examples: Run Examples from the Documentation

Description Usage Arguments Details Warning References Examples

View source: R/examples.R

Description

Run the examples contained in each of the documentation topics.

Usage

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  examples(save.png = FALSE)
  demos(which = c("sources", "protein.equil", "affinity", "NaCl",
    "density", "ORP", "findit", "ionize", "buffer", "protbuff",
    "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold",
    "contour", "sphalerite", "wjd", "bugstab", "Shh", "saturation",
    "adenine", "DEW", "lambda", "TCA", "aluminum", "bison", "AkDi",
    "comproportionation"),
    save.png=FALSE)

Arguments

save.png

logical, generate PNG image files for the plots?

which

character, which example to run

Details

examples runs all the examples in the help pages for the package. example is called for each topic with ask set to FALSE (so all of the figures are shown without prompting the user).

demos runs all the demos in the package. The demo(s) to run is/are specified by which; the default is to run them in the order of the list below.

sources Cross-check the reference list with the thermodynamic database
protein.equil Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011)
affinity Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001)
NaCl Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)
density Density of \H2O, inverted from IAPWS-95 equations (rho.IAPWS95)
ORP Temperature dependence of oxidation-reduction potential for redox standards
findit Minimize the standard deviation of logarithms of activities of sulfur species
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995)
protbuff Chemical activities buffered by thiol peroxidases or sigma factors
glycinate Metal-glycinate complexes (Shock and Koretsky, 1995; Azadi et al., 2019)
mosaic Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965)
copper Another example of mosaic: complexation of Cu with glycine (Aksu and Doyle, 2001)
arsenic Another example of mosaic: Eh-pH diagram for the system As-O-H-S (Lu and Zhu, 2011)
solubility Solubility of calcite (cf. Manning et al., 2013) and \CO2 (cf. Stumm and Morgan, 1996)
gold Solubility of gold (Akinfiev and Zotov; 2001; Stef\aacutensson and Seward, 2004; Williams-Jones et al., 2009)
contour Gold solubility contours on a log fO2 - pH diagram (Williams-Jones et al., 2009)
sphalerite Solubility of sphalerite (Akinfiev and Tagirov, 2014)
wjd G minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast
dehydration \logK of dehydration reactions; SVG file contains tooltips and links
bugstab Formation potential of microbial proteins in colorectal cancer (Dick, 2016)
Shh Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015)
saturation Equilibrium activity diagram showing activity ratios and mineral saturation limits (Bowers et al., 1984)
adenine HKF regression of heat capacity and volume of aqueous adenine (Lowe et al., 2017)
DEW Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b)
lambda Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988)
TCA Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016)
aluminum Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014)
carboxylase Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase
bison Average oxidation state of carbon in proteins for phyla at Bison Pool (Dick and Shock, 2013)
AkDi Henry's constant of dissolved gases (Akinfiev and Diamond, 2003)
comproportionation Gibbs energy of sulfur comproportionation (Amend et al., 2020)

For either function, if save.png is TRUE, the plots are saved in png files whose names begin with the names of the help topics or demos.

Two of the demos have external dependencies and are not automatically run by demos. dehydration creates an interactive SVG file; this demo depends on RSVGTipsDevice, which is not available for Windows. carboxylase creates an animated GIF; this demo requires that the ImageMagick convert commmand be available on the system (tested on Linux and Windows).

carboxylase animates diagrams showing rankings of calculated chemical activities along a combined \T and \logaH2 gradient, or makes a single plot on the default device (without conversion to animated GIF) if a single temperature (T) is specified in the code. To run this demo, an empty directory named png must be present (as a subdirectory of the R working directory). The proteins in the calculation are 24 carboxylases from a variety of organisms. There are 12 ribulose phosphate carboxylase and 12 acetyl-coenzyme A carboxylase; 6 of each type are from nominally mesophilic organisms and 6 from nominally thermophilic organisms, shown as blue and red symbols on the diagrams. The activities of hydrogen at each temperature are calculated using logaH2 = -11 + 3/40 * T(degC); this equation comes from a model of relative stabilities of proteins in a hot-spring environment (Dick and Shock, 2011).

Warning

The discontinuities apparent in the plot made by the NaCl demo illustrate limitations of the "g function" for charged species in the revised HKF model (the 355 \degC boundary of region II in Figure 6 of Shock et al., 1992). Note that SUPCRT92 (Johnson et al., 1992) gives similar output at 500 bar. However, SUPCRT does not output thermodynamic properties above 350 \degC at \Psat; see Warning in subcrt.

References

Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. Geochim. Cosmochim. Acta 67, 613–629. https://doi.org/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. Geochem. Int. 52, 197–214. https://doi.org/10.1134/S0016702914030021

Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. Geochem. Int. 39, 990–1006. http://pleiades.online/cgi-perl/search.pl/?type=abstract&name=geochem&number=10&year=1&page=990

Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. J. Electrochem. Soc. 148, B51–B57. https://doi.org/10.1149/1.1344532

Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. Science 281, 1659–1662. https://doi.org/10.1126/science.281.5383.1659

Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25, 175–243. https://doi.org/10.1016/S0168-6445(00)00062-0

Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. Environ. Microbiol. https://doi.org/10.1111/1462-2920.14982

Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. Fluid Phase Equilib. 480, 25-40. https://doi.org/10.1016/j.fluid.2018.10.002

Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na\s2O-K\s2O-CaO-MgO-FeO-Fe\s2O\s3-Al\s2O\s3-SiO\s2-TiO\s2-H\s2O-CO\s2. J. Petrol. 29, 445-522. https://doi.org/10.1093/petrology/29.2.445

Bowers, T. S., Jackson, K. J. and Helgeson, H. C. (1984) Equilibrium Activity Diagrams for Coexisting Minerals and Aqueous Solutions at Pressures and Temperatures to 5 kb and 600\degC, Springer-Verlag, Berlin, 397 p. http://www.worldcat.org/oclc/11133620

Canovas, P. A., III and Shock, E. L. (2016) Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle. Geochim. Cosmochim. Acta 195, 293–322. https://doi.org/10.1016/j.gca.2016.08.028

Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. Science 146, 1461–1464. https://doi.org/10.1126/science.146.3650.1461

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. PLoS ONE 6, e22782. https://doi.org/10.1371/journal.pone.0022782

Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. PLoS ONE 8, e72395. https://doi.org/10.1371/journal.pone.0072395

Dick, J. M. (2015) Chemical integration of proteins in signaling and development. bioRxiv. https://doi.org/10.1101/015826

Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238. https://doi.org/10.7717/peerj.2238

Garrels, R. M. and Christ, C. L. (1965) Solutions, Minerals, and Equilibria, Harper & Row, New York, 450 p. http://www.worldcat.org/oclc/517586

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. Comp. Geosci. 18, 899–947. https://doi.org/10.1016/0098-3004(92)90029-Q

Lowe, A. R., Cox, J. S. and Tremaine, P. R. (2017) Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from T = 278.15 K to 393.15 K. J. Chem. Thermodyn. 112, 129–145. https://doi.org/10.1016/j.jct.2017.04.005

Lu, P. and Zhu, C. (2011) Arsenic Eh–pH diagrams at 25\degC and 1 bar. Environ. Earth Sci. 62, 1673–1683. https://doi.org/10.1007/s12665-010-0652-x

Manning, C. E., Shock, E. L. and Sverjensky, D. A. (2013) The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints. Rev. Mineral. Geochem. 75, 109–148. https://doi.org/10.2138/rmg.2013.75.5

Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. Orig. Life Evol. Biosph. 25, 161–173. https://doi.org/10.1007/BF01581580

Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim. Cosmochim. Acta 59, 1497–1532. https://doi.org/10.1016/0016-7037(95)00058-8

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 \degC and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803–826. https://doi.org/10.1039/FT9928800803

Stef\aacutensson, A. and Seward, T. M. (2004) Gold(I) complexing in aqueous sulphide solutions to 500\degC at 500 bar. Geochim. Cosmochim. Acta 68, 4121–4143. https://doi.org/10.1016/j.gca.2004.04.006

Stumm, W. and Morgan, J. J. (1996) Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, John Wiley & Sons, New York, 1040 p. http://www.worldcat.org/oclc/31754493

Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014a) Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 \degC. Geochim. Cosmochim. Acta 129, 125–145. https://doi.org/10.1016/j.gca.2013.12.019

Sverjensky, D. A., Hemley, J. J. and D'Angelo, W. M. (1991) Thermodynamic assessment of hydrothermal alkali feldspar-mica-aluminosilicate equilibria. Geochim. Cosmochim. Acta 55, 989-1004. https://doi.org/10.1016/0016-7037(91)90157-Z

Sverjensky, D. A., Stagno, V. and Huang, F. (2014b) Important role for organic carbon in subduction-zone fluids in the deep carbon cycle. Nat. Geosci. 7, 909–913. https://doi.org/10.1038/ngeo2291

Tutolo, B. M., Kong, X.-Z., Seyfried, W. E., Jr. and Saar, M. O. (2014) Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. Geochim. Cosmochim. Acta 133, 216–234. https://doi.org/10.1016/j.gca.2014.02.036

Williams-Jones, A. E., Bowell, R. J. and Migdisov, A. A. (2009) Gold in solution. Elements 5, 281–287. https://doi.org/10.2113/gselements.5.5.281

Zimmer, K., Zhang, Y., Lu, P., Chen, Y., Zhang, G., Dalkilic, M. and Zhu, C. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Comp. Geosci. 90, 97–111. https://doi.org/10.1016/j.cageo.2016.02.013

Examples

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demos(c("ORP", "NaCl"))

CHNOSZ documentation built on July 7, 2020, 3 p.m.