[CHNOSZ-commits] r944 - in pkg/CHNOSZ: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 9 06:00:47 CET 2025
Author: jedick
Date: 2025-12-09 06:00:46 +0100 (Tue, 09 Dec 2025)
New Revision: 944
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/Berman.Rd
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/DEW.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/IAPWS95.Rd
pkg/CHNOSZ/man/NaCl.Rd
pkg/CHNOSZ/man/add.OBIGT.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/logK.to.OBIGT.Rd
pkg/CHNOSZ/man/mod.buffer.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/phosphorylate.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/thermo.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.protein.Rd
pkg/CHNOSZ/man/util.water.Rd
pkg/CHNOSZ/man/water.Rd
Log:
Use Elementa reference style in Rd files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/DESCRIPTION 2025-12-09 05:00:46 UTC (rev 944)
@@ -1,6 +1,6 @@
-Date: 2025-12-08
+Date: 2025-12-09
Package: CHNOSZ
-Version: 2.2.0-10
+Version: 2.2.0-11
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -15,7 +15,7 @@
\newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
\newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
-\section{Changes in CHNOSZ version 2.2.0-9 (2025-12-08)}{
+\section{Changes in CHNOSZ version 2.2.0-11 (2025-12-09)}{
\itemize{
@@ -37,6 +37,10 @@
\item Add \code{hyphen.in.pdf()} for replacing minus signs with
hyphens in text added to PDF plots.
+ \item Use \href{https://online.ucpress.edu/elementa}{Elementa} reference
+ style (like \href{https://www.csemanual.org}{CSE} name-year style but all
+ authors are listed) in Rd files.
+
}
}
Modified: pkg/CHNOSZ/man/Berman.Rd
===================================================================
--- pkg/CHNOSZ/man/Berman.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/Berman.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -118,15 +118,15 @@
}
\references{
-Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{https://www.worldcat.org/oclc/474880901}
+Anderson GM. 2005. \emph{Thermodynamics of Natural Systems}. 2nd ed. Cambridge, UK: Cambridge University Press. 648 p. \url{https://www.worldcat.org/oclc/474880901}
-Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \doi{10.1093/petrology/29.2.445}
+Berman RG. 1988. Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J Petrol} \bold{29}: 445--522. \doi{10.1093/petrology/29.2.445}
-Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib. Mineral. Petrol.} \bold{126}, 1-24. \doi{10.1007/s004100050233}
+Berman RG, Aranovich LYa. 1996. Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al{\s2}O{\s3}-TiO{\s2}-SiO{\s2}. \emph{Contrib Mineral Petrol} \bold{126}: 1--24. \doi{10.1007/s004100050233}
-Berman, R. G. (2007) winTWQ (version 2.3): A software package for performing internally-consistent thermobarometric calculations. \emph{Open File} \bold{5462}, Geological Survey of Canada, 41 p. \doi{10.4095/223425}
+Berman RG. 2007. winTWQ (version 2.3): A software package for performing internally-consistent thermobarometric calculations. \emph{Open File} \bold{5462}, Geological Survey of Canada. 41 p. \doi{10.4095/223425}
-Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{https://www.worldcat.org/oclc/13594862}
+Helgeson HC, Delany JM, Nesbitt HW, Bird DK. 1978. Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am J Sci} \bold{278-A}: 1--229. \url{https://www.worldcat.org/oclc/13594862}
}
\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -49,7 +49,7 @@
}
\references{
-Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \doi{10.1016/0098-3004(92)90029-Q}
+Johnson JW, Oelkers EH, Helgeson HC. 1992. SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000°C. \emph{Comput Geosci} \bold{18}: 899--947. \doi{10.1016/0098-3004(92)90029-Q}
}
\keyword{package}
Modified: pkg/CHNOSZ/man/DEW.Rd
===================================================================
--- pkg/CHNOSZ/man/DEW.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/DEW.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -51,9 +51,9 @@
}
\references{
-Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014) Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 \degC. \emph{Geochim. Cosmochim. Acta} \bold{129}, 125--145. \doi{10.1016/j.gca.2013.12.019}
+Sverjensky DA, Harrison B, Azzolini D. 2014. Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200°C. \emph{Geochim Cosmochim Acta} \bold{129}: 125--145. \doi{10.1016/j.gca.2013.12.019}
-Zhang, Z. and Duan, Z. (2005) Prediction of the \emph{PVT} properties of water over wide range of temperatures and pressures from molecular dynamics simulation. \emph{Phys. Earth Planet. Inter.} \bold{149}, 335--354. \doi{10.1016/j.pepi.2004.11.003}
+Zhang Z, Duan Z. 2005. Prediction of the \emph{PVT} properties of water over wide range of temperatures and pressures from molecular dynamics simulation. \emph{Phys Earth Planet Inter} \bold{149}: 335--354. \doi{10.1016/j.pepi.2004.11.003}
}
\concept{Water properties}
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -90,7 +90,7 @@
Here, \eqn{\sigma}{sigma} and \eqn{\xi}{xi} are calculated from a1, a2, a3 and a4 in \code{thermo()$OBIGT} at the pressure indicated by \code{P} (default 1 bar).
The original motivation for writing these functions was to explore alternatives or possible modifications to the revised Helgeson-Kirkham-Flowers equations applied to aqueous nonelectrolytes.
-As pointed out by Schulte et al., 2001, the functional forms of the equations do not permit retrieving values of the solvation parameter (\eqn{\omega}{omega}) that closely represent the observed trends in both heat capacity and volume at high temperatures (above ca. 200 \degC).
+As pointed out by Schulte et al. (2001), the functional forms of the equations do not permit retrieving values of the solvation parameter (\eqn{\omega}{omega}) that closely represent the observed trends in both heat capacity and volume at high temperatures (above ca. 200 \degC).
The examples below assume that the \eqn{\omega}{omega} parameter in the HKF functions is a constant (does not depend on T and P), as is appropriate for nonelectrolytes.
For charged species, the variables \code{Cp_s_var} and \code{V_s_var} can be used in the regressions.
@@ -111,9 +111,9 @@
}
\references{
- Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \doi{10.1006/jcht.1997.0192}
+Hnědkovský L, Wood RH. 1997. Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J Chem Thermodyn} \bold{29}: 731--747. \doi{10.1006/jcht.1997.0192}
- Schulte, M. D., Shock, E. L. and Wood, R. H. (1995) The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3919--3930. \doi{10.1016/S0016-7037(01)00717-7}
+Schulte MD, Shock EL, Wood RH. 2001. The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. \emph{Geochim Cosmochim Acta} \bold{65}: 3919--3930. \doi{10.1016/S0016-7037(01)00717-7}
}
Modified: pkg/CHNOSZ/man/IAPWS95.Rd
===================================================================
--- pkg/CHNOSZ/man/IAPWS95.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/IAPWS95.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -43,7 +43,7 @@
}
\references{
-Wagner, W. and Pruss, A. (2002) The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J. Phys. Chem. Ref. Data} \bold{31}, 387--535. \doi{10.1063/1.1461829}
+Wagner W, Pruss A. 2002. The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J Phys Chem Ref Data} \bold{31}: 387--535. \doi{10.1063/1.1461829}
}
\concept{Water properties}
Modified: pkg/CHNOSZ/man/NaCl.Rd
===================================================================
--- pkg/CHNOSZ/man/NaCl.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/NaCl.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -85,7 +85,7 @@
}
\references{
-Shvarov, Y. and Bastrakov, E. (1999) HCh: A software package for geochemical equilibrium modelling. User's Guide. \emph{Australian Geological Survey Organisation} \bold{1999/25}. \url{https://pid.geoscience.gov.au/dataset/ga/25473}
+Shvarov Y, Bastrakov E. 1999. HCh: A software package for geochemical equilibrium modelling. User's Guide. \emph{Australian Geological Survey Organisation} \bold{1999/25}. \url{https://pid.geoscience.gov.au/dataset/ga/25473}
}
\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/add.OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/add.OBIGT.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/add.OBIGT.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -164,17 +164,17 @@
}
\references{
-Apps, J. and Spycher, N. (2004) \emph{Data qualification for thermodynamic data used to support THC calculations}. DOC.20041118.0004 ANL-NBS-HS-000043 REV 00. Bechtel SAIC Company, LLC.
+Apps J, Spycher N. 2004. \emph{Data qualification for thermodynamic data used to support THC calculations}. DOC.20041118.0004 ANL-NBS-HS-000043 REV 00. Bechtel SAIC Company, LLC.
-Bazarkina, E. F., Zotov, A. V., and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1-1000 bar and 25°C. \emph{Geology of Ore Deposits} \bold{52}, 167--178. \doi{10.1134/S1075701510020054}
+Bazarkina EF, Zotov AV, Akinfiev NN. 2010. Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1--1000 bar and 25°C. \emph{Geol Ore Deposits} \bold{52}: 167--178. \doi{10.1134/S1075701510020054}
-Kitadai, N. (2014) Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. \emph{J. Mol. Evol.} \bold{78}, 171--187. \doi{10.1007/s00239-014-9616-1}
+Kitadai N. 2014. Thermodynamic prediction of glycine polymerization as a function of temperature and pH consistent with experimentally obtained results. \emph{J Mol Evol} \bold{78}: 171--187. \doi{10.1007/s00239-014-9616-1}
-Shock, E. L., Helgeson, H. C. and Sverjensky, D. A. (1989) Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. \emph{Geochim. Cosmochim. Acta} \bold{53}, 2157--2183. \doi{10.1016/0016-7037(89)90341-4}
+Shock EL, Helgeson HC, Sverjensky DA. 1989. Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. \emph{Geochim Cosmochim Acta} \bold{53}: 2157--2183. \doi{10.1016/0016-7037(89)90341-4}
-Stef{\aacute}nsson, A. (2001) Dissolution of primary minerals of basalt in natural waters. I. Calculation of mineral solubilities from 0\degC to 350\degC. \emph{Chem. Geol.} \bold{172}, 225--250. \doi{10.1016/S0009-2541(00)00263-1}
+Stefánsson A. 2001. Dissolution of primary minerals of basalt in natural waters. I. Calculation of mineral solubilities from 0°C to 350°C. \emph{Chem Geol} \bold{172}: 225--250. \doi{10.1016/S0009-2541(00)00263-1}
-Sverjensky, D. A., Shock, E. L., and Helgeson, H. C. (1997) Prediction of the thermodynamic properties of aqueous metal complexes to 1000 °C and 5 kbar. \emph{Geochim. Cosmochim. Acta} \bold{61}, 1359--1412. \doi{10.1016/S0016-7037(97)00009-4}
+Sverjensky DA, Shock EL, Helgeson HC. 1997. Prediction of the thermodynamic properties of aqueous metal complexes to 1000°C and 5 kbar. \emph{Geochim Cosmochim Acta} \bold{61}: 1359--1412. \doi{10.1016/S0016-7037(97)00009-4}
}
\concept{Thermodynamic data}
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/affinity.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -102,7 +102,7 @@
}
\references{
-Helgeson, H. C., Richard, L, McKenzie, W. F., Norton, D. L. and Schmitt, A. (2009) A chemical and thermodynamic model of oil generation in hydrocarbon source rocks. \emph{Geochim. Cosmochim. Acta} \bold{73}, 594--695. \doi{10.1016/j.gca.2008.03.004}
+Helgeson HC, Richard L, McKenzie WF, Norton DL, Schmitt A. 2009. A chemical and thermodynamic model of oil generation in hydrocarbon source rocks. \emph{Geochim Cosmochim Acta} \bold{73}: 594--695. \doi{10.1016/j.gca.2008.03.004}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/basis.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -77,9 +77,9 @@
}
\references{
-Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \doi{10.7717/peerj.2238}
+Dick JM. 2016. Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}: e2238. \doi{10.7717/peerj.2238}
-Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{PeerJ} \bold{5}:e3421 \doi{10.7717/peerj.3421}
+Dick JM. 2017. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{PeerJ} \bold{5}: e3421. \doi{10.7717/peerj.3421}
}
\examples{
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/diagram.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -315,23 +315,21 @@
}
\references{
+Aksu S, Doyle FM. 2001. Electrochemistry of copper in aqueous glycine solutions. \emph{J Electrochem Soc} \bold{148}: B51--B57. \doi{10.1149/1.1344532}
-Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57.
+Dick JM. 2019. CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. \emph{Front Earth Sci} \bold{7}: 180. \doi{10.3389/feart.2019.00180}
-Dick, J. M. (2019) CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. \emph{Front. Earth Sci.} \bold{7}:180. \doi{10.3389/feart.2019.00180}
+Dick JM, Shock EL. 2011. Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLOS One} \bold{6}: e22782. \doi{10.1371/journal.pone.0022782}
-Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLOS One} \bold{6}, e22782. \doi{10.1371/journal.pone.0022782}
+Helgeson HC. 1970. A chemical and thermodynamic model of ore deposition in hydrothermal systems. \emph{Mineral Soc Am Spec Pap} \bold{3}: 155--186. \url{https://www.worldcat.org/oclc/583263}
-Helgeson, H. C. (1970) A chemical and thermodynamic model of ore deposition in hydrothermal systems. \emph{Mineral. Soc. Amer. Spec. Pap.} \bold{3}, 155--186. \url{https://www.worldcat.org/oclc/583263}
+Helgeson HC, Delany JM, Nesbitt HW, Bird DK. 1978. Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am J Sci} \bold{278-A}: 1--229. \url{https://www.worldcat.org/oclc/13594862}
-Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{https://www.worldcat.org/oclc/13594862}
+LaRowe DE, Helgeson HC. 2007. Quantifying the energetics of metabolic reactions in diverse biogeochemical systems: electron flow and ATP synthesis. \emph{Geobiology} \bold{5}: 153--168. \doi{10.1111/j.1472-4669.2007.00099.x}
-LaRowe, D. E. and Helgeson, H. C. (2007) Quantifying the energetics of metabolic reactions in diverse biogeochemical systems: electron flow and ATP synthesis. \emph{Geobiology} \bold{5}, 153--168. \doi{10.1111/j.1472-4669.2007.00099.x}
+Majzlan J, Navrotsky A, McClesky RB, Alpers CN. 2006. Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe\s{2}(SO\s{4})\s{3}(H\s{2}O)\s{5}. \emph{Eur J Mineral} \bold{18}: 175--186. \doi{10.1127/0935-1221/2006/0018-0175}
-Majzlan, J., Navrotsky, A., McClesky, R. B. and Alpers, C. N. (2006) Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe\s{2}(SO\s{4})\s{3}(H\s{2}O)\s{5}. \emph{Eur. J. Mineral.} \bold{18}, 175--186. \doi{10.1127/0935-1221/2006/0018-0175}
-
-Tagirov, B. and Schott, J. (2001) Aluminum speciation in crustal fluids revisited. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3965--3992. \doi{10.1016/S0016-7037(01)00705-0}
-
+Tagirov B, Schott J. 2001. Aluminum speciation in crustal fluids revisited. \emph{Geochim Cosmochim Acta} \bold{65}: 3965--3992. \doi{10.1016/S0016-7037(01)00705-0}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -141,7 +141,7 @@
}
\references{
- Dick, J. M. (2008) Calculation of the relative metastabilities of proteins using the CHNOSZ software package. \emph{Geochem. Trans.} \bold{9}:10. \doi{10.1186/1467-4866-9-10}
+Dick JM. 2008. Calculation of the relative metastabilities of proteins using the CHNOSZ software package. \emph{Geochem Trans} \bold{9}: 10. \doi{10.1186/1467-4866-9-10}
}
\concept{Main workflow}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2025-12-08 07:05:24 UTC (rev 943)
+++ pkg/CHNOSZ/man/examples.Rd 2025-12-09 05:00:46 UTC (rev 944)
@@ -65,7 +65,7 @@
\item{E_coli}{Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016)}
\item{rank.affinity}{Affinity ranking for proteins in yeast nutrient limitation (data from Tai et al., 2005)}
\item{yttrium}{\code{\link{logK.to.OBIGT}} fits at 800 and 1000 bar and Y speciation in \code{\link{NaCl}} solution at varying pH (Guan et al., 2020)}
- \item{uranyl}{Total (carbonate|sulfate)-pH diagrams for uranyl species (Migdisov et al., 2024)}
+ \item{uranyl}{Total (carbonate|sulfate)-pH diagrams for uranyl species (Migdisov et al., 2025)}
\item{sum_S}{Summed molality of S species and solubility contours for iron and gold (Skirrow and Walshe, 2002)}
\item{MgATP}{Speciation of ATP with H+ and Mg+2 (Alberty, 2003)}
\item{rubisco_Zc}{Zc of Rubisco vs optimal growth temperature}
@@ -92,81 +92,81 @@
}
\references{
-Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim. Cosmochim. Acta} \bold{67}, 613--629. \doi{10.1016/S0016-7037(02)01141-9}
+Akinfiev NN, Diamond LW. 2003. Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. \emph{Geochim Cosmochim Acta} \bold{67}: 613--629. \doi{10.1016/S0016-7037(02)01141-9}
-Akinfiev, N. N. and Tagirov, B. R. (2014) Zn in hydrothermal systems: Thermodynamic description of hydroxide, chloride, and hydrosulfide complexes. \emph{Geochem. Int.} \bold{52}, 197--214. \doi{10.1134/S0016702914030021}
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