Chemical Thermodynamics and Activity Diagrams


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Documentation for package ‘CHNOSZ’ version 0.9-7

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

CHNOSZ-package Chemical Thermodynamics and Activity Diagrams

-- A --

add.obigt Functions to Work with the Thermodynamic Database
add.protein Functions to Work with the Thermodynamic Database
affinity Chemical Affinities of Formation Reactions
allparents Extract Data from NCBI Taxonomy Files
aminoacids Functions to Work with Sequence Data
anim Functions to Make Animations
anim.carboxylase Functions to Make Animations
anim.plasma Functions to Make Animations
anim.TCA Functions to Make Animations
apc Mass Transfer Calculations
axis.label Functions to Create and Modify Plots

-- B --

basis Basis Species
basis.comp Functions for Miscellaneous Tasks
browse.refs Functions to Work with the Thermodynamic Database
buffer Calculating Buffered Chemical Activities
buffers Thermodynamic Database and System Definition

-- C --

c2s Functions to Manipulate Character Objects
caller.name Functions for Miscellaneous Tasks
can.be.numeric Functions to Manipulate Character Objects
cgl Equations of State
change Functions to Work with the Thermodynamic Database
check.obigt Functions to Work with the Thermodynamic Database
checkEOS Functions to Work with the Thermodynamic Database
checkGHS Functions to Work with the Thermodynamic Database
convert Functions to Convert Units
cvrmsd Functions for Various Statistical Operations

-- D --

def2gi Functions to Work with BLAST Output Files
describe Functions for Miscellaneous Tasks
diagram Calculate and Plot Equilibrium Chemical Activities of Species
dimSums Functions to Work with Multidimensional Arrays
dPdTtr Functions for Miscellaneous Tasks
draw.transfer Mass Transfer Calculations

-- E --

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
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.boltz Calculate Logarithms of Activity of Species
equil.react Calculate Logarithms of Activity of Species
examples Run examples from the documentation
expand.formula Functions to Work with Chemical Formulas
extdata Extra Data
extremes Diversity Calculations for Chemical Species

-- F --

feldspar Mass Transfer Calculations
findit Multidimensionally Optimize Chemical Activities

-- G --

get.expr Protein Expression Data
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 Database and System Definition

-- H --

hkf Equations of State

-- I --

id.blast Functions to Work with BLAST Output Files
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
lograt Functions for Various Statistical Operations
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 Calculating Buffered Chemical Activities
mod.obigt Functions to Work with the Thermodynamic Database
MP90.cp Functions for Miscellaneous Tasks
mtitle Functions to Create and Modify Plots
mylapply Functions to Work with Lists

-- N --

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

-- O --

OBIGT Thermodynamic Database and System Definition
obigt2eos Functions to Work with the Thermodynamic Database
opt Thermodynamic Database and System Definition
outvert Functions to Convert Units

-- P --

parent Extract Data from NCBI Taxonomy Files
plot.findit Multidimensionally Optimize Chemical Activities
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 Functions for Miscellaneous Tasks
protein.residue Properties of Proteins
psum Functions to Work with Lists

-- Q --

qqr Functions for Various Statistical Operations

-- R --

read.blast Functions to Work with BLAST Output Files
read.fasta Functions for Accessing FASTA Files
read.supcrt Properties of Species and Reactions
refs Thermodynamic Database and System Definition
residualsplot Functions to Create and Modify Plots
residue.formula Functions to Work with Chemical Formulas
residue.info Properties of Proteins
revisit Diversity Calculations for Chemical Species
richness Diversity Calculations for Chemical Species
rmsd Functions for Various Statistical Operations

-- S --

s2c Functions to Manipulate Character Objects
sciname Extract Data from NCBI Taxonomy Files
slice Functions to Work with Multidimensional Arrays
slice.affinity Functions to Work with Multidimensional Arrays
spearman Functions for Various Statistical Operations
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 Database and System Definition
strip Calculate and Plot Equilibrium Chemical Activities 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 Database and System Definition
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 Functions for Miscellaneous Tasks

-- U --

unitize Functions for Miscellaneous Tasks
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 Work with 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 Functions for Miscellaneous Tasks
util.plot Functions to Create and Modify Plots
util.seq Functions to Work with Sequence Data
util.stat Functions for Various Statistical Operations
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 Functions for Miscellaneous Tasks
which.pmax Functions to Work with Lists
write.blast Functions to Work with BLAST Output Files
write.supcrt Properties of Species and Reactions

-- Y --

yeastgfp Proteins from Model Organisms

-- Z --

ZC Functions to Work with Chemical Formulas