data
nuts Functions to Convert Units

-- O --

OBIGT Thermodynamic Properties and Compositional Data
opt Thermodynamic Properties and Compositional Data
outvert Functions to Convert Units

-- P --

parent Extract Data from NCBI Taxonomy Files
PM90 Thermodynamic Properties and Compositional Data
pprod Functions to Work with Lists
protein Properties of Proteins
protein.formula Functions to Work with Chemical Formulas
protein.info Properties of Proteins
protein.length Miscellaneous Utility Functions
protein.residue Properties of Proteins
proteins Thermodynamic Properties and Compositional Data
psum Functions to Work with Lists

-- R --

read.fasta Functions for Accessing FASTA Files
read.supcrt Properties of Species and Reactions
residue.formula Functions to Work with Chemical Formulas
residue.info Properties of Proteins
revisit Diversity Calculations for Chemical Species
RH95 Thermodynamic Properties and Compositional Data
richness Diversity Calculations for Chemical Species
RT71 Thermodynamic Properties and Compositional Data

-- S --

s2c Functions to Manipulate Character Objects
sciname Extract Data from NCBI Taxonomy Files
SGD Thermodynamic Properties and Compositional Data
slice Functions to Work with Multidimensional Arrays
SOJSH Thermodynamic Properties and Compositional Data
source Thermodynamic Properties and Compositional Data
spearman Miscellaneous Utility Functions
species Species of Interest
species.label Functions to Create and Modify Plots
splitline Functions for Accessing FASTA Files
state.args Functions for Processing Argument Lists
stress Thermodynamic Properties and Compositional Data
strip Calculate and Plot Relative Abundances of Species
subcrt Properties of Species and Reactions
sum.refseq Functions for Accessing FASTA Files

-- T --

taxonomy Extract Data from NCBI Taxonomy Files
thermo Thermodynamic Properties and Compositional Data
thermo.axis Functions to Create and Modify Plots
thermo.plot.new Functions to Create and Modify Plots
thermo.postscript Functions to Create and Modify Plots
TP.args Functions for Processing Argument Lists
transfer Mass Transfer Calculations
trimfas Functions for Accessing FASTA Files
Ttr Miscellaneous Utility Functions

-- U --

unitize Miscellaneous Utility Functions
util.args Functions for Processing Argument Lists
util.array Functions to Work with Multidimensional Arrays
util.blast Functions to Work with BLAST Output Files
util.character Functions to Manipulate Character Objects
util.data Functions to Modify the Thermodynamic Database
util.fasta Functions for Accessing FASTA Files
util.formula Functions to Work with Chemical Formulas
util.list Functions to Work with Lists
util.misc Miscellaneous Utility Functions
util.plot Functions to Create and Modify Plots
util.seq Functions to Work with Sequence Data
util.units Functions to Convert Units

-- W --

water Properties of Water
water.AW90 Properties of Water
water.IAPWS95 Properties of Water
water.lines Functions to Create and Modify Plots
water.SUPCRT92 Properties of Water
water.WP02 Properties of Water
where.extreme Diversity Calculations for Chemical Species
which.balance Miscellaneous Utility Functions
which.pmax Functions to Work with Lists
write.supcrt Properties of Species and Reactions

-- Y --

yeastgfp Proteins from Model Organisms

-- Z --

ZC Functions to Work with Chemical Formulas