[CHNOSZ-commits] r249 - in pkg/CHNOSZ: . data demo inst inst/extdata/OBIGT man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Oct 9 17:16:40 CEST 2017 

Author: jedick
Date: 2017-10-09 17:16:40 +0200 (Mon, 09 Oct 2017)
New Revision: 249

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/demo/adenine.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/obigt.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
use Lowe et al., 2017 parameters for adenine


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-09 15:16:40 UTC (rev 249)
@@ -1,6 +1,6 @@
 Date: 2017-10-09
 Package: CHNOSZ
-Version: 1.1.0-47
+Version: 1.1.0-48
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/data/refs.csv	2017-10-09 15:16:40 UTC (rev 249)
@@ -88,7 +88,7 @@
 HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013
 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
 LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010
-LH06a.2,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","adenine GHS",https://doi.org/10.1016/j.gca.2006.04.010
+LH06a.2,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","adenine-old, HKF parameters superseded by @LCT17",https://doi.org/10.1016/j.gca.2006.04.010
 LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",https://doi.org/10.1016/j.tca.2006.06.008
 LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",https://doi.org/10.1016/j.tca.2006.06.008
 DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006
@@ -134,7 +134,7 @@
 CHNOSZ.6,"J. M. Dick",2017,"CHNOSZ package documentation","dipeptides not included in slop files after slop98.dat",http://chnosz.net
 CHNOSZ.7,"J. M. Dick",2017,"CHNOSZ package documentation","charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99",http://chnosz.net
 CHNOSZ.8,"J. M. Dick",2017,"CHNOSZ package documentation","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
-LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine Cp and V",https://doi.org/10.1016/j.jct.2017.04.005
+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,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","other data from Aqueous Species Table in spreadsheet (see detailed references there)",http://www.dewcommunity.org
 DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for ions",http://www.dewcommunity.org
 DEW17.2,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for cations",http://www.dewcommunity.org

Modified: pkg/CHNOSZ/demo/adenine.R
===================================================================
--- pkg/CHNOSZ/demo/adenine.R	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/demo/adenine.R	2017-10-09 15:16:40 UTC (rev 249)
@@ -57,7 +57,10 @@
 # error bars (arrows trick from https://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars)
 arrows(AdH$T, AdH$Cp - AdH$Cp_SD, AdH$T, AdH$Cp + AdH$Cp_SD, length = 0.05, angle = 90, code = 3)
 # get LH06 predictions using HKF model
-LH06 <- subcrt("adenine", T = TK)$out$adenine
+# this version of adenine parameters has been superseded by LCT17
+# but are still available as optional data
+add.obigt("CHNOSZ", "adenine-old")
+LH06 <- subcrt("adenine-old", T = TK)$out$adenine
 lines(TK, LH06$Cp, lty = 3)
 # density model (parameters from LCT17 Table 11)
 lines(TK, Cpfun(160.4, -653239, -7930.3, TK), lty = 2)
@@ -104,9 +107,7 @@
 lines(TK, LH06$V, lty = 3)
 # density model with coefficients from LCT17
 lines(TK, Vfun(73.9, -917.0, -7930.3, TK), lty = 2)
-# load HKF coefficients for adenine reported by LCT17
-# note that the Cp coefficients here are very close to those regressed above!
-add.obigt("CHNOSZ_aq", "adenine")
+# HKF heat capacity coefficients from LCT17
 LCT17 <- subcrt("adenine", T = TK)$out$adenine
 lines(TK, LCT17$V, lwd = 2, col = "royalblue")
 legend("bottomright", lty = c(3, 2, 1), lwd = c(1, 1, 2), col = c("black", "black", "royalblue"), bty = "n",

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-09 15:16:40 UTC (rev 249)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-45 (2017-10-08)
+CHANGES IN CHNOSZ 1.1.0-48 (2017-10-09)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -75,10 +75,13 @@
   minerals from the Helgeson data. The parameters themselves are
   stored in extdata/Berman/*.csv.
 
+- Update HKF parameters of adenine based on experimental heat capacity
+  and volume data (Lowe et al., 2017). Add demo/adenine.R comparing
+  the updates with the previous data (LaRowe and Helgeson, 2006).
+
 - Data file CHNOSZ_aq.csv is no longer added to the database by default.
-  It is now intended to hold provisional updates. Updated heat capacity
-  and volume HKF parameters for adenine (Lowe et al., 2017) have been
-  added to this file.
+  It is now intended to hold optional data. Currently it contains
+  pseudo-H4SiO4 and adenine-old.
 
 - Remove H2O(gas) from the database (taken from SUPCRT92), as it gives
   inconsistent results for metastable steam (Zavarin et al., 2016,

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv	2017-10-09 15:16:40 UTC (rev 249)
@@ -1,3 +1,3 @@
 name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
 pseudo-H4SiO4,NA,H4SiO4,aq,CHNOSZ.4,NA,18.Feb.17,-312565,-346409,51.4246,-40.0964,52.1998,89.2031,-176.5071,-452.1431,101.36051,67.0854,-52.0776,0.1215745,0
-adenine,NA,C5H5N5,aq,LCT17,LH06a.2,26.Jul.17,74770,31235,53.41,51.63,90.6,23.53,0,-17.75,0,48.54,-3.318,-1.093,0
+adenine-old,NA,C5H5N5,aq,LH06a.2,NA,03.Mar.17,74770,31235,53.41,56.24,89.59,21.5046,8.501,-2.6632,-5.3561,87.88,-15.87,0.065,0

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2017-10-09 15:16:40 UTC (rev 249)
@@ -1,4 +1,4 @@
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\ No newline at end of file

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2017-10-09 03:14:34 UTC (rev 248)
+++ pkg/CHNOSZ/man/examples.Rd	2017-10-09 15:16:40 UTC (rev 249)
@@ -31,32 +31,33 @@
 \code{demos} is a function to run other examples that are provided as \code{\link{demo}s}.
 \code{\link{demo}} is called with settings to not echo the source code and to not ask before making each plot.
 The demo(s) to run is/are specified by \code{which}; the default is to run them in the order of the list below.
+Demos that are displayed on the CHNOSZ website (\url{http://chnosz.net/demos}) are indicated with an asterisk.
 See the comments in the source code for more information about each demo.
 
   \tabular{ll}{
     \code{sources} \tab cross-check the reference list with the thermodynamic database \cr
     \code{protein.equil} \tab chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011) \cr
-    \code{affinity} \tab affinities of metabolic reactions and amino acid synthesis \cr
-    \code{NaCl} \tab equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
-    \code{density} \tab density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
-    \code{ORP} \tab temperature dependence of oxidation-reduction potential for redox standards \cr
-    \code{revisit} \tab coefficient of variation of metastable equilibrium activities of proteins \cr
-    \code{findit} \tab minimize the standard deviation of logarithms of activities of sulfur species \cr
+    \code{affinity} \tab affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001) \cr
+    \code{NaCl} \tab * equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
+    \code{density} \tab * density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
+    \code{ORP} \tab * temperature dependence of oxidation-reduction potential for redox standards \cr
+    \code{revisit} \tab * coefficient of variation of metastable equilibrium activities of proteins \cr
+    \code{findit} \tab * minimize the standard deviation of logarithms of activities of sulfur species \cr
     \code{ionize} \tab ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK \cr
-    \code{buffer} \tab  minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
+    \code{buffer} \tab  * minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
     \code{protbuff} \tab chemical activities buffered by thiol peroxidases or sigma factors \cr
-    \code{yeastgfp} \tab subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams (Dick, 2009) \cr
-    \code{mosaic} \tab Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
-    \code{copper} \tab another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
-    \code{solubility} \tab solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996) \cr
-    \code{wjd} \tab Gibbs energy minimization: prebiological atmospheres and cell periphery of yeast \cr
-    \code{dehydration} \tab log K of dehydration reactions; SVG file contains tooltips and links \cr
-    \code{bugstab} \tab formation potential of microbial proteins in colorectal cancer (Dick, 2016) \cr
-    \code{Shh} \tab affinities of transcription factors relative to Sonic hedgehog \cr
-    \code{activity_ratios} \tab mineral stability plots with activity ratios on the axes \cr
-    \code{adenine} \tab HKF parameters regressed from heat capacity and volume of aqueous adenine (Lowe et al., 2017) \cr
-    \code{adenine} \tab Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b) \cr
-    \code{lambda} \tab Effects of lambda transtion on thermodynamic properties of quartz (Berman, 1988) \cr
+    \code{yeastgfp} \tab * subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams (Dick, 2009) \cr
+    \code{mosaic} \tab * Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
+    \code{copper} \tab * another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
+    \code{solubility} \tab * solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996) \cr
+    \code{wjd} \tab * Gibbs energy minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast \cr
+    \code{dehydration} \tab * log K of dehydration reactions; SVG file contains tooltips and links \cr
+    \code{bugstab} \tab * formation potential of microbial proteins in colorectal cancer (Dick, 2016) \cr
+    \code{Shh} \tab * affinities of transcription factors relative to Sonic hedgehog (Dick, 2015) \cr
+    \code{activity_ratios} \tab * mineral stability plots with activity ratios on the axes \cr
+    \code{adenine} \tab * HKF parameters regressed from heat capacity and volume of aqueous adenine (Lowe et al., 2017) \cr
+    \code{DEW} \tab * Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b) \cr
+    \code{lambda} \tab * Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988) \cr
   }
 
 }
@@ -64,12 +65,20 @@
 \references{
 Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57. \url{https://doi.org/10.1149/1.1344532}
 
+Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. \emph{Science} \bold{281}, 1659--1662. \url{https://doi.org/10.1126/science.281.5383.1659}
+
[TRUNCATED]

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    svnlook diff /svnroot/chnosz -r 249

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