[CHNOSZ-commits] r556 - in pkg/CHNOSZ: . inst/extdata/OBIGT vignettes

Sun Jul 12 02:00:39 CEST 2020

Author: jedick
Date: 2020-07-12 02:00:38 +0200 (Sun, 12 Jul 2020)
New Revision: 556

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/vignettes/equilibrium.Rmd
Log:
Remove sulfur example from equilibrium.Rmd


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

--- pkg/CHNOSZ/DESCRIPTION	2020-07-11 08:14:53 UTC (rev 555)
+++ pkg/CHNOSZ/DESCRIPTION	2020-07-12 00:00:38 UTC (rev 556)
@@ -1,6 +1,6 @@
-Date: 2020-07-11
+Date: 2020-07-12
 Package: CHNOSZ
-Version: 1.3.6-29
+Version: 1.3.6-30
 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/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-07-11 08:14:53 UTC (rev 555)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-07-12 00:00:38 UTC (rev 556)
@@ -270,6 +270,6 @@
 DEW19.3,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","CaO: Fitted by Dimitri to high PT retrievals from Fang",http://www.dewcommunity.org
 DEW19.4,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","glycinate: @AH97b for the G, H, S, Cp, V",http://www.dewcommunity.org
 DEW19.5,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Ca<sup>+2</sup>: values listed in DEW spreadsheet)",http://www.dewcommunity.org
-DEW19.6,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Fe<sup>+2</sup>: take HKF a<sub>1</sub>-a<sub>4</sub> parameters from @HS19, which are different from 2019 DEW spreadsheet)",http://www.dewcommunity.org
+DEW19.6,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Fe<sup>+2</sup>: HKF a<sub>1</sub>-a<sub>4</sub> parameters taken from @HS19, which are different from 2019 DEW spreadsheet)",http://www.dewcommunity.org
 HS19,"F. Huang and D. A. Sverjensky",2019,"Geochim. Cosmochim. Acta 254, 192-230","ions and metal complexes",https://doi.org/10.1016/j.gca.2019.03.027
 LA19,"D. E. LaRowe and J. P. Amend",2019,"Geomicrobiol. J. 36, 492-505","dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid",https://doi.org/10.1080/01490451.2019.1573278

Modified: pkg/CHNOSZ/vignettes/equilibrium.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rmd	2020-07-11 08:14:53 UTC (rev 555)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rmd	2020-07-12 00:00:38 UTC (rev 556)
@@ -434,8 +434,8 @@
 
 ## Example 3: Normalization
 
-Here are two more figures showing the effects of normalization.
-The first one is like Figure 5 of @Dic08, extended to more extreme conditions.
+Here is another figure showing the effects of normalization.
+This is like Figure 5 of @Dic08, extended to more extreme conditions.
 If you wish to reproduce the diagram from the 2008 paper more closely, uncomment the `add.OBIGT()` command.
 
 ```{r ProteinSpeciation, results = "hide", message = FALSE, fig.width = 8, fig.height = 5.5, out.width = "100%", pngquant = pngquant}
@@ -463,50 +463,11 @@
 is an interesting convergence of the metastable equilibrium activities of some
 proteins at low log *f*~O2~.
 
-Normalization may also be useful for calculations with inorganic molecules that
-are in various stages of polymerization. The first diagram below is similar to
-the one shown by @See96, with the addition of color and the water stability
-line. Normalization of the chemical formulas (scaling them to each contain one
-S atom) brings up the activities of the larger molecules, yielding a much
-smaller range of activities.
-
-```{r SulfurSpeciation, results = "hide", message = FALSE, fig.width = 7, fig.height = 3.5, out.width = "100%", pngquant = pngquant}
-basis("CHNOS+")
-basis("pH", 5)
-species(c("H2S", "S2-2", "S3-2", "S2O3-2", "S2O4-2",
-          "S3O6-2", "S5O6-2", "S2O6-2", "HSO3-", "SO2", "HSO4-"))
-T <- 325
-P <- 350
-loga_S <- -2
-a <- affinity(O2 = c(-50, -15), T = T, P = P)
-layout(matrix(1:3, nrow = 1), widths = c(4, 4, 1))
-col <- rep(c("blue", "black", "red"), each = 4)
-lty <- 1:4
-for(normalize in c(FALSE, TRUE)) {
-  e <- equilibrate(a, loga.balance = loga_S, normalize = normalize)
-  diagram(e, ylim = c(-30, 0), legend.x = NULL, col = col, lty = lty)
-  water.lines(e, col = 4)
-  par(xpd = NA)
-  title(main = paste0("Total sulfur activity = ",
-                      10^loga_S, "; normalize = ", normalize))
-  par(xpd = FALSE)
-  dp <- describe.property(c("T", "P"), c(T, P))
-  db <- describe.basis(ibasis = 6)
-  dpb <- c(dp, db)
-  if(!normalize) legend("topleft", dpb, bg = "white")
-}
-par(mar = c(0, 0, 0, 0))
-plot.new()
-leg <- lapply(species()$name, expr.species)
-legend("center", lty = lty, col = col, lwd = 1.5, bty = "n",
-       legend = as.expression(leg), y.intersp = 1.3)
-```
-
 ## Document history
 
 * 2009-11-29 Initial version with CSG example, titled "Calculating relative abundances of proteins"
 * 2012-09-30 Renamed to "Equilibrium in CHNOSZ"; remove activity comparisons and add maximum affinity method.
 * 2015-11-08 Move previous material to Appendix and add sections on concepts, organization, examples, and applications; use knitr vignette engine.
-* 2020-07-10 Simplify to concepts and examples (amino acids, proteins, normalization); convert document from LaTeX (Rnw) to Rmarkdown (Rmd).
+* 2020-07-10 Simplify to concepts and examples (amino acids, proteins, normalization); convert document from LaTeX (Rnw) to R Markdown (Rmd).
 
 ## References

