[CHNOSZ-commits] r199 - in pkg/CHNOSZ: . data demo inst inst/extdata/cpetc man man/macros tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 4 05:43:05 CEST 2017
Author: jedick
Date: 2017-05-04 05:43:04 +0200 (Thu, 04 May 2017)
New Revision: 199
Added:
pkg/CHNOSZ/man/macros/
pkg/CHNOSZ/man/macros/macros.Rd
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/NaCl.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/activity_ratios.R
pkg/CHNOSZ/demo/affinity.R
pkg/CHNOSZ/demo/bugstab.R
pkg/CHNOSZ/demo/dehydration.R
pkg/CHNOSZ/demo/wjd.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/cpetc/rubisco.csv
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/IAPWS95.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/anim.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.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/objective.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/read.expr.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/transfer.Rd
pkg/CHNOSZ/man/util.blast.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
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/tests/testthat/test-IAPWS95.R
pkg/CHNOSZ/tests/testthat/test-eos.R
pkg/CHNOSZ/tests/testthat/test-equilibrate.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa_pK.R
pkg/CHNOSZ/tests/testthat/test-protein.info.R
pkg/CHNOSZ/tests/testthat/test-subcrt.R
pkg/CHNOSZ/tests/testthat/test-util.data.R
pkg/CHNOSZ/tests/testthat/test-water.R
pkg/CHNOSZ/tests/testthat/test-wjd.R
pkg/CHNOSZ/vignettes/equilibrium.Rnw
pkg/CHNOSZ/vignettes/equilibrium.lyx
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
pkg/CHNOSZ/vignettes/rubisco.svg
pkg/CHNOSZ/vignettes/wjd.Rnw
pkg/CHNOSZ/vignettes/wjd.lyx
Log:
minor documentation changes #4
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-05-03 14:38:51 UTC (rev 198)
+++ pkg/CHNOSZ/DESCRIPTION 2017-05-04 03:43:04 UTC (rev 199)
@@ -1,6 +1,6 @@
-Date: 2017-05-03
+Date: 2017-05-04
Package: CHNOSZ
-Version: 1.0.8-87
+Version: 1.0.8-88
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-05-03 14:38:51 UTC (rev 198)
+++ pkg/CHNOSZ/data/refs.csv 2017-05-04 03:43:04 UTC (rev 199)
@@ -10,95 +10,95 @@
RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452
RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
-PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.doi.org/10.1016/0016-7037(82)90056-4
+PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO<sub>4</sub>,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
-BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2
-Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845
-JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
-SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",http://dx.doi.org/10.1016/0016-7037(88)90181-0
-SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",http://dx.doi.org/10.1016/0016-7037(89)90341-4
-SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",http://dx.doi.org/10.1016/0016-7037(90)90429-O
+BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
+Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
+JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
+SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0
+SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
+SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
Joh92a,"J. W. Johnson",1992,"personal communication","steam, Cp represented by the Maier-Kelley equation",
SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
SPRONS92.3,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file",""Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."",
-Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",http://dx.doi.org/10.1016/0016-7037(92)90392-V
-Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",http://dx.doi.org/10.1016/0016-7037(93)90542-5
-Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",http://dx.doi.org/10.1016/0016-7037(93)90542-5
-SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",http://dx.doi.org/10.1016/0016-7037(93)90128-J
-SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",http://dx.doi.org/10.1006/icar.1993.1185
-SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,http://dx.doi.org/10.1016/0016-7037(93)90337-V
-HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",http://dx.doi.org/10.1016/0016-7037(95)00314-P
-PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,http://dx.doi.org/10.1063/1.555964
+Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",https://doi.org/10.1016/0016-7037(92)90392-V
+Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5
+Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5
+SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
+SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185
+SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V
+HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
+PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",http://pubs.er.usgs.gov/publication/b2131
-SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",http://dx.doi.org/10.1016/0016-7037(95)00058-8
-SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes not included in later slop files.",http://dx.doi.org/10.1016/0016-7037(95)00058-8
-Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",http://dx.doi.org/10.2475/ajs.295.5.496
-AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",http://dx.doi.org/10.1039/A608126F
-DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO<sub>4</sub>, NaSO<sub>4</sub><sup>-</sup>, and HCl",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
-MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,http://dx.doi.org/10.1016/S0016-7037(97)00241-X
-SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",http://dx.doi.org/10.1016/S0016-7037(97)00009-4
-SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","inorganic ions and hydroxide complexes",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
-TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",http://dx.doi.org/10.1016/S1251-8050(97)83981-X
-HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
-HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
-RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",http://dx.doi.org/10.1016/S0016-7037(97)00345-1
+SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
+SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes not included in later slop files.",https://doi.org/10.1016/0016-7037(95)00058-8
+Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
+AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
+DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
+DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
+DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
+MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO<sub>4</sub>, NaSO<sub>4</sub><sup>-</sup>, and HCl",https://doi.org/10.1016/S0016-7037(97)00241-X
+MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,https://doi.org/10.1016/S0016-7037(97)00241-X
+SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8
+SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8
+SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
+SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","inorganic ions and hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
+SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",https://doi.org/10.1016/S0016-7037(96)00339-0
+TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X
+HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
+HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
+RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1
SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "G<sub>f</sub> and H<sub>f</sub> from @SS93a TMM"",http://geopig.asu.edu/?q=tools
SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools
SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools
-SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",http://dx.doi.org/10.1016/S0016-7037(99)00276-8
+SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
+SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0
+SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,https://doi.org/10.1016/S0016-7037(98)00049-0
+HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8
MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221
-PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
-SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",http://dx.doi.org/10.2138/rmg.2000.40.9
-AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,http://dx.doi.org/10.1016/S0016-7037(01)00707-4
-AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N<sub>2</sub>O",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x
-AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x
-MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
-PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
-Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",http://dx.doi.org/10.1016/S0016-7037(01)00761-X
-SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",http://dx.doi.org/10.1016/S0016-7037(01)00717-7
-MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",http://dx.doi.org/10.2138/am-2003-5-614
-MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",http://dx.doi.org/10.2138/am-2003-5-613
-MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",http://dx.doi.org/10.1007/s00269-004-0405-z
-SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",http://dx.doi.org/10.1016/j.gca.2003.06.001
-HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org/10.1016/j.jct.2005.10.013
-LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",http://dx.doi.org/10.1016/j.gca.2006.04.010
-LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",http://dx.doi.org/10.1016/j.gca.2006.04.010
-LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",http://dx.doi.org/10.1016/j.tca.2006.06.008
-LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",http://dx.doi.org/10.1016/j.tca.2006.06.008
-DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",http://dx.doi.org/10.5194/bg-3-311-2006
-DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",http://dx.doi.org/10.5194/bg-3-311-2006
-DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",http://dx.doi.org/10.5194/bg-3-311-2006
-MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175
+PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
+SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9
+AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://doi.org/10.1016/S0016-7037(01)00707-4
+AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N<sub>2</sub>O",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x
+AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x
+MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",https://doi.org/10.1016/S0883-2927(00)00025-1
+PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",https://doi.org/10.1016/S0016-7037(01)00678-0
+Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X
+SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
+MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614
+MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",https://doi.org/10.2138/am-2003-5-613
+MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z
+SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001
+HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013
+LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
+LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010
+LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",https://doi.org/10.1016/j.tca.2006.06.008
+LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",https://doi.org/10.1016/j.tca.2006.06.008
+DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006
+DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",https://doi.org/10.5194/bg-3-311-2006
+MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
-MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes",http://dx.doi.org/10.1007/s00254-006-0578-5
+MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes",https://doi.org/10.1007/s00254-006-0578-5
SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)+2",http://geopig.asu.edu/?q=tools
SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",http://geopig.asu.edu/?q=tools
Ric08,"L. Richard",2008,"personal communication",alkenes,
-GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815","kieserite, starkeyite, hexahydrite, and epsomite",http://dx.doi.org/10.1016/j.gca.2009.08.005
-HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",kerogens,http://dx.doi.org/10.1016/j.gca.2008.03.004
-AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010
-MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",http://dx.doi.org/10.1007/s12665-009-0369-x
-Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",http://dx.doi.org/10.1007/s10498-010-9102-3
-RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",http://dx.doi.org/10.1016/j.gca.2011.07.030
-LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",http://dx.doi.org/10.1016/j.gca.2011.11.041
-LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",http://dx.doi.org/10.1016/j.gca.2011.11.041
-LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041
-LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041
-DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",http://dx.doi.org/10.1016/j.gca.2013.08.020
+GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005
+HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",kerogens,https://doi.org/10.1016/j.gca.2008.03.004
+AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010
+MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",https://doi.org/10.1007/s12665-009-0369-x
+Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",https://doi.org/10.1007/s10498-010-9102-3
+RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",https://doi.org/10.1016/j.gca.2011.07.030
+LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",https://doi.org/10.1016/j.gca.2011.11.041
+LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",https://doi.org/10.1016/j.gca.2011.11.041
+LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",https://doi.org/10.1016/j.gca.2011.11.041
+LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",https://doi.org/10.1016/j.gca.2011.11.041
+DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",https://doi.org/10.1016/j.gca.2013.08.020
SLOP15.1,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools
SLOP15.2,"E. L. Shock et al.",2015,"slop15.dat computer data file","Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",http://geopig.asu.edu/?q=tools
SLOP15.3,"E. L. Shock et al.",2015,"slop15.dat computer data file","formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."",http://geopig.asu.edu/?q=tools
@@ -106,8 +106,8 @@
SLOP15.5,"E. L. Shock et al.",2015,"slop15.dat computer data file","n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."",http://geopig.asu.edu/?q=tools
SLOP15.6,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools
SLOP15.7,"E. L. Shock et al.",2015,"slop15.dat computer data file","hexanol, heptanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a<sub>1</sub>, a<sub>2</sub>, a<sub>3</sub>, a<sub>4</sub> and c<sub>1</sub> values compared to @SH90."",http://geopig.asu.edu/?q=tools
-CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",http://dx.doi.org/10.1016/j.gca.2016.08.028
-CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters",http://dx.doi.org/10.1016/j.gca.2016.08.028
+CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",https://doi.org/10.1016/j.gca.2016.08.028
+CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters",https://doi.org/10.1016/j.gca.2016.08.028
CHNOSZ.1,"J. M. Dick",2017,"CHNOSZ package documentation","GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.",http://chnosz.net
CHNOSZ.2,"J. M. Dick",2017,"CHNOSZ package documentation","alanate and glycinate: GHS as used by @DLH06",http://chnosz.net
CHNOSZ.3,"J. M. Dick",2017,"CHNOSZ package documentation","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net
Modified: pkg/CHNOSZ/demo/NaCl.R
===================================================================
--- pkg/CHNOSZ/demo/NaCl.R 2017-05-03 14:38:51 UTC (rev 198)
+++ pkg/CHNOSZ/demo/NaCl.R 2017-05-04 03:43:04 UTC (rev 199)
@@ -3,7 +3,7 @@
## (Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992)
## Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures:
## Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 degrees C and 5 kbar.
-## J. Chem. Soc. Faraday Trans. 88, 803-826. http://dx.doi.org/10.1039/FT9928800803 )
+## J. Chem. Soc. Faraday Trans. 88, 803-826. https://doi.org/10.1039/FT9928800803 )
species <- c("NaCl", "Na+", "Cl-")
coeffs <- c(-1, 1, 1)
# start a new plot and show the experimental logK
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2017-05-03 14:38:51 UTC (rev 198)
+++ pkg/CHNOSZ/demo/Shh.R 2017-05-04 03:43:04 UTC (rev 199)
@@ -1,5 +1,5 @@
# Compare affinities of Sonic hedgehog and transcription factors involved in dorsal-ventral patterning
-# (Dick, 2015. Chemical integration of proteins in signaling and development. http://dx.doi.org/10.1101/015826)
+# (Dick, 2015. Chemical integration of proteins in signaling and development. https://doi.org/10.1101/015826)
# UniProt names of the proteins
pname <- c("SHH", "OLIG2", "NKX22", "FOXA2", "IRX3", "PAX6", "NKX62", "DBX1",
Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R 2017-05-03 14:38:51 UTC (rev 198)
+++ pkg/CHNOSZ/demo/activity_ratios.R 2017-05-04 03:43:04 UTC (rev 199)
@@ -35,7 +35,7 @@
# with accordingly different axis ranges
## MgO-CaO-SiO2-H2O at 300 degree C and Psat
-## Russell et al., 2010 (http://dx.doi.org/10.1111/j.1472-4669.2010.00249.x)
+## Russell et al., 2010 (https://doi.org/10.1111/j.1472-4669.2010.00249.x)
basis(c("Mg+2", "Ca+2", "SiO2", "H2O", "O2", "H+"))
species(c("brucite", "chrysotile", "talc", "tremolite", "diopside", "akermanite"))
a <- affinity(SiO2 = c(-10, 0, res), `Ca+2` = c(0, 20, res), T = 300)
@@ -45,7 +45,7 @@
## CaO-MgO-SiO2-H2O and
## CaO-Al2O3-MgO-SiO2-H2O at 300 degree C and 500 bar
-## Bach and Klein, 2009 (http://dx.doi.org/10.1016/j.lithos.2008.10.022)
+## Bach and Klein, 2009 (https://doi.org/10.1016/j.lithos.2008.10.022)
basis(c("Ca+2", "Al+3", "Mg+2", "SiO2", "H2O", "O2", "H+"))
species(c("clinochlore,14a", "clinozoisite", "prehnite", "grossular"))
a <- affinity(SiO2 = c(-5, 0, res), `Ca+2` = c(6, 11, res), T = 300, P = 500)
Modified: pkg/CHNOSZ/demo/affinity.R
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 199
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