[CHNOSZ-commits] r901 - in pkg/CHNOSZ: . R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 22 02:12:16 CEST 2025
Author: jedick
Date: 2025-05-22 02:12:15 +0200 (Thu, 22 May 2025)
New Revision: 901
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Reorganize NEWS.Rd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-05-16 02:18:11 UTC (rev 900)
+++ pkg/CHNOSZ/DESCRIPTION 2025-05-22 00:12:15 UTC (rev 901)
@@ -1,6 +1,6 @@
-Date: 2025-05-16
+Date: 2025-05-21
Package: CHNOSZ
-Version: 2.1.0-72
+Version: 2.1.0-73
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/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2025-05-16 02:18:11 UTC (rev 900)
+++ pkg/CHNOSZ/R/diagram.R 2025-05-22 00:12:15 UTC (rev 901)
@@ -211,7 +211,7 @@
# Some additional steps for affinity values, but not for equilibrated activities
if(eout.is.aout) {
for(i in 1:length(pv)) {
- # NOTE: CHNOSZ_equilibrium.Rmd in JMDplots shows predominance diagrams using
+ # NOTE: equilibrium.Rmd in JMDplots shows predominance diagrams using
# 'normalize' and 'as.residue' settings that are consistent with equilibrate()
# TODO: what is the derivation of these equations?
if(normalize) pv[[i]] <- (pv[[i]] + eout$species$logact[i] / n.balance[i]) - log10(n.balance[i])
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2025-05-16 02:18:11 UTC (rev 900)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2025-05-22 00:12:15 UTC (rev 901)
@@ -15,11 +15,17 @@
\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 2.1.0-71 (2025-05-14)}{
+\section{Changes in CHNOSZ version 2.1.0-73 (2025-05-21)}{
\subsection{OBIGT DEFAULT DATA}{
\itemize{
+ \item Add tantalum species from
+ \href{https://doi.org/10.1016/j.gca.2024.10.019}{Hu et al. (2024)}.
+
+ \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 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
@@ -33,28 +39,22 @@
\item Add alkylamines, benzylamines, and aminiums from
\href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
- \item Add tantalum species from
- \href{https://doi.org/10.1016/j.gca.2024.10.019}{Hu et al. (2024)}.
-
- \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 Move americium complexes from \file{SLOP98.csv} back to
- \file{inorganic_aq.csv} (entropy of the element Am has been available for
- checking GHS self-consistency since version 1.4.0).
+ \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)}.
- \item \file{inorganic_cr.csv}: 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)}.
+ \item Move americium complexes from \file{SLOP98.csv} (entropy of the
+ element Am has been available for checking GHS self-consistency since
+ version 1.4.0).
- \item Fix sign of \emph{c} parameter for nesquehonite. Thanks to
- James Leong and Grayson Boyer.
+ \item Fix sign of \emph{c} parameter for nesquehonite. Thanks to James
+ Leong and Grayson Boyer.
- \item Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}.
+ \item Restore steam (H\s{2}O,g).
}
}
@@ -66,20 +66,20 @@
for testing, including \file{SiO2.csv} (renamed from \file{AS04.csv}) and
\file{GEMSFIT.csv} in addition to those listed below.
+ \item Add \file{testing/GA.csv}: Germanium, indium, gallium, and cadmium
+ species from \href{https://doi.org/10.1080/08120099.2024.2423772}{Huston
+ and Bastrakov (2024)}.
+
\item Add \file{testing/IGEM.csv}: Au and Cu complexes and
SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.
-
- \item Add \file{testing/Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
- \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
- (2024)}.
\item Add \file{testing/REE.csv}: REE(III) fluoride and chloride complexes from
\href{https://doi.org/10.1016/j.gca.2009.08.023}{Migdisov et al. (2009)}
(previously available in CHNOSZ verisons 0.9-5 to 1.0.8).
- \item Add \file{testing/GA.csv}: Germanium, indium, gallium, and cadmium
- species from \href{https://doi.org/10.1080/08120099.2024.2423772}{Huston
- and Bastrakov (2024)}.
+ \item Add \file{testing/Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+ \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
+ (2024)}.
}
}
@@ -87,26 +87,12 @@
\subsection{DOCUMENTATION}{
\itemize{
- \item Revise \file{anintro.Rmd}. Text before \dQuote{Building Up} was
- revised and shortened with AI assistance.
+ \item Major revision of \file{anintro.Rmd}.
- \item Add FAQ question: Why are mineral stability boundaries curved on
- mosaic diagrams?
-
- \item Add \file{demo/total_S.R}: total activity of S--pH diagram for
- Fe-S-O-C minerals.
-
- \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)}.
-
- \item Revise \file{demo/sum_S.R} for log \emph{f}O\s{2} - log \emph{m} ΣS
- diagram and add solubility contours for Fe and Au.
-
\item Add \file{demo/MgATP.R}: speciation of ATP with H\S{+} and
Mg\S{+2}, based on
- \href{https://search.worldcat.org/title/51242181}{Alberty (2003)}
- (example moved here from \file{anintro.Rmd}).
+ \href{https://search.worldcat.org/title/51242181}{Alberty (2003)} (moved
+ from \file{anintro.Rmd}).
\item Update \file{demo/contour.R} to use conditions taken from
\href{https://doi.org/10.1016/j.oregeorev.2022.105231}{Ding et al.
@@ -113,14 +99,21 @@
(2023)} and optional data for Au species from IGEM RAS, including
polynuclear Au\s{2}S\s{2}\S{-2}.
- \item Move \file{equilibrium.Rmd} from CHNOSZ to
- \file{CHNOSZ_equilibrium.Rmd} in the [JMDplots
- package](https://github.com/jedick/JMDplots).
+ \item Add \file{demo/rubisco_Zc.R}, moved from \file{anintro.Rmd}.
- \item \file{demo/rubisco_Zc.R} extracted from old version of
- \file{anintro.Rmd}.
+ \item Add \file{demo/sum_S.R}: log \emph{f}O\s{2}--log \emph{m} ΣS
+ diagram for Fe-S-O-C minerals with solubility contours for Fe and Au.
+ \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)}.
+ \item Add FAQ question: Why are mineral stability boundaries curved on
+ mosaic diagrams?
+
+ \item Move \file{equilibrium.Rmd} to
+ \href{https://github.com/jedick/JMDplots}{JMDplots}.
+
}
}
@@ -127,12 +120,6 @@
\subsection{NEW FEATURES}{
\itemize{
- \item Rename \code{logB.to.OBIGT()} to \code{logK.to.OBIGT()} and add a
- \strong{state} argument which accepts \samp{aq} (aqueous species using
- heat capacity parameters in the \samp{HKF} model; the previous method and
- current default) or \samp{cr} (minerals using the Maier-Kelley equation
- in the \samp{CGL} model; a new method)).
-
\item \code{OBIGT} now uses \samp{CGL_Ttr} as the \code{model} for
species whose \code{T} value denotes a phase stability limit above which
\code{subcrt()} returns NA values, in contrast to \samp{CGL}, for which
@@ -147,6 +134,12 @@
and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending
on the \code{model} defined in OBIGT (HKF or DEW, respectively).
+ \item Rename \code{logB.to.OBIGT()} to \code{logK.to.OBIGT()} and add a
+ \strong{state} argument which accepts \samp{aq} (aqueous species using
+ heat capacity parameters in the \samp{HKF} model; the previous method and
+ current default) or \samp{cr} (minerals using the Maier-Kelley equation
+ in the \samp{CGL} model; a new method)).
+
}
}
@@ -199,15 +192,17 @@
\itemize{
\item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to
- the canprot package with different names.
+ [canprot](https://cran.r-project.org/package=canprot) with different
+ names.
\item Remove \code{seq2aa()}.
- \item Remove \code{add.alpha()}. Instead, \code{grDevices::adjustcolor()}
- is now used in \code{stack_mosaic()} to add transparency.
+ \item Remove \code{add.alpha()}. Instead of this function,
+ \code{grDevices::adjustcolor()} is now used in \code{stack_mosaic()} to
+ add transparency.
\item Move \code{protein.equil()} to JMDplots; the associated demo has
- been moved to the \file{CHNOSZ_equilibrium.Rmd} vignette in that package.
+ been moved to the \file{equilibrium.Rmd} vignette in that package.
}
}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-16 02:18:11 UTC (rev 900)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-22 00:12:15 UTC (rev 901)
@@ -158,7 +158,7 @@
info("CH4")
```
-When searching by formula, aqueous species are returned if they are available.
+Searching by formula returns the aqueous species if it is available.
Use a species name or add the state to get a particular physical state - `aq`, `cr`, `gas`, or `liq`:
```{r info_methane}
@@ -211,8 +211,10 @@
### Working with reactions
-Define reactions with species names, states (optional), and coefficients:
+Define reactions with species names or formulas, states (optional), and coefficients:
+NOTE: Reaction coefficients are negative for reactants and positive for products.
+
```{r subcrt_CO2_reaction}
# CO2 dissolution reaction
subcrt(c("CO2", "CO2"), c("gas", "aq"), c(-1, 1), T = 25)
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