Move uranium.R to uranyl.R

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@848 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
jedick · Nov 17, 2024 · d5ed796 · d5ed796
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Date: 2024-11-17
 Package: CHNOSZ
-Version: 2.1.0-20
+Version: 2.1.0-21
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

diff --git a/R/examples.R b/R/examples.R
@@ -34,7 +34,7 @@ demos <- function(which = c("sources", "protein.equil", "affinity", "NaCl", "den
   "ORP", "ionize", "buffer", "protbuff", "glycinate",
   "mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "minsol",
   "Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum",
-  "AD", "comproportionation", "Pourbaix", "E_coli", "yttrium", "rank.affinity", "uranium"),
+  "AD", "comproportionation", "Pourbaix", "E_coli", "yttrium", "rank.affinity", "uranyl"),
   save.png = FALSE) {
   # Run one or more demos from CHNOSZ with ask = FALSE, and return the value of the last one
   out <- NULL

diff --git a/demo/00Index b/demo/00Index
@@ -33,4 +33,4 @@ Pourbaix        Eh-pH diagram for Fe-O-H with equisolubility lines
 E_coli          Gibbs energy of biomass synthesis in E. coli
 rank.affinity   Affinity ranking for proteins in yeast nutrient limitation
 yttrium         logB.to.OBIGT fits at 800 and 1000 bar and Y speciation in NaCl solution at varying pH
-uranium         Total (carbonate|sulfate)-pH diagrams for uranium
+uranyl          Total (carbonate|sulfate)-pH diagrams for uranyl species
diff --git a/demo/uranium.R → demo/uranyl.R b/demo/uranium.R → demo/uranyl.R
@@ -1,5 +1,5 @@
-# CHNOSZ/demo/uranium.R
-# Total (carbonate|sulfate)-pH diagrams for U, after Migdisov et al., 2024
+# CHNOSZ/demo/uranyl.R
+# Total (carbonate|sulfate)-pH diagrams for uranyl species, after Migdisov et al., 2024
 # 20241116 jmd
 library(CHNOSZ)
 

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -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{&Delta;<I>G</I>&deg;}}{ΔG°}}}
 
-\section{Changes in CHNOSZ version 2.1.0-20 (2024-11-17)}{
+\section{Changes in CHNOSZ version 2.1.0-21 (2024-11-17)}{
 
     \itemize{
 
@@ -52,8 +52,8 @@
 
       \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to James Leong and Grayson Boyer.
 
-      \item Add \file{demo/uranium.R}, total (carbonate|sulfate)-pH diagrams
-      for uranium, after
+      \item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams
+      for uranyl species, after
       \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}.
 
     }

diff --git a/man/examples.Rd b/man/examples.Rd
@@ -65,7 +65,7 @@ The demo(s) to run is/are specified by \code{which}; the default is to run them
     \item{E_coli}{Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016)}
     \item{rank.affinity}{Affinity ranking for proteins in yeast nutrient limitation (data from Tai et al., 2005)}
     \item{yttrium}{\code{\link{logB.to.OBIGT}} fits at 800 and 1000 bar and Y speciation in \code{\link{NaCl}} solution at varying pH (Guan et al., 2020)}
-    \item{uranium}{Total (carbonate|sulfate)-pH diagrams for uranium (Migdisov et al., 2024)}
+    \item{uranyl}{Total (carbonate|sulfate)-pH diagrams for uranyl species (Migdisov et al., 2024)}
   }
 
 For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos.