examples(do.png = FALSE)
demos(which = c("sources", "NaCl", "cordierite",
"phosphate", "nucleobase", "orp", "diagram", "revisit", "findit",
"CO2Ac", "nonideal", "ionize", "buffer", "yeastgfp", "mosaic",
"solubility", "wjd"))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)
cordierite equilibrium constant of hydrous cordierite dehydration
phosphate phosphate speciation with pH, temperature and ionic strength
nucleobase relative stabilities of nucleobases and some amino acids
orp oxidation-reduction potential of redox standards as a function of temperature
diagram comparison of methods for calculating stability fields
revisit detailed example of usage of revisit
findit detailed example of usage of findit
CO2Ac activity of CO2 buffered by acetic acid; comparing affinity with diagram
nonideal activity coefficient of charged species (Alberty, 2003), using the IS argument of subcrt
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)
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
}
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.
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.
Stumm, W. and Morgan, J. J. (1996) Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, John Wiley & Sons, New York, 1040 p.
data(thermo)
demos(c("orp", "NaCl"))
par(thermo$opar)
# use the following to run examples in all help topics
examples()Run the code above in your browser using DataLab