[CHNOSZ-commits] r948 - in pkg/CHNOSZ: . R demo inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 6 07:10:47 CET 2026
Author: jedick
Date: 2026-01-06 07:10:46 +0100 (Tue, 06 Jan 2026)
New Revision: 948
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/util.legend.R
pkg/CHNOSZ/demo/contour.R
pkg/CHNOSZ/demo/minsol.R
pkg/CHNOSZ/demo/mosaic.R
pkg/CHNOSZ/demo/sphalerite.R
pkg/CHNOSZ/demo/sum_S.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/mix.Rd
pkg/CHNOSZ/man/solubility.Rd
pkg/CHNOSZ/man/stack_mosaic.Rd
pkg/CHNOSZ/man/util.legend.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Remove lex()
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/DESCRIPTION 2026-01-06 06:10:46 UTC (rev 948)
@@ -1,6 +1,6 @@
-Date: 2026-01-05
+Date: 2026-01-06
Package: CHNOSZ
-Version: 2.2.0-14
+Version: 2.2.0-15
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/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/NAMESPACE 2026-01-06 06:10:46 UTC (rev 948)
@@ -52,7 +52,7 @@
"dumpdata", "thermo.axis", "solubility", "NaCl",
# added 20190213 or later
"CHNOSZ", "thermo", "reset", "OBIGT", "retrieve", "moles",
- "lNaCl", "lS", "lT", "lP", "lTP", "lex",
+ "lNaCl", "lS", "lT", "lP", "lTP",
# added 20200716 or later
"mash", "mix", "rebalance",
# added 20220324
Modified: pkg/CHNOSZ/R/util.legend.R
===================================================================
--- pkg/CHNOSZ/R/util.legend.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/R/util.legend.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -11,5 +11,3 @@
lP <- function(x, digits = 0) if(identical(x, "Psat")) quote(italic(P)[sat]) else substitute(x~bar, list(x = round(x, digits)))
lTP <- function(x, y, digits = 0) substitute(list(x, y), list(x = lT(x, digits), y = lP(y, digits)))
-
-lex <- function(...) as.expression(c(...))
Modified: pkg/CHNOSZ/demo/contour.R
===================================================================
--- pkg/CHNOSZ/demo/contour.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/demo/contour.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -56,8 +56,8 @@
diagram(s, levels = c(1, 10, 100, 1000), col = 1, add = TRUE)
# Add legend and title
dP <- describe.property(c("T", "P"), c(T, P))
- lexpr <- lex(dP, lNaCl(m_NaCl), lS(sum_S))
- legend("topright", lexpr, bty = "n")
+ lexpr <- c(dP, lNaCl(m_NaCl), lS(sum_S))
+ legend("topright", legend = lexpr, bty = "n")
if(i == 1) title(main = ("Gold solubility (ppb), after Ding et al., 2023 (default data)"), font.main = 1)
if(i == 2) title(main = ("Gold solubility (ppb), after Ding et al., 2023 (optional data)"), font.main = 1)
Modified: pkg/CHNOSZ/demo/minsol.R
===================================================================
--- pkg/CHNOSZ/demo/minsol.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/demo/minsol.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -52,7 +52,7 @@
lNaCl(mNaCl),
lS(Stot)
)
-legend("topleft", legend = lex(l), bty = "n", cex = 1.5)
+legend("topleft", legend = l, bty = "n", cex = 1.5)
# Describe steps
par(xpd = NA)
legend("bottomleft", c("Predominance diagram: molality of aqueous", "species defines one solubility contour.",
Modified: pkg/CHNOSZ/demo/mosaic.R
===================================================================
--- pkg/CHNOSZ/demo/mosaic.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/demo/mosaic.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -76,15 +76,13 @@
bquote(sum("S(aq)") == 10^.(loga_S)~m),
bquote(sum("C(aq)") == 10^.(loga_C)~m)
)
-legend1 <- lex(TP, SC)
-legend("topright", legend1, bty = "n")
+legend("topright", legend = c(TP, SC), bty = "n")
Fe <- c(
bquote(10^-4~"m Fe"),
bquote(10^-6~"m Fe")
)
-legend2 <- lex(Fe)
-legend("bottomleft", legend2, lty = c(3, 1), bty = "n")
+legend("bottomleft", legend = Fe, lty = c(3, 1), bty = "n")
title(main = paste("Iron oxides, sulfides, and carbonate in water,",
"after Garrels and Christ, 1965, Figure 7.21", sep = "\n"), font.main = 1)
Modified: pkg/CHNOSZ/demo/sphalerite.R
===================================================================
--- pkg/CHNOSZ/demo/sphalerite.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/demo/sphalerite.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -32,7 +32,7 @@
abline(v = pKw / 2, lty = 2, lwd = 2, col = "blue1")
# Add legend
- l <- lex(lNaCl(m_NaCl), lTP(T, P))
+ l <- c(lNaCl(m_NaCl), lTP(T, P))
legend("topright", legend = l, bty = "n")
}
Modified: pkg/CHNOSZ/demo/sum_S.R
===================================================================
--- pkg/CHNOSZ/demo/sum_S.R 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/demo/sum_S.R 2026-01-06 06:10:46 UTC (rev 948)
@@ -5,7 +5,7 @@
library(CHNOSZ)
# Define conditions
-res <- 500
+res <- 300
loga_S <- c(-6, 0, res)
logf_O2 <- c(-45, -20, res)
pH <- 5
@@ -22,7 +22,7 @@
# Setup chemical system
# Use oxygen instead of O2 to get the gas
-basis(c("Fe", "SO4-2", "oxygen", "H+", "Cl-", "H2O"))
+basis(c("Fe", "H2S", "oxygen", "H+", "Cl-", "H2O"))
basis("pH", pH)
basis("Cl-", log10(NaCl$m_Clminus))
# Add minerals as formed species
@@ -31,7 +31,7 @@
# List basis species to swap through
bases <- list( c("H2S", "HS-", "S3-", "SO2", "HSO4-", "SO4-2") )
# Calculate mosaic for Fe minerals
-m <- mosaic(bases, "SO4-2" = loga_S, O2 = logf_O2, T = T, P = P, IS = IS)
+m <- mosaic(bases, "H2S" = loga_S, O2 = logf_O2, T = T, P = P, IS = IS)
# Loop over metals for solubility contours
for(metal in c("Fe", "Au")) {
@@ -44,7 +44,7 @@
if(metal == "Au") {
# Put Au as the first basis species for solubility() calculation
- basis(c("Au", "SO4-2", "oxygen", "H+", "Cl-", "H2O"))
+ basis(c("Au", "H2S", "oxygen", "H+", "Cl-", "H2O"))
basis("pH", pH)
# This is the species whose solubility we want to calculate
species("Au")
@@ -60,7 +60,7 @@
cols <- c(2, 2)
}
# Calculate solubility and convert log molality to ppb
- s <- solubility(iaq, bases = bases, "SO4-2" = loga_S, O2 = logf_O2, T = T, P = P, IS = IS, in.terms.of = metal)
+ s <- solubility(iaq, bases = bases, "H2S" = loga_S, O2 = logf_O2, T = T, P = P, IS = IS, in.terms.of = metal)
sp <- convert(s, "ppb")
# Plot twice to get deeper colors
for(col in cols) {
@@ -70,7 +70,7 @@
# Add legend and title
T_P <- describe.property(c("T", "P"), c(T, P))
P_Cl <- c(bquote(pH == .(pH)), bquote(NaCl == .(m_NaCl)~mol~kg^-1))
- legend <- lex(T_P, P_Cl)
+ legend <- c(T_P, P_Cl)
legend("topright", legend, bty = "n")
main <- paste("Fe minerals with summed aq species: S (x-axis) and ppb", metal, "(contours)")
title(main, font.main = 1)
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2026-01-06 06:10:46 UTC (rev 948)
@@ -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 2.2.0-14 (2026-01-05)}{
+\section{Changes in CHNOSZ version 2.2.0-15 (2026-01-06)}{
\itemize{
@@ -47,6 +47,9 @@
calculations in examples, demos, and vignettes. Thanks to Evgeniy
Bastrakov for suggesting this change.
+ \item Remove \code{lex()}, which only wrapped its argument in
+ \code{as.expression(c())}.
+
}
}
Modified: pkg/CHNOSZ/man/mix.Rd
===================================================================
--- pkg/CHNOSZ/man/mix.Rd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/man/mix.Rd 2026-01-06 06:10:46 UTC (rev 948)
@@ -88,7 +88,7 @@
ad <- rebalance(dFe, dCu)
diagram(ad, xlab = xlab, balance = 1, main = "Cu-Fe-S-O-H with rebalance()")
db <- describe.basis(3)
-leg <- lex(lTP(400, 2000), db)
+leg <- c(lTP(400, 2000), db)
legend("bottomleft", legend = leg, bty = "n")
\dontshow{par(opar)}}
Modified: pkg/CHNOSZ/man/solubility.Rd
===================================================================
--- pkg/CHNOSZ/man/solubility.Rd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/man/solubility.Rd 2026-01-06 06:10:46 UTC (rev 948)
@@ -118,7 +118,7 @@
S_ <- expr.species("SO2", "gas", -20, TRUE)
pH_ <- quote(pH == 6)
T_ <- lT(125)
-lexpr <- lex(S_, pH_, T_)
+lexpr <- c(S_, pH_, T_)
# Make diagrams from the results of solubility calculations
layout(matrix(c(1, 3, 2, 3), nrow = 2))
Modified: pkg/CHNOSZ/man/stack_mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/stack_mosaic.Rd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/man/stack_mosaic.Rd 2026-01-06 06:10:46 UTC (rev 948)
@@ -92,7 +92,7 @@
species1, species2, species12, dx = dx,
pH = pH, O2 = O2, T = T, P = P, IS = NaCl$IS)
# Add legend and title
-lTP <- lex(lTP(T, P))
+lTP <- lTP(T, P)
db <- describe.basis(c(3:4))
legend("topright", c(lTP, db), bg = "white")
title("Fe-Cu-S-O-H-Cl", font.main = 1)
Modified: pkg/CHNOSZ/man/util.legend.Rd
===================================================================
--- pkg/CHNOSZ/man/util.legend.Rd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/man/util.legend.Rd 2026-01-06 06:10:46 UTC (rev 948)
@@ -6,7 +6,6 @@
\alias{lT}
\alias{lP}
\alias{lTP}
-\alias{lex}
\title{Functions to make legend text}
\description{Generate expressions describing system conditions that can be added to legends of plots.}
@@ -16,7 +15,6 @@
lT(x, digits = 0)
lP(x, digits = 0)
lTP(x, y, digits = 0)
- lex(...)
}
\arguments{
@@ -23,7 +21,6 @@
\item{x}{numeric, value of the property}
\item{digits}{numeric, digits for rounding}
\item{y}{numeric, value of pressure}
- \item{...}{language, objects to combine in an expression}
}
\details{
@@ -31,9 +28,6 @@
\code{lNaCl} describe the molality of NaCl, and \code{lS} the total molality of sulfur.
\code{lT} and \code{lP} describe the temperature and pressure.
\code{lTP} describe the temperature and pressure together, separated by a comma.
-
-The above functions return language objects, which can be combined with \code{lex} to make an expression that when used in \code{\link{legend}} appears on multiple lines.
-
}
\seealso{
@@ -42,8 +36,8 @@
\examples{
plot.new()
-l <- lex(lTP(100, "Psat"), lNaCl(1), lS(1e-3))
-legend("center", l)
+l <- c(lTP(100, "Psat"), lNaCl(1), lS(1e-3))
+legend("center", legend = l)
}
\concept{Utility functions}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2026-01-06 06:10:46 UTC (rev 948)
@@ -457,8 +457,7 @@
lNaCl(1.9),
lS(Stot)
)
-leg_expr <- lex(leg_list)
-legend("bottomleft", legend = leg_expr, bg = "white")
+legend("bottomleft", legend = leg_list, bg = "white")
title("Total solubility is higher than quasisolubility", font.main = 1)
## Second plot: activities of aqueous species in solubility calculation
@@ -820,8 +819,7 @@
lNaCl(m_NaCl),
lS(Stot)
)
-leg_expr <- lex(leg_list)
-legend("topright", legend = leg_expr, bty = "n")
+legend("topright", legend = leg_list, bty = "n")
# Make diagram for aqueous species
species(iaq)
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2026-01-05 07:51:47 UTC (rev 947)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2026-01-06 06:10:46 UTC (rev 948)
@@ -993,7 +993,7 @@
label.plot("E")
db <- describe.basis(3)
-leg <- lex(lTP(400, 2000), db)
+leg <- c(lTP(400, 2000), db)
legend("bottomleft", legend = leg, bty = "n")
```
</div>
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