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git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@831 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
jedick · Mar 3, 2024 · 7a05c0a · 7a05c0a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
-Date: 2024-03-02
+Date: 2024-03-04
 Package: CHNOSZ
-Version: 2.1.0-3
+Version: 2.1.0-4
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

diff --git a/man/Berman.Rd b/man/Berman.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{Berman}
 \alias{Berman}
-\title{Thermodynamic Properties of Minerals}
+\title{Thermodynamic properties of minerals}
 \description{
 Calculate thermodynamic properties of minerals using the equations of Berman (1988).
 }

diff --git a/man/CHNOSZ-package.Rd b/man/CHNOSZ-package.Rd
@@ -2,7 +2,7 @@
 \name{CHNOSZ-package}
 \alias{CHNOSZ-package}
 \docType{package}
-\title{Thermodynamic Calculations and Diagrams for Geochemistry}
+\title{Thermodynamic calculations and diagrams for geochemistry}
 \description{
 CHNOSZ is a package for thermodynamic calculations, primarily with applications in geochemistry and compositional biology.
 It can be used to calculate the standard molal thermodynamic properties and chemical affinities of reactions relevant to geobiochemical processes, and to visualize the equilibrium activities of species on chemical speciation and predominance diagrams.

diff --git a/man/DEW.Rd b/man/DEW.Rd
@@ -5,7 +5,7 @@
 \alias{calculateGibbsOfWater}
 \alias{calculateEpsilon}
 \alias{calculateQ}
-\title{Deep Earth Water (DEW) Model}
+\title{Deep Earth Water (DEW) model}
 \description{
 Calculate thermodynamic properties of water using the Deep Earth Water (DEW) model.
 }

diff --git a/man/EOSregress.Rd b/man/EOSregress.Rd
@@ -8,7 +8,7 @@
 \alias{EOScoeffs}
 \alias{Cp_s_var}
 \alias{V_s_var}
-\title{Regress Equations-of-State Parameters for Aqueous Species}
+\title{Regress equations-of-state parameters for aqueous species}
 \description{
 Fit experimental volumes and heat capacities using regression equations.
 Possible models include the Helgeson-Kirkham-Flowers (HKF) equations of state, or other equations defined using any combination of terms derived from the temperature, pressure and thermodynamic and electrostatic properties of water.

diff --git a/man/IAPWS95.Rd b/man/IAPWS95.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{IAPWS95}
 \alias{IAPWS95}
-\title{Properties of Water from IAPWS-95}
+\title{Properties of water from IAPWS-95}
 \description{
 Calculate thermodynamic properties of water following the IAPWS-95 formulation.
 }

diff --git a/man/NaCl.Rd b/man/NaCl.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{NaCl}
 \alias{NaCl}
-\title{Simple NaCl-Water Solution}
+\title{Simple NaCl-water solution model}
 \description{
 Calculate speciation and ionic strength of aqueous solutions with a given molality of NaCl.
 }

diff --git a/man/add.OBIGT.Rd b/man/add.OBIGT.Rd
@@ -2,7 +2,7 @@
 \name{add.OBIGT}
 \alias{add.OBIGT}
 \alias{mod.OBIGT}
-\title{Functions to Work with the Thermodynamic Database}
+\title{Functions to work with the thermodynamic database}
 \description{
 Add or modify species in the thermodynamic database.
 }

diff --git a/man/add.protein.Rd b/man/add.protein.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{add.protein}
 \alias{add.protein}
-\title{Amino Acid Compositions of Proteins}
+\title{Amino acid compositions of proteins}
 \description{
   Functions to get amino acid compositions and add them to protein list for use by other functions.
 }

diff --git a/man/affinity.Rd b/man/affinity.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{affinity}
 \alias{affinity}
-\title{Chemical Affinities of Formation Reactions}
+\title{Chemical affinities of formation reactions}
 \description{
 Calculate the chemical affinities of formation reactions of species.
 }

diff --git a/man/basis.Rd b/man/basis.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{basis}
 \alias{basis}
-\title{Define Basis Species}
+\title{Define basis species}
 \description{
 Define the basis species of a chemical system.
 }

diff --git a/man/buffer.Rd b/man/buffer.Rd
@@ -2,7 +2,7 @@
 \name{buffer}
 \alias{buffer}
 \alias{mod.buffer}
-\title{Calculating Buffered Chemical Activities}
+\title{Calculating buffered chemical activities}
 \description{
 Calculate values of activity or fugacity of basis species buffered by an assemblage of one or more species.
 }

diff --git a/man/diagram.Rd b/man/diagram.Rd
@@ -2,7 +2,7 @@
 \name{diagram}
 \alias{diagram}
 \alias{find.tp}
-\title{Chemical Activity Diagrams}
+\title{Chemical activity diagrams}
 \description{
 Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis species, temperature and/or pressure.
 }

diff --git a/man/equilibrate.Rd b/man/equilibrate.Rd
@@ -4,7 +4,7 @@
 \alias{equil.boltzmann}
 \alias{equil.reaction}
 \alias{moles}
-\title{Equilibrium Chemical Activities of Species}
+\title{Equilibrium chemical activities of species}
 \description{
 Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity. 
 }

diff --git a/man/examples.Rd b/man/examples.Rd
@@ -2,7 +2,7 @@
 \name{examples}
 \alias{examples}
 \alias{demos}
-\title{Run Examples from the Documentation}
+\title{Run examples from the documentation}
 \description{
   Run the examples contained in each of the documentation topics. }
 

diff --git a/man/extdata.Rd b/man/extdata.Rd
@@ -2,7 +2,7 @@
 \name{extdata}
 \alias{extdata}
 \docType{data}
-\title{Extra Data}
+\title{Extra data}
 
 \description{
   The files in the subdirectories of \code{extdata} provide additional thermodynamic data and other data to support the examples in the package documentation and vignettes. 

diff --git a/man/info.Rd b/man/info.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{info}
 \alias{info}
-\title{Search the Thermodynamic Database}
+\title{Search the thermodynamic database}
 \description{
   Search for species by name or formula, retrieve their thermodynamic properties and parameters, and add proteins to the thermodynamic database.
 }

diff --git a/man/ionize.aa.Rd b/man/ionize.aa.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{ionize.aa}
 \alias{ionize.aa}
-\title{Properties of Ionization of Proteins}
+\title{Properties of ionization of proteins}
 \description{
   Calculate the charges of proteins and contributions of ionization to the thermodynamic properties of proteins.
 }

diff --git a/man/logB.to.OBIGT.Rd b/man/logB.to.OBIGT.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{logB.to.OBIGT}
 \alias{logB.to.OBIGT}
-\title{Fit Thermodynamic Parameters to Formation Constants (\logB)}
+\title{Fit thermodynamic parameters to formation constants (\logB)}
 \description{
 Fit thermodynamic parameters to experimental formation constants for an aqueous species and add the parameters to OBIGT.
 }

diff --git a/man/makeup.Rd b/man/makeup.Rd
@@ -2,7 +2,7 @@
 \name{makeup}
 \alias{makeup}
 \alias{count.elements}
-\title{Parse Chemical Formulas}
+\title{Parse chemical formulas}
 \description{
 Count the elements and charges in a chemical formula.
 }

diff --git a/man/mix.Rd b/man/mix.Rd
@@ -3,7 +3,7 @@
 \alias{mash}
 \alias{rebalance}
 \alias{mix}
-\title{Combine Diagrams for Multi-Metal Systems}
+\title{Combine diagrams for multi-metal systems}
 \description{
   Combine diagrams for different systems by mashing or rebalancing two diagrams or mixing two diagrams with a third.
 }

diff --git a/man/mosaic.Rd b/man/mosaic.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{mosaic}
 \alias{mosaic}
-\title{Chemical Affinities with Changing Basis Species}
+\title{Chemical affinities with changing basis species}
 \description{
 Calculate chemical affinities of formation reactions of species using basis species that change with the conditions.
 }

diff --git a/man/nonideal.Rd b/man/nonideal.Rd
@@ -2,7 +2,7 @@
 \name{nonideal}
 \alias{nonideal}
 \alias{bgamma}
-\title{Activity Coefficients of Aqueous Species}
+\title{Activity coefficients of aqueous species}
 \description{
 Calculate activity coefficients and adjusted molal properties of aqueous species.
 }

diff --git a/man/palply.Rd b/man/palply.Rd
@@ -2,7 +2,7 @@
 \name{palply}
 \alias{palply}
 
-\title{Conditional Parallel Processing}
+\title{Conditional parallel processing}
 \description{
   Use multiple processors for large calculations.
 }

diff --git a/man/protein.info.Rd b/man/protein.info.Rd
@@ -7,7 +7,7 @@
 \alias{protein.OBIGT}
 \alias{protein.basis}
 \alias{protein.equil}
-\title{Summaries of Thermodynamic Properties of Proteins}
+\title{Summaries of thermodynamic properties of proteins}
 
 \description{
   Protein information, length, chemical formula, thermodynamic properties by group additivity, reaction coefficients of basis species, and metastable equilibrium example calculation.

diff --git a/man/rank.affinity.Rd b/man/rank.affinity.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{rank.affinity}
 \alias{rank.affinity}
-\title{Average Ranks of Chemical Affinities}
+\title{Average ranks of chemical affinities}
 \description{
 Affinity rankings for groups of species.
 }

diff --git a/man/retrieve.Rd b/man/retrieve.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{retrieve}
 \alias{retrieve}
-\title{Retrieve Species by Element}
+\title{Retrieve species by element}
 \description{
 Retrieve species in the database containing one or more chemical elements.
 }

diff --git a/man/solubility.Rd b/man/solubility.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{solubility}
 \alias{solubility}
-\title{Equilibrium Chemical Activities of Species}
+\title{Equilibrium chemical activities of species}
 \description{
 Calculate chemical activities of aqueous species in equilibrium with a mineral or gas.
 }

diff --git a/man/species.Rd b/man/species.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{species}
 \alias{species}
-\title{Species of Interest}
+\title{Species of interest}
 \description{
   Define the species of interest in a system; modify their physical states and logarithms of activities.
 }

diff --git a/man/subcrt.Rd b/man/subcrt.Rd
@@ -1,7 +1,7 @@
 \encoding{UTF-8}
 \name{subcrt}
 \alias{subcrt}
-\title{Properties of Species and Reactions}
+\title{Properties of species and reactions}
 \description{
   Calculate the standard molal thermodynamic properties of one or more species or a reaction between species as a function of temperature and pressure.
 }

diff --git a/man/swap.basis.Rd b/man/swap.basis.Rd
@@ -5,7 +5,7 @@
 \alias{basis.logact}
 \alias{swap.basis}
 \alias{ibasis}
-\title{Swap Basis Species}
+\title{Swap basis species}
 \description{
   Swap the basis species defining a chemical system. One basis species is replaced by a new one with a different chemical formula.
 }

diff --git a/man/taxonomy.Rd b/man/taxonomy.Rd
@@ -7,7 +7,7 @@
 \alias{allparents}
 \alias{getnames}
 \alias{sciname}
-\title{Extract Data from NCBI Taxonomy Files}
+\title{Extract data from NCBI taxonomy files}
 
 \description{
   Read data from NCBI taxonomy files, traverse taxonomic ranks, get scientific names of taxonomic nodes.

diff --git a/man/thermo.Rd b/man/thermo.Rd
@@ -4,7 +4,7 @@
 \alias{OBIGT}
 \alias{thermo}
 \alias{CHNOSZ}
-\title{Thermodynamic Database and System Settings}
+\title{Thermodynamic database and system settings}
 \description{
 Run \code{reset()} to reset all of the data used in CHNOSZ to default values.
 This includes the computational settings, thermodynamic database, and system settings (chemical species).

diff --git a/man/util.array.Rd b/man/util.array.Rd
@@ -5,7 +5,7 @@
 \alias{slice}
 \alias{dimSums}
 \alias{slice.affinity}
-\title{Functions to Work with Multidimensional Arrays}
+\title{Functions to work with multidimensional arrays}
 \description{
   These functions can be used to turn a list into an array and extract or replace values or take the sum along a certain dimension of an array.
 }

diff --git a/man/util.data.Rd b/man/util.data.Rd
@@ -7,7 +7,7 @@
 \alias{check.OBIGT}
 \alias{dumpdata}
 \alias{RH2OBIGT}
-\title{Functions for Checking Thermodynamic Data}
+\title{Functions for checking thermodynamic data}
 \description{
 Show table of references in a web browser or get individual references for species.
 Check self consistency of individual entries in database.

diff --git a/man/util.expression.Rd b/man/util.expression.Rd
@@ -10,7 +10,7 @@
 \alias{describe.reaction}
 \alias{syslab}
 \alias{ratlab}
-\title{Functions to Express Chemical Formulas and Properties}
+\title{Functions to express chemical formulas and properties}
 \description{Generate expressions suitable for axis labels and plot legends describing chemical species, properties and reactions.}
 
 \usage{

diff --git a/man/util.formula.Rd b/man/util.formula.Rd
@@ -7,7 +7,7 @@
 \alias{GHS}
 \alias{ZC}
 \alias{i2A}
-\title{Functions to Work with Chemical Formulas}
+\title{Functions to work with chemical formulas}
 
 \description{
 Calculate the standard molal entropy of elements in a compound; calculate the standard molal Gibbs energy or enthalpy of formation, or standard molal entropy, from the other two; list coefficients of selected elements in a chemical formula; calculate the average oxidation state of carbon. Create a stoichiometric matrix for selected species.

diff --git a/man/util.legend.Rd b/man/util.legend.Rd
@@ -7,7 +7,7 @@
 \alias{lP}
 \alias{lTP}
 \alias{lex}
-\title{Functions to Make Legend Text}
+\title{Functions to make legend text}
 \description{Generate expressions describing system conditions that can be added to legends of plots.}
 
 \usage{

diff --git a/man/util.list.Rd b/man/util.list.Rd
@@ -2,7 +2,7 @@
 \name{util.list}
 \alias{util.list}
 \alias{which.pmax}
-\title{Functions to Work with Lists}
+\title{Functions to work with lists}
 
 \description{
   Identify list elements that have the maximum (or minimum) values.

diff --git a/man/util.misc.Rd b/man/util.misc.Rd
@@ -5,7 +5,7 @@
 \alias{Ttr}
 \alias{GHS_Tr}
 \alias{unitize}
-\title{Functions for Miscellaneous Tasks}
+\title{Functions for miscellaneous tasks}
 \description{
 Calculate \eqn{dP/dT}{dP/dT} and temperature of polymorphic transitions; scale logarithms of activity to a desired total activity.
 }

diff --git a/man/util.plot.Rd b/man/util.plot.Rd
@@ -9,7 +9,7 @@
 \alias{water.lines}
 \alias{mtitle}
 \alias{ZC.col}
-\title{Functions to Create and Modify Plots}
+\title{Functions to create and modify plots}
 
 \description{
   Initialize a new plot window using preset parameters, add an axis or title to a plot, generate labels for axes and subplots, add stability lines for water, get colors for a set of numeric values.

diff --git a/man/util.protein.Rd b/man/util.protein.Rd
@@ -3,7 +3,7 @@
 \alias{util.protein}
 \alias{group.formulas}
 \alias{MP90.cp}
-\title{Functions for Proteins (Other Calculations)}
+\title{Functions for proteins (other calculations)}
 
 \description{
   Return chemical formulas of groups in proteins, and calculate heat capacity using an additivity model from the literature.

diff --git a/man/util.seq.Rd b/man/util.seq.Rd
@@ -3,7 +3,7 @@
 \alias{util.seq}
 \alias{aminoacids}
 
-\title{Functions to Work with Sequence Data}
+\title{Functions to work with sequence data}
 
 \description{
   Return names or one- or three-letter abbreviations of amino acids.

diff --git a/man/util.units.Rd b/man/util.units.Rd
@@ -5,7 +5,7 @@
 \alias{T.units}
 \alias{E.units}
 \alias{convert}
-\title{Functions to Convert Units}
+\title{Functions to convert units}
 \description{
 These functions convert values between units and set the user's preferred units.
 }