[CHNOSZ-commits] r284 - in pkg/CHNOSZ: . vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2017-11-09 14:22:52 +0100 (Thu, 09 Nov 2017)
New Revision: 284

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: use water.lines() for all Cu-S-Cl-H2O projections


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-11-09 11:47:07 UTC (rev 283)
+++ pkg/CHNOSZ/DESCRIPTION	2017-11-09 13:22:52 UTC (rev 284)
@@ -1,6 +1,6 @@
 Date: 2017-11-09
 Package: CHNOSZ
-Version: 1.1.0-81
+Version: 1.1.0-82
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2017-11-09 11:47:07 UTC (rev 283)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2017-11-09 13:22:52 UTC (rev 284)
@@ -691,7 +691,7 @@
 The key argument is `bases`, which identifies the candidate basis species, starting with the one in the current basis.
 The other arguments, like those of <span style="color:green">`affinity()`</span>, specify the ranges of the variables; `res` indicates the grid resolution to use for each variable (the default is 128).
 The first call to <span style="color:green">`diagram()`</span> plots the species of interest; the second adds the predominance fields of the basis species.
-We turn off the gray coloring beyond the water stability limits (`limit.water`) but plot the lines using <span style="color:green">`water.lines()`</span>:
+We turn off the gray coloring beyond the water stability limits (`limit.water`) but plot the red dotted lines using <span style="color:green">`water.lines()`</span>:
 
 ```{r copper_mosaic, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", message=FALSE, cache=TRUE, fig.cap="Copper minerals and aqueous complexes with chloride, 200 °C.", pngquant=pngquant, timeit=timeit}
 T <- 200
@@ -701,7 +701,7 @@
 diagram(m1$A.species, lwd = 2, fill = NA, limit.water = FALSE)
 diagram(m1$A.bases, add = TRUE, col = "blue", col.names = "blue", lty = 2,
         limit.water = FALSE)
-water.lines(m1$A.species, col = "red", lwd = 2, lty = 2)
+water.lines(m1$A.species, col = "red", lwd = 2, lty = 3)
 ```
 
 The argument `blend = TRUE` is used to combine the diagrams according to the equilibrium activities of the basis species by themselves ([see below](#equilibration)).
@@ -724,12 +724,13 @@
           limit.water = FALSE)
   diagram(m1$A.bases, add = TRUE, col = "blue", col.names = "blue", lty = 3,
           limit.water = FALSE)
+  water.lines(m1$A.species, col = "red", lwd = 2, lty = 3)
   swap.basis(names(newvar), "e-")
 }
 par(mfrow = c(1, 3))
 mosaicfun(list(Eh = c(-1, 1, res)))
-mosaicfun(list(H2 = c(-25, 10, res)))
-mosaicfun(list(O2 = c(-70, 0, res)))
+mosaicfun(list(H2 = c(-30, 10, res)))
+mosaicfun(list(O2 = c(-70, 5, res)))
 ```
 
 ## *T*, *P*, activity transects