[CHNOSZ-commits] r781 - in pkg/CHNOSZ: . R demo inst/extdata/OBIGT man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Mar 21 05:10:46 CET 2023 

Author: jedick
Date: 2023-03-21 05:10:46 +0100 (Tue, 21 Mar 2023)
New Revision: 781

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/demo/density.R
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/vignettes/OBIGT.Rmd
Log:
Change some URLs to https


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/DESCRIPTION	2023-03-21 04:10:46 UTC (rev 781)
@@ -1,6 +1,6 @@
-Date: 2023-03-13
+Date: 2023-03-21
 Package: CHNOSZ
-Version: 2.0.0
+Version: 2.0.0-1
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -30,4 +30,4 @@
 Encoding: UTF-8
 License: GPL-3
 VignetteBuilder: knitr
-URL: http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/
+URL: https://www.chnosz.net/, https://r-forge.r-project.org/projects/chnosz/

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/R/util.data.R	2023-03-21 04:10:46 UTC (rev 781)
@@ -105,11 +105,11 @@
     .cat("</head>")
     ### Boilerplate text
     .cat("<body>")
-    .cat(paste0('<h1>References for thermodynamic data in <a href="http://chnosz.net"><font color="red">CHNOSZ</font></a> ',
+    .cat(paste0('<h1>References for thermodynamic data in <a href="https://chnosz.net"><font color="red">CHNOSZ</font></a> ',
                packageDescription("CHNOSZ")$Version), " (", packageDescription("CHNOSZ")$Date, ')</h1>')
     .cat("<h3>Click on a column header to sort, or on a citation to open the URL in new window.</h3>")
     .cat("<h4>Column 'number' gives the number of times each reference appears in thermo()$OBIGT.</h4>")
-    .cat('<p>See also the vignette <a href="http://chnosz.net/vignettes/OBIGT.html">OBIGT thermodynamic database</a>.</p>')
+    .cat('<p>See also the vignette <a href="https://chnosz.net/vignettes/OBIGT.html">OBIGT thermodynamic database</a>.</p>')
     ### Start table and headers
     .cat("<table id='thermorefs' border='1'>")
     .cat("<tr>")

Modified: pkg/CHNOSZ/demo/density.R
===================================================================
--- pkg/CHNOSZ/demo/density.R	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/demo/density.R	2023-03-21 04:10:46 UTC (rev 781)
@@ -9,8 +9,10 @@
 blue <- "blue"
 if(TPrange == "low") {
   T <- seq(300, 800, 10)
-  #P <- seq(1, 600, 11.98)
   P <- seq(0, 600, 12)
+  ## Uncomment these lines to make high-resolution plot (used on https://chnosz.net/demos/)
+  #T <- seq(300, 800, 2)
+  #P <- seq(0, 600, 2)
   bias <- 1.68
 } else {
   # Upper T,P limit for SUPCRT92: 2250 degC, 30000 bar

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2023-03-21 04:10:46 UTC (rev 781)
@@ -96,7 +96,7 @@
 TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3
 ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327
 ST97.1,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylamine HKF parameters",https://doi.org/10.1023/A:1022977006327
-proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",http://chnosz.net
+proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net
 HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
 HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
 RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1
@@ -161,7 +161,7 @@
 LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006
 MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
 SGX+06,"A. V. Sharygin et al.",2006,"Geochim. Cosmochim. Acta 70, 5169-5182",KSO<sub>4</sub><sup>-</sup>,https://doi.org/10.1016/j.gca.2006.07.034
-electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",http://chnosz.net
+electron,OBIGT,2006,"See CHNOSZ vignette OBIGT.Rmd for more information","Non-zero entropy of the electron based on the hydrogen-ion convention",https://chnosz.net
 Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
 MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes; linked to properties of arsenate and arsenite from @SSWS97",https://doi.org/10.1007/s00254-006-0578-5
 SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)<sup>+2</sup>",http://geopig.asu.edu/?q=tools
@@ -218,14 +218,14 @@
 ZZL+16.1,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","As(α): V listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
 ZZL+16.2,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","Cp parameters listed in spronsbl.dat",https://doi.org/10.1016/j.cageo.2016.02.013
 ZZL+16.3,"K. Zimmer et al.",2016,"Comp. Geosci. 90, 97-111","dawsonite GHS",https://doi.org/10.1016/j.cageo.2016.02.013
-OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.",http://chnosz.net
-OBIGT.3,"J. M. Dick",2017,"OBIGT database in CHNOSZ","AuCl<sub>4</sub><sup>-</sup> renamed to AuCl<sub>4</sub><sup>-3</sup>",http://chnosz.net
-OBIGT.4,"J. M. Dick",2017,"OBIGT database in CHNOSZ","charge of NpO<sub>2</sub>(Oxal), La(Succ)<sup>+</sup>, NH<sub>4</sub>(Succ)<sup>-</sup>, and NpO<sub>2</sub>(Succ) as listed by @PSK99",http://chnosz.net
-OBIGT.5,"J. M. Dick",2017,"OBIGT database in CHNOSZ","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH<sub>2</sub>NH<sub>2</sub>] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
-OBIGT.6,"J. M. Dick",2019,"OBIGT database in CHNOSZ","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",http://chnosz.net
-OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",http://chnosz.net
-OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",http://chnosz.net
-OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",http://chnosz.net
+OBIGT.1,"J. M. Dick",2017,"OBIGT database in CHNOSZ","GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.",https://chnosz.net
+OBIGT.3,"J. M. Dick",2017,"OBIGT database in CHNOSZ","AuCl<sub>4</sub><sup>-</sup> renamed to AuCl<sub>4</sub><sup>-3</sup>",https://chnosz.net
+OBIGT.4,"J. M. Dick",2017,"OBIGT database in CHNOSZ","charge of NpO<sub>2</sub>(Oxal), La(Succ)<sup>+</sup>, NH<sub>4</sub>(Succ)<sup>-</sup>, and NpO<sub>2</sub>(Succ) as listed by @PSK99",https://chnosz.net
+OBIGT.5,"J. M. Dick",2017,"OBIGT database in CHNOSZ","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH<sub>2</sub>NH<sub>2</sub>] were printed in Table 6 of @DLH06; corrected values are used here.",https://chnosz.net
+OBIGT.6,"J. M. Dick",2019,"OBIGT database in CHNOSZ","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",https://chnosz.net
+OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",https://chnosz.net
+OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",https://chnosz.net
+OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",https://chnosz.net
 LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine HKF parameters",https://doi.org/10.1016/j.jct.2017.04.005
 DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as in @PS01)",http://www.dewcommunity.org
 DEW17.02,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(ethanol: parameters in DEW spreadsheet are different from @PS01; no comment provided)",http://www.dewcommunity.org

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/man/examples.Rd	2023-03-21 04:10:46 UTC (rev 781)
@@ -62,6 +62,7 @@
     \item{comproportionation}{Gibbs energy of sulfur comproportionation (Amend et al., 2020)}
     \item{Pourbaix}{Eh-pH diagram for Fe-O-H with equisolubility lines (Pourbaix, 1974)}
     \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)}
   }
 
@@ -142,6 +143,8 @@
 
 Sverjensky, D. A., Stagno, V. and Huang, F. (2014b) Important role for organic carbon in subduction-zone fluids in the deep carbon cycle. \emph{Nat. Geosci.} \bold{7}, 909--913. \doi{10.1038/ngeo2291}
 
+Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J.-M. and Pronk, J. T. (2005) Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in \emph{Saccharomyces cerevisiae}. \emph{J. Biol. Chem.} \bold{280}, 437--447. \doi{10.1074/jbc.M410573200}
+
 Tutolo, B. M., Kong, X.-Z., Seyfried, W. E., Jr. and Saar, M. O. (2014) Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. \emph{Geochim. Cosmochim. Acta} \bold{133}, 216--234. \doi{10.1016/j.gca.2014.02.036}
 
 Williams-Jones, A. E., Bowell, R. J. and Migdisov, A. A. (2009) Gold in solution. \emph{Elements} \bold{5}, 281--287. \doi{10.2113/gselements.5.5.281}

Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd	2023-03-13 23:54:01 UTC (rev 780)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd	2023-03-21 04:10:46 UTC (rev 781)
@@ -361,7 +361,7 @@
 ## <a id="optional-DEW" class="anchor"></a> `r setfile("DEW.csv")`
 The Deep Earth Water (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar.
 Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the <i>a</i><sub>1</sub> HKF parameter, as described by [Sverjensky et al. (2014)](https://doi.org/10.1016/j.gca.2013.12.019).
-The data here were taken from the May 2017 and January 2019 versions of the at http://www.dewcommunity.org/resources.html.
+The thermodynamic parameters for species were taken from the May 2017 and January 2019 versions of the DEW spreadsheet.
 The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)<sub>3</sub>, Br<sup>-</sup>, Ca<sup>+2</sup>, Cl<sup>-</sup>, Cs<sup>+</sup>, F<sup>-</sup>, H<sup>+</sup>, H<sub>2</sub>, He, I<sup>-</sup>, K<sup>+</sup>, Kr, Li<sup>+</sup>, Mg<sup>+2</sup>, Na<sup>+</sup>, Ne, O<sub>2</sub>, Rb<sup>+</sup>, Rn, SO<sub>4</sub><sup>-2</sup>.
 
 Besides using `add.OBIGT("DEW")` to load these data, you should also run `water("DEW")` to activate the DEW equations in CHNOSZ.

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