examples: Run Examples from the Documentation

Description Usage Arguments Details References Examples

View source: R/examples.R


Run the examples contained in each of the documentation topics.


  examples(do.png = FALSE)
  demos(which = c("sources", "protein.equil", "affinity", "NaCl",
    "density", "ORP", "revisit", "findit", "ionize", "buffer",
    "protbuff", "yeastgfp", "mosaic", "copper", "solubility",
    "wjd", "dehydration", "bugstab", "Shh", "activity_ratios",



logical, generate PNG files for the plots?


character, which example to run


logical, generate image files for the plots?


examples runs all the examples in the documentation 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). If do.png is TRUE, the plots in the examples are saved as png files having names beginning with the name of each of the help topics.

demos is a function to run other examples that are provided as demos. demo is called with settings to not echo the source code and to not ask before making each plot. The demo(s) to run is/are specified by which; the default is to run them in the order of the list below. See the comments in the source code for more information about each demo.

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
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
revisit coefficient of variation of metastable equilibrium activities of proteins
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
yeastgfp subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams (Dick, 2009)
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)
solubility solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996)
wjd Gibbs energy minimization: prebiological atmospheres and cell periphery of yeast
dehydration log K 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
activity_ratios mineral stability plots with activity ratios on the axes
adenine HKF parameters regressed from heat capacity and volume of aqueous adenine (Lowe et al., 2017)


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

Dick, J. M. (2009) Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. BMC Syst. Biol. 3:75. https://doi.org/10.1186/1752-0509-3-75

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. (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

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

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

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


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

## Not run: 
# use the following to run examples in all help topics
## End(Not run)

CHNOSZ documentation built on Sept. 25, 2017, 3:01 p.m.