[CHNOSZ-commits] r740 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Sep 18 01:47:19 CEST 2022
Author: jedick
Date: 2022-09-18 01:47:19 +0200 (Sun, 18 Sep 2022)
New Revision: 740
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/man/util.plot.Rd
Log:
OBIGT/organic_aq.csv: Correct formulas of Na(Mal)-, K(Mal)-, and Dy(Mal)+
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-07-24 10:43:17 UTC (rev 739)
+++ pkg/CHNOSZ/DESCRIPTION 2022-09-17 23:47:19 UTC (rev 740)
@@ -1,6 +1,6 @@
-Date: 2022-07-24
+Date: 2022-09-18
Package: CHNOSZ
-Version: 1.9.9-31
+Version: 1.9.9-32
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 2022-07-24 10:43:17 UTC (rev 739)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-09-17 23:47:19 UTC (rev 740)
@@ -12,7 +12,7 @@
% links to vignettes 20220723
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
-\section{Changes in CHNOSZ version 1.9.9-30 (2022-07-23)}{
+\section{Changes in CHNOSZ version 1.9.9-32 (2022-09-18)}{
\subsection{MAJOR CHANGE}{
\itemize{
@@ -47,6 +47,9 @@
(Co\s{3}O\s{4}), and zinc from \href{https://doi.org/10.3133/b2131}{Robie
and Hemingway (1995)}.
+ \item \samp{OBIGT/organic_aq.csv}: Correct formulas of Na(Mal)-, K(Mal)-,
+ and Dy(Mal)+. Thanks to Grayson Boyer.
+
}
}
@@ -154,6 +157,9 @@
\item Change default for \code{affinity()} to \code{loga.protein = 0}
(was -3).
+ \item Add tests stack_mosaic.R and stack_solubility.R (these create PDF
+ files for visual inspection of results).
+
\item Change license from GPL (>= 2) to GPL-3.
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-07-24 10:43:17 UTC (rev 739)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-09-17 23:47:19 UTC (rev 740)
@@ -501,8 +501,8 @@
K(Oxal)-,NA,KC2O4-,aq,PSK99,NA,2006-08-24,cal,-229702,-256488,42.1,8.7,0,0,0,0,0,19.5508,-1.2623,0.9911,-1
Fe(Oxal)+,NA,FeC2O4+,aq,PSK99,NA,2006-08-24,cal,-177951,-209886,-15.4,-27.4,0,0,0,0,0,-3.2911,-8.6159,0.7895,1
Cu(Oxal),NA,CuC2O4,aq,PSK99,NA,2006-08-24,cal,-153871,-181609,15.7,1,0,0,0,0,0,7.6072,-2.8308,0.1022,0
-Na(Mal)-,NA,NaC4H4O5-,aq,PSK99,NA,2006-08-24,cal,-227252,-265366,33.5,23.7,0,0,0,0,0,29.43,1.7931,1.1213,-1
-K(Mal)-,NA,KC4H4O5-,aq,PSK99,NA,2006-08-24,cal,-232648,-268321,44.9,16.6,0,0,0,0,0,23.826,0.3468,0.9486,-1
+Na(Mal)-,NA,NaC3H2O4-,aq,PSK99,NA,2006-08-24,cal,-227252,-265366,33.5,23.7,0,0,0,0,0,29.43,1.7931,1.1213,-1
+K(Mal)-,NA,KC3H2O4-,aq,PSK99,NA,2006-08-24,cal,-232648,-268321,44.9,16.6,0,0,0,0,0,23.826,0.3468,0.9486,-1
Cu(Mal),NA,CuC3H2O4,aq,PSK99,NA,2006-08-24,cal,-155944,-192837,17.6,8.9,0,0,0,0,0,11.9966,-1.2216,0.0735,0
La(Mal)+,NA,LaC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-334582,-376503,-9.2,-22.6,0,0,0,0,0,-1.3006,-7.6381,0.6911,1
Gd(Mal)+,NA,GdC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-329715,-371001,-4.4,-21.3,0,0,0,0,0,-1.1139,-7.3733,0.6223,1
@@ -516,7 +516,7 @@
Pr(Mal)+,NA,PrC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-333756,-375646,-5.2,-33.1,0,0,0,0,0,-7.961,-9.777,0.6305,1
Eu(Mal)+,NA,EuC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-308524,-351636,-8.2,-22,0,0,0,0,0,-1.099,-7.5159,0.6732,1
Tb(Mal)+,NA,TbC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-331392,-374477,-9.2,-25.9,0,0,0,0,0,-3.2346,-8.3103,0.6911,1
-Dy(Mal)+,NA,DyCC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-330783,-373740,-8.4,-17.1,0,0,0,0,0,1.8472,-6.5178,0.6821,1
+Dy(Mal)+,NA,DyC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-330783,-373740,-8.4,-17.1,0,0,0,0,0,1.8472,-6.5178,0.6821,1
Tm(Mal)+,NA,TmC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-331888,-376252,-13.3,-19.7,0,0,0,0,0,0.8771,-7.0474,0.7483,1
Ho(Mal)+,NA,HoC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-333361,-377876,-13.5,-18.7,0,0,0,0,0,1.5473,-6.8437,0.7484,1
Er(Mal)+,NA,ErC3H2O4+,aq,PSK99,NA,2006-08-24,cal,-331861,-376225,-13.5,-19.7,0,0,0,0,0,0.9612,-7.0407,0.7584,1
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-07-24 10:43:17 UTC (rev 739)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-09-17 23:47:19 UTC (rev 740)
@@ -155,8 +155,8 @@
"OBIGT",1382,"Na(Oxal)-","aq","cal",,-3.14,
"OBIGT",1383,"K(Oxal)-","aq","cal",,-2.75,
"OBIGT",1384,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1386,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1387,"K(Mal)-","aq","cal",,-2.63,17013
+"OBIGT",1386,"Na(Mal)-","aq","cal",,-3.11,
+"OBIGT",1387,"K(Mal)-","aq","cal",,-2.63,
"OBIGT",1389,"La(Mal)+","aq","cal",,-1.92,
"OBIGT",1390,"Gd(Mal)+","aq","cal",,-1.73,
"OBIGT",1391,"Lu(Mal)+","aq","cal",,-2.25,
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/man/util.plot.Rd
===================================================================
--- pkg/CHNOSZ/man/util.plot.Rd 2022-07-24 10:43:17 UTC (rev 739)
+++ pkg/CHNOSZ/man/util.plot.Rd 2022-09-17 23:47:19 UTC (rev 740)
@@ -30,8 +30,8 @@
label.figure(x, xfrac = 0.05, yfrac = 0.95, paren = FALSE,
italic = FALSE, ...)
water.lines(eout, which = c("oxidation","reduction"),
- lty = 2, lwd=1, col = par("fg"), plot.it = TRUE)
- mtitle(main, line=0, spacing=1, ...)
+ lty = 2, lwd = 1, col = par("fg"), plot.it = TRUE)
+ mtitle(main, line = 0, spacing = 1, ...)
ZC.col(z)
}
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