[CHNOSZ-commits] r826 - in pkg/CHNOSZ: . inst/extdata/OBIGT inst/tinytest man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Feb 10 13:30:38 CET 2024 

Author: jedick
Date: 2024-02-10 13:30:37 +0100 (Sat, 10 Feb 2024)
New Revision: 826

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/tinytest/test-subcrt.R
   pkg/CHNOSZ/man/logB.to.OBIGT.Rd
   pkg/CHNOSZ/man/util.fasta.Rd
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Minor documentation updates


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/DESCRIPTION	2024-02-10 12:30:37 UTC (rev 826)
@@ -1,6 +1,6 @@
-Date: 2024-02-06
+Date: 2024-02-10
 Package: CHNOSZ
-Version: 2.0.0-45
+Version: 2.0.0-46
 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/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2024-02-10 12:30:37 UTC (rev 826)
@@ -36,7 +36,7 @@
 Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.",
 OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-Hückel extended term parameter (<i>b</i><sub>$\gamma$</sub>)",https://doi.org/10.1016/0016-7037(90)90368-U
 SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
-HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.er.usgs.gov/publication/70016664
+HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.usgs.gov/publication/70016664
 SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
 SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
 SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4

Modified: pkg/CHNOSZ/inst/tinytest/test-subcrt.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-subcrt.R	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/inst/tinytest/test-subcrt.R	2024-02-10 12:30:37 UTC (rev 826)
@@ -253,8 +253,8 @@
 # Added on 20240206
 info <- "High-temperature polymorph is not shown as stable below the transition temperature"
 # This checks that the below-transition temperature code in subcrt() is working.
-# If not, then cr2 is incorrectly identified as stable at 25 and 103 degC
-# (that is, cr2 has a lower Delta G0, than cr at those temperature,
+# If not, then cr2 is incorrectly identified as stable at 25 and 103 °C
+# (that is, cr2 has a lower ΔG° than cr at those temperatures,
 #  but should only be shown as stable above the transition temperature of 377 K)
 T <- c(25, 50, 103, 104)
 sout <- subcrt("carrollite", T = T, P = 1)$out[[1]]

Modified: pkg/CHNOSZ/man/logB.to.OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/logB.to.OBIGT.Rd	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/man/logB.to.OBIGT.Rd	2024-02-10 12:30:37 UTC (rev 826)
@@ -36,7 +36,7 @@
 The fitted parameters for the formed species are then added to OBIGT.
 Finally, \code{\link{all.equal}} is used to test for approximate equivalence of the input values of \logB and calculated equilibrium constants; if the mean absolute difference exceeds \code{tolerance}, an error occurs.
 
-To avoid overfitting, only the first three parameters (code{G}, \code{S}, and \code{c1}) are used by default.
+To avoid overfitting, only the first three parameters (\code{G}, \code{S}, and \code{c1}) are used by default.
 More parameters (up to 5) or fewer (down to 1) can be selected by changing \code{npar}.
 Volumetric parameters (\a1 to \a4) in the HKF equations currently aren't included, so the resulting fits are valid only at the input pressure values.
 

Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/man/util.fasta.Rd	2024-02-10 12:30:37 UTC (rev 826)
@@ -36,7 +36,7 @@
 If the line numbers of the header lines were previously determined, they can be supplied in \code{ihead}. 
 Optionally, the lines of a previously read file may be supplied in \code{lines} (in this case no file is needed so \code{file} should be set to "").
 When \code{ret} is \samp{count}, the names of the proteins in the resulting data frame are parsed from the header lines of the file, unless \code{id} is provided.
-If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
+If \code{id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and \code{organism} columns of the resulting data frame.
 
 \code{count.aa} counts the occurrences of each amino acid or nucleic-acid base in a sequence (\code{seq}).
 For amino acids, the columns in the returned data frame are in the same order as \code{thermo()$protein}.

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2024-02-06 14:31:48 UTC (rev 825)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2024-02-10 12:30:37 UTC (rev 826)
@@ -327,11 +327,11 @@
 In these diagrams, changing the Fe:V ratio affects the fully reduced metallic species.
 In the 1:1 mixture, the FeV~3~ + Fe~3~V assemblage is predicted to be stable instead of FeV.
 This result is unlike Figure 1 of @SZS_17 but is consistent with the [MP page for FeV](https://doi.org/10.17188/1189535) where it is shown to decompose to this assemblage.
-On the other hand, [FeV~3~ is stable](https://materialsproject.org/materials/mp-1079399/) in the 1:3 mixture.
+On the other hand, [FeV~3~ is stable](https://next-gen.materialsproject.org/materials/mp-1079399/) in the 1:3 mixture.
 For an even higher proportion of V, the V + FeV~3~ assemblage is stable, which can be seen for instance in the Pourbaix diagram linked from the [MP page for FeV~5~O~12~](https://doi.org/10.17188/1305091).
 
 Let's make another diagram for the 1:1 Fe:V composition over a broader range of Eh and pH.
-The diagram shows a stable assemblage of Fe~2~O~3~ with an oxidized bimetallic material, [Fe~2~V~4~O~13~](https://materialsproject.org/materials/mp-1200054/).
+The diagram shows a stable assemblage of Fe~2~O~3~ with an oxidized bimetallic material, [Fe~2~V~4~O~13~](https://next-gen.materialsproject.org/materials/mp-1200054/).
 ```{r FeVO4, eval = FALSE, echo = 1:29}
 layout(t(matrix(1:3)), widths = c(1, 1, 0.2))
 par(cex = 1)
@@ -445,7 +445,7 @@
 stopifnot(round(eV_atom, 3) == 0.415)
 ```
 
-This is equal to the value for the energy above the hull / atom for [triclinic FeVO~4~ on the MP website](https://materialsproject.org/materials/mp-504509/) (0.415 eV, accessed on 2020-11-09 and 2021-02-19).
+This is equal to the value for the energy above the hull / atom for [triclinic FeVO~4~ on the MP website](https://next-gen.materialsproject.org/materials/mp-504509/) (0.415 eV, accessed on 2020-11-09 and 2021-02-19).
 This shows that we successfully made a round trip starting with the input formation energies (eV/atom) from the Materials API, to standard Gibbs energy (J/mol) in the OBIGT database, and back out to energy above the hull (eV/atom).
 
 The concept of using the stable minerals and aqueous species to calculate reaction energetics is formalized in the `mosaic()` function, which is described next.

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