From 7a05c0a7beeb5c2f08e6abf2a7b2ffba73bcf95f Mon Sep 17 00:00:00 2001 From: Jeffrey Dick Date: Sun, 3 Mar 2024 23:50:42 +0000 Subject: [PATCH] Use sentence case for help page titles git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@831 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- DESCRIPTION | 4 ++-- man/Berman.Rd | 2 +- man/CHNOSZ-package.Rd | 2 +- man/DEW.Rd | 2 +- man/EOSregress.Rd | 2 +- man/IAPWS95.Rd | 2 +- man/NaCl.Rd | 2 +- man/add.OBIGT.Rd | 2 +- man/add.protein.Rd | 2 +- man/affinity.Rd | 2 +- man/basis.Rd | 2 +- man/buffer.Rd | 2 +- man/diagram.Rd | 2 +- man/equilibrate.Rd | 2 +- man/examples.Rd | 2 +- man/extdata.Rd | 2 +- man/info.Rd | 2 +- man/ionize.aa.Rd | 2 +- man/logB.to.OBIGT.Rd | 2 +- man/makeup.Rd | 2 +- man/mix.Rd | 2 +- man/mosaic.Rd | 2 +- man/nonideal.Rd | 2 +- man/palply.Rd | 2 +- man/protein.info.Rd | 2 +- man/rank.affinity.Rd | 2 +- man/retrieve.Rd | 2 +- man/solubility.Rd | 2 +- man/species.Rd | 2 +- man/subcrt.Rd | 2 +- man/swap.basis.Rd | 2 +- man/taxonomy.Rd | 2 +- man/thermo.Rd | 2 +- man/util.array.Rd | 2 +- man/util.data.Rd | 2 +- man/util.expression.Rd | 2 +- man/util.formula.Rd | 2 +- man/util.legend.Rd | 2 +- man/util.list.Rd | 2 +- man/util.misc.Rd | 2 +- man/util.plot.Rd | 2 +- man/util.protein.Rd | 2 +- man/util.seq.Rd | 2 +- man/util.units.Rd | 2 +- man/util.water.Rd | 2 +- man/water.Rd | 2 +- 46 files changed, 47 insertions(+), 47 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7d21aa1..97f49a9 100644 --- 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", , "j3ffdick@gmail.com", role = c("aut", "cre"), diff --git a/man/Berman.Rd b/man/Berman.Rd index 169150b..5307798 100644 --- 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 index 2e2a328..69b51ca 100644 --- 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 index f2bd024..1ef77d9 100644 --- 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 index 70241a3..96b9768 100644 --- 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 index cc7de7d..9159283 100644 --- 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 index 538ba0c..7eec5ca 100644 --- 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 index 55e247a..7c5544a 100644 --- 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 index 4721e8b..f1bb11f 100644 --- 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 index e7e8fe4..f7e88ac 100644 --- 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 index 83aec80..f8dc996 100644 --- 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 index a8837b1..db026ac 100644 --- 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 index b116915..4f5bd07 100644 --- 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 index b832ce6..7173b02 100644 --- 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 index 1146d7d..0cad1b6 100644 --- 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 index c1e32e3..c721abd 100644 --- 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 index 2d5d3ff..f3b267a 100644 --- 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 index 4236408..90c4b77 100644 --- 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 index cd889e5..99d8bef 100644 --- 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 index 1d4fdb7..af00e5f 100644 --- 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 index bb5b36f..23222ee 100644 --- 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 index 62d9b47..f969d67 100644 --- 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 index bfc74e0..f6ddb91 100644 --- 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 index 5f379cb..bd537ea 100644 --- 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 index 6c60837..64599db 100644 --- 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 index ac9368e..aecea80 100644 --- 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 index 6eccee0..a945c6b 100644 --- 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 index 11d8b50..1afe7ed 100644 --- 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 index b961d99..26bddfa 100644 --- 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 index 9f06bd1..5ef5c5e 100644 --- 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 index 9a24568..f9c37df 100644 --- 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 index b4add8c..51a9162 100644 --- 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 index f19a17b..c8f319e 100644 --- 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 index 6925ffc..dd34c01 100644 --- 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 index 05d3ab3..c92609a 100644 --- 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 index 41d5d39..66f2bb1 100644 --- 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 index 2ff15b6..cc22cd8 100644 --- 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 index 8cbdb51..1fd98be 100644 --- 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 index e9bd10f..41294b1 100644 --- 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 index 67de3fa..5dbd292 100644 --- 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 index 1975039..0d69540 100644 --- 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 index 2a337ba..87732e9 100644 --- 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 index d1d7fa4..a8c99ee 100644 --- 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 index bd67273..d9a95ed 100644 --- 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. } diff --git a/man/util.water.Rd b/man/util.water.Rd index e1cafae..e3b9b61 100644 --- a/man/util.water.Rd +++ b/man/util.water.Rd @@ -4,7 +4,7 @@ \alias{WP02.auxiliary} \alias{rho.IAPWS95} \alias{water.AW90} -\title{Functions for Properties of Water and Steam} +\title{Functions for properties of water and steam} \description{ Utility functions for properties of water and steam. } diff --git a/man/water.Rd b/man/water.Rd index a2e12ed..b019f1b 100644 --- a/man/water.Rd +++ b/man/water.Rd @@ -4,7 +4,7 @@ \alias{water.SUPCRT92} \alias{water.IAPWS95} \alias{water.DEW} -\title{Properties of Water} +\title{Properties of water} \description{ Calculate thermodynamic and electrostatic properties of water. }