[CHNOSZ-commits] r616 - in pkg/CHNOSZ: . demo inst man

Tue Nov 10 06:39:32 CET 2020

Author: jedick
Date: 2020-11-10 06:39:31 +0100 (Tue, 10 Nov 2020)
New Revision: 616

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/zinc.R
   pkg/CHNOSZ/inst/TODO
   pkg/CHNOSZ/man/diagram.Rd
Log:
Document type = 'loga.balance' in diagram.Rd


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2020-11-09 13:16:48 UTC (rev 615)
+++ pkg/CHNOSZ/DESCRIPTION	2020-11-10 05:39:31 UTC (rev 616)
@@ -1,6 +1,6 @@
-Date: 2020-11-09
+Date: 2020-11-10
 Package: CHNOSZ
-Version: 1.3.6-89
+Version: 1.3.6-90
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/demo/zinc.R
===================================================================
--- pkg/CHNOSZ/demo/zinc.R	2020-11-09 13:16:48 UTC (rev 615)
+++ pkg/CHNOSZ/demo/zinc.R	2020-11-10 05:39:31 UTC (rev 616)
@@ -53,7 +53,7 @@
 par(xpd = NA)
 legend("bottomleft", c("Predominance diagram: molality of aqueous", "species defines one solubility contour.",
   "Take away aqueous species to see", "all possible minerals.",
-  "Calculate solubility for each mineral separately", "then take the minimum to plot solubilities", "of stable minerals across the diagram."),
+  "Calculate solubility for each mineral separately", "then find the minimum to plot solubilities", "of stable minerals across the diagram."),
        pch = c("A", "", "B", "", "C", "", ""), inset = c(-0.1, 0), cex = 0.95)
 par(xpd = FALSE)
 

Modified: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO	2020-11-09 13:16:48 UTC (rev 615)
+++ pkg/CHNOSZ/inst/TODO	2020-11-10 05:39:31 UTC (rev 616)
@@ -6,8 +6,6 @@
 
 - move protein.equil() example (previously in equilibrium.Rnw) to JMDplots.
 
-- change add.obigt --> add.OBIGT on website (Fe-O-H-S example) when package is submitted to CRAN.
-
 - move extdata/bison to JMDplots package.
 
 - OBIGT.Rmd: change "CHNOSZ" references to "OBIGT".
@@ -16,8 +14,6 @@
 
 - add check to mosaic() that 'stable' values have the right dimensions.
 
-- remove stopifnot() from examples.
-
 - get water limits on logfO2-logfS2 diagram (multi-metal.Rmd)
 
 - anintro.Rmd, help files: make it clear that species with
@@ -33,5 +29,3 @@
 (CoCl2-4 has been added to OBIGT).
 
 - add wustite from Robie and Hemingway (1995).
-
-- document type = 'loga.balance' (for solubility contours) in ?diagram.

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2020-11-09 13:16:48 UTC (rev 615)
+++ pkg/CHNOSZ/man/diagram.Rd	2020-11-10 05:39:31 UTC (rev 616)
@@ -97,16 +97,6 @@
 2-D diagrams, for two variables, are plotted as predominance fields.
 The allowed variables are any that \code{\link{affinity}} or the other functions accepts: temperature, pressure, or the chemical activities of the basis species.
 
-The \code{type} argument only applies when the output from \code{affinity} is being used.
-For \code{type} set to \samp{auto}, and 0 or 1 variables, the property computed by \code{\link{affinity}} for each species is plotted.
-This is usually the affinity of the formation reaction, but can be set to some other property, such as the equilibrium constant (\samp{logK}).
-For two variables, equilibrium predominance (maximum affinity) fields are plotted.
-This \dQuote{maximum affinity method} (Dick, 2019) uses balancing coefficients that are specified by the \code{balance} argument.
-If \code{type} is \samp{saturation}, the function plots the line for each species where the affinity of formation equals zero (see \code{demo("saturation")} for an example).
-If for a given species no saturation line is possible or the range of the diagram does not include the saturation line, the function prints a message instead.
-If \code{type} is the name of a basis species, then the equilibrium activity of the selected basis species in each of the formation reactions is plotted (see the \CO2-acetic acid example in \code{\link{buffer}}).
-In the case of 2-D diagrams, both of these options use \code{\link{contour}} to draw the lines, with the method specified in \code{contour.method}.
-
 A new plot is started unless \code{add} is TRUE.
 If \code{plot.it} is FALSE, no plot will be generated but all the intermediate computations will be performed and the results returned.
 
@@ -122,6 +112,23 @@
 
 }
 
+\section{\code{type} argument}{
+This paragraph describes the effect of the \code{type} argument when the output from \code{affinity} is being used.
+For \code{type} set to \samp{auto}, and with 0 or 1 variables defined in \code{\link{affinity}}, the property computed by \code{affinity} for each species is plotted.
+This is usually the affinity of the formation reactions, but can be set to some other property (using the \code{property} argument of \code{affinity}), such as the equilibrium constant (\samp{logK}).
+For two variables, equilibrium predominance (maximum affinity) fields are plotted.
+This \dQuote{maximum affinity method} (Dick, 2019) uses balancing coefficients that are specified by the \code{balance} argument.
+If \code{type} is \samp{saturation}, the function plots the line for each species where the affinity of formation equals zero (see \code{demo("saturation")} for an example).
+If for a given species no saturation line is possible or the range of the diagram does not include the saturation line, the function prints a message instead.
+If \code{type} is the name of a basis species, then the equilibrium activity of the selected basis species in each of the formation reactions is plotted (see the \CO2-acetic acid example in \code{\link{buffer}}).
+In the case of 2-D diagrams, both of these options use \code{\link{contour}} to draw the lines, with the method specified in \code{contour.method}.
+
+This paragraph describes the effect of the \code{type} argument when the output from \code{solubility} is being used.
+For \code{type} set to \samp{auto}, the equilibrium activities (i.e. computed solubilities) of each species are plotted.
+If \code{type} is \samp{loga.balance}, the activity of the balancing basis species (i.e. total solubility) is plotted; this is represented by contours on a 2-D diagram.
+For examples that use these features, see \code{\link{solubility}} and various \code{\link{demos}}: \samp{DEW}, \samp{contour}, \samp{gold}, \samp{solubility}, \samp{sphalerite}, \samp{zinc}.
+}
+
 \section{1-D diagrams}{
 For 1-D diagrams, the default setting for the y-axis is a logarithmic scale (unless \code{alpha} is TRUE) with limits corresponding to the range of logarithms of activities (or 0,1 if \code{alpha} is TRUE); these actions can be overridden by \code{ylog} and \code{ylim}.
 If \code{legend.x} is NA (the default), the lines are labeled with the names of the species near the maximum value.

