[CHNOSZ-commits] r907 - in pkg/CHNOSZ: . inst vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue May 27 02:31:06 CEST 2025 

Author: jedick
Date: 2025-05-27 02:31:05 +0200 (Tue, 27 May 2025)
New Revision: 907

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/eos-regress.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
Fix issues from winbuilder checks


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2025-05-26 03:46:14 UTC (rev 906)
+++ pkg/CHNOSZ/DESCRIPTION	2025-05-27 00:31:05 UTC (rev 907)
@@ -1,6 +1,6 @@
-Date: 2025-05-26
+Date: 2025-05-27
 Package: CHNOSZ
-Version: 2.1.0-78
+Version: 2.1.0-79
 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/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2025-05-26 03:46:14 UTC (rev 906)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2025-05-27 00:31:05 UTC (rev 907)
@@ -15,7 +15,7 @@
 \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
 \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
 
-\section{Changes in CHNOSZ version 2.1.0-75 (2025-05-23)}{
+\section{Changes in CHNOSZ version 2.1.0-78 (2025-05-26)}{
 
   \subsection{OBIGT DEFAULT DATA}{
     \itemize{
@@ -26,6 +26,10 @@
       \item Add Pd(HS)\s{4}\S{-2} and Pt(HS)\s{4}\S{-2} from
       \href{https://doi.org/10.1016/j.gca.2024.12.019}{Laskar et al. (2024)}.
 
+      \item Add Sn chloride complexes and updated parameters for Sn\S{+2} and
+      Th\S{+4} from \href{https://doi.org/10.1016/j.gsf.2023.101624}{Liu et al.
+        (2023)}.
+
       \item Add aqueous uranyl complexes from
       \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}
       and related U-bearing minerals from
@@ -39,10 +43,6 @@
       \item Add alkylamines, benzylamines, and aminiums from
       \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
 
-      \item Add Sn chloride complexes and updated parameters for Sn\S{+2} and
-      Th\S{+4} from \href{https://doi.org/10.1016/j.gsf.2023.101624}{Liu et al.
-        (2023)}.
-
       \item Add cerianite (CeO\s{2}), chromite (FeCr\s{2}O\s{4}), and
       cassiterite (SnO\s{2}) from \href{https://doi.org/10.3133/b2131}{Robie
         and Hemingway (1995)}.

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2025-05-26 03:46:14 UTC (rev 906)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2025-05-27 00:31:05 UTC (rev 907)
@@ -1532,7 +1532,7 @@
 # Scale protein abundance so total abundance of residues is unity
 scaled_abundance <- 10^unitize(log10(abundance), pl)
 # Check that sum for residues is unity
-stopifnot(sum(scaled_abundance * pl) == 1)
+stopifnot(all.equal(sum(scaled_abundance * pl), 1))
 ```
 
 Unit total activity of residues is set by `equilibrate(loga.balance = 0)`, allowing comparison between experimental and predicted abundances:

Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/eos-regress.Rmd	2025-05-26 03:46:14 UTC (rev 906)
+++ pkg/CHNOSZ/vignettes/eos-regress.Rmd	2025-05-27 00:31:05 UTC (rev 907)
@@ -9,12 +9,7 @@
     toc: true
     mathjax: null
     highlight: null
-  tufte::tufte_handout:
-    citation_package: natbib
-    latex_engine: xelatex
-  tufte::tufte_book:
-    citation_package: natbib
-    latex_engine: xelatex
+    margin_references: false
 vignette: >
   %\VignetteIndexEntry{Regressing thermodynamic data}
   %\VignetteEngine{knitr::rmarkdown}
@@ -443,17 +438,19 @@
 text(225, 1000, describe.reaction(s1$reaction))
 ```
 
-Let's compare `H4SiO4` from Stefánsson (2001) and the `calc-H4SiO4` we just made with the calculated properties of `r sio2` + 2 `r h2o` as a function of temperature:
+Let's compare `H4SiO4` from @Ste01 and the `calc-H4SiO4` we just made with the calculated properties of `r sio2` + 2 `r h2o` as a function of temperature:
 ```{r subcrt_H4SiO4, eval=FALSE}
 ```
 
 Ideally, the lines would be horizontal with a _y_-interecept of 0.
-However, both the `calc-H4SiO4` we made here and the `H4SiO4` from Stefánsson (2001) show deviations that increase at higher temperatures.
+However, both the `calc-H4SiO4` we made here and the `H4SiO4` from @Ste01 show deviations that increase at higher temperatures.
 While they are not quite negligible, these deviations are comparatively small.
 For example, the almost 800 J/mol offset in Δ<i>G</i>° at 350 °C corresponds to a difference in log<i>K</i> of only -0.07.
 
-The following example uses the `H4SiO4` from Stefánsson (2001) to make an activity diagram for the K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
-This is similar to the diagram on p. 361 of [Garrels and Christ, 1965](https://www.worldcat.org/oclc/517586), but is quantitatively a closer match to the diagram in the [User's Guide to PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-75.html).
+The following example uses the `H4SiO4` from @Ste01 to make an activity diagram for the
+K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
+This is similar to the diagram on p. 361 of @GC65, but the positions of the stability boundaries
+are closer to those shown on p. 316 of the User's Guide for PHRREQC v3 [@PA13].
 
 ```{r activity_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=TRUE, results="hide", message=FALSE, out.width="100%", cache=TRUE, fig.cap="Activity diagram for K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O.", pngquant=pngquant}
 basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))
@@ -462,3 +459,5 @@
 diagram(a, ylab = ratlab("K+"), fill = "terrain", yline = 1.7)
 legend("bottomleft", describe.property(c("T", "P"), c(25, 1)), bty = "n")
 ```
+
+## References

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2025-05-26 03:46:14 UTC (rev 906)
+++ pkg/CHNOSZ/vignettes/vig.bib	2025-05-27 00:31:05 UTC (rev 907)
@@ -818,6 +818,14 @@
   doi       = {10.1111/j.1525-1314.1998.00140.x},
 }
 
+ at TechReport{PA13,
+  author      = {David L. Parkhurst and C. A. J. Appelo},
+  institution = {U.S. Geological Survey},
+  title       = {Description of Input and Examples for {PHREEQC} Version 3—A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations},
+  year        = {2013},
+  doi         = {10.3133/tm6A43},
+}
+
 @Article{SW02,
   author    = {Skirrow, Roger G. and Walshe, John L.},
   journal   = {Economic Geology},

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