examples: Run Examples from the Documentation

Description

Run the examples contained in each of the documentation topics.

Usage

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"),
    to.file=FALSE)

Arguments

do.png

logical, generate PNG files for the plots?

which

character, which example to run

to.file

logical, generate image files for the plots?

Details

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 , 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 (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

References

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

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 \(^{\circ}\)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

Examples

Run this code

# NOT RUN {
demos(c("ORP", "NaCl"))
# }
# NOT RUN {
# use the following to run examples in all help topics
examples()
# }

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