Run Examples from the Documentation


Run the examples contained in each of the documentation topics.


  examples(do.png = FALSE)
  demos(which = c("sources", "NaCl", "density",
    "nucleobase", "ORP", "revisit", "findit", 
    "ionize", "buffer", "yeastgfp", "mosaic",
    "copper", "solubility", "wjd", "dehydration"), to.file=FALSE)



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
NaCl equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)
density density of H2O, inverted from IAPWS-95 equations (rho.IAPWS95)
nucleobase relative stabilities of nucleobases and some amino acids
ORP oxidation-reduction potential of redox standards as a function of temperature
revisit detailed example of usage of revisit
findit detailed example of usage of findit
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer ionized proteins as a chemical activity buffer (1. thiol peroxidases 2. sigma factors)
yeastgfp logfO2-logaH2O diagrams for model proteins based on YeastGFP localizations (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(gas) (cf. Stumm and Morgan, 1996)
wjd run.wjd() with proteins: cell periphery of yeast
dehydration log K of dehydration reactions; SVG file contains tooltips and links


Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. J. Electrochem. Soc. 148, B51–B57.

Dick, J. M. (2009) Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. BMC Syst. Biol. 3:75.

Garrels, R. M. and Christ, C. L. (1965) Solutions, Minerals, and Equilibria, Harper & Row, New York, 450 p.

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.

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.

Stumm, W. and Morgan, J. J. (1996) Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, John Wiley & Sons, New York, 1040 p.


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

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

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