thermo.plot.new(xlim, ylim, xlab, ylab, cex = par("cex"), mar = NULL, lwd = par("lwd"), side = c(1,2,3,4), mgp = c(1.5, 0.3, 0), cex.axis = par("cex"), col = par("col"), yline = NULL, axs = "i", do.box = TRUE, ticks = NULL, las = 1, xline = NULL) thermo.axis(lab = "x-axis", side = 1, line = 1.5, cex = par("cex"), lwd = par("lwd"), T = NULL, col = par("col")) label.plot(x, xfrac = 0.05, yfrac = 0.95, paren = FALSE, italic = FALSE, ...) usrfig() label.figure(x, xfrac = 0.05, yfrac = 0.95, paren = FALSE, italic = FALSE, ...) water.lines(xaxis = "pH", yaxis = "Eh", T = 298.15, P = "Psat", which = c("oxidation","reduction"), logaH2O = 0, lty = 2, lwd=1, col = par("fg"), xpoints = NULL, O2state="gas") mtitle(main, line=0, ...) residualsplot(residuals, property = "Cp", model = "big")side (retained for backwards compatibility)mtext thermo.plot.new sets parameters for a new plot, creates a new plot using plot.new, and adds axes and major and minor ticks to the plot. Plot parameters (see par) including cex, mar, lwd, mgp and axs can be given, as well as a numeric vector in ticks identifying which sides of the plot receive tick marks. yline, if present, denotes the margin line (default par('mgp')[1]) where the y-axis name is plotted. The very first time thermo.plot.new is called, it stores the existing value of par(no.readonly=TRUE) in thermo$opar so that the plot device can be reset to the previous state later on.
water.lines plots lines representing the oxidation and reduction stability limits of water on yaxis-xaxis diagrams, where yaxis can be Eh or O2, and xaxis can be pH or T.
which controls which lines are drawn (oxidation, reduction, or both (the default)).
logaH2O denotes the logarithm of the activity of water.
With O2state set to gas (the default), the logarithm of oxygen fugacity is plotted.
Change this to aq to plot the logarithm of oxygen activity (do not change it if plotting Eh).
xpoints is an optional list of points on the x axis to which to restrict the plotting (default of NULL refers to the axis limits).
label.plot and label.figure add identifying text within the plot region and figure region.
The value given for x is made into a label, optionally italicized and with parentheses (like html(a)(a)).
The location of the label is controlled by xfrac and yfrac (the fractional coordinates of either the plot or figure region), and ... can include other parameters such as cex and adj that are passed to text.
usrfig returns the limits of the figure region in “user” coordinates (i.e. the limits of the plot region, from par("usr")).
It is a supporting function for label.figure but is also useful for other circumstances where information must be added at a particular location in a figure.
thermo.axis is used to add axes and axis labels to plots, with some default style settings (rotation of numeric labels) and conversions between oxidation-reduction scales (called by thermo.plot.new). It also adds minor tick marks.
mtitle can be used to add a multi-line title to a plot.
It loops over each element of main and places it on a separate margin line using mtext.
The spacing of the last (bottom) line from the edge of the plot is specified by line.
This function exists to facilitate using expressions in multiline titles (see revisit for an example.)
residualsplot produces a barchart with options useful for plotting residuals of group contribution models for thermodynamic properties. It plots horizontal bars stacked with largest on top. The names of the residuals argument (i.e., the names of model species) are plotted across from each respective bar. The axis title is taken from the property (probably Cp or V), and the plot title includes the model name. See the ‘xadditivity’ vignette for examples of these plots.