[CHNOSZ-commits] r283 - in pkg/CHNOSZ: . data demo

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Nov 9 12:47:07 CET 2017 

Author: jedick
Date: 2017-11-09 12:47:07 +0100 (Thu, 09 Nov 2017)
New Revision: 283

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/demo/sources.R
Log:
clean up data/refs.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-11-09 07:43:29 UTC (rev 282)
+++ pkg/CHNOSZ/DESCRIPTION	2017-11-09 11:47:07 UTC (rev 283)
@@ -1,6 +1,6 @@
-Date: 2017-11-08
+Date: 2017-11-09
 Package: CHNOSZ
-Version: 1.1.0-80
+Version: 1.1.0-81
 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	2017-11-09 07:43:29 UTC (rev 282)
+++ pkg/CHNOSZ/data/refs.csv	2017-11-09 11:47:07 UTC (rev 283)
@@ -99,7 +99,6 @@
 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 Acta 70, 4680-4724","adenine-old, HKF parameters superseded by @LCT17",https://doi.org/10.1016/j.gca.2006.04.010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
@@ -154,40 +153,8 @@
 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
 DEW17.3,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for complex species",http://www.dewcommunity.org
-DEW17.4,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","with revised a1 equal to the sum of the ions",http://www.dewcommunity.org
-DEW17.5,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","BaCl+, CaCl+, CaCl2: with new V from the sum of a1 values of ions",http://www.dewcommunity.org
-DEW17.6,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions",http://www.dewcommunity.org
 DEW17.7,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","acetate: revised January 26th, 2016; new a1 value from complexes and organics correlation.",http://www.dewcommunity.org
-DEW17.10,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","CaSO4: revised using exptl V and pred. a1 from new correlation",http://www.dewcommunity.org
-DEW17.11,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","diglycine: Jamie & Dimitri fit to exptl Cp(T) and pred. a1-a4; delGf and S from fitting logK dimerisation values from Lemke et al. (2009).",http://www.dewcommunity.org
-DEW17.12,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","diketopiperazine: Jamie & Dimitri fit delGf and S from to logK dimerisation values from Lemke et al. (2009);  pred. a1-a4;",http://www.dewcommunity.org
-DEW17.13,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","FeOH+, FeO, HFeO2-: 31/1/17: V from estimate to have similar behavior to MgO,aq",http://www.dewcommunity.org
-DEW17.14,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","FeCl+2: 29/11/16: Fit to Tagirov et al. (2000) with revised volume increased in order that a1 of the complex a bit greater than the sum of the a1 values of the ions",http://www.dewcommunity.org
-DEW17.15,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","FeCl2+, FeCl4-: 29/11/16: Fit to Liu et al. (2006) with revised volume increased in order that a1 of the complex a bit greater than the sum of the a1 values of the ions",http://www.dewcommunity.org
-DEW17.16,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","FeCl3: 29/11/16: Fit to Liu et al. (2006) with revised volume increased in order that a1 of the complex is equal to the sum of the a1 values of the ions",http://www.dewcommunity.org
-DEW17.17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","glutamate: Revised 1/22/15 based on V at 25 C from Ziemer & Woolley (2007) and predicted a1, a2, and a4; c1 and c2 from fits to delCpr protonation of Ziemer & Woolley (2007); S from fitting temperature dependence of logK from Ziemer & Woolley (2007); omega predicted from S using ion correlation.",http://www.dewcommunity.org
-DEW17.18,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","glutamic acid: Revised 1/22/15 based on fitting Cp and V vs T data from Hakin et al. (1994) + revised correlation for a1 from Sverjensky et al. (2014); omega from delCPr above 100 °C (Ziemer & Woolley, 2007); G, H, and S from Amend & Helgeson (1997).",http://www.dewcommunity.org
-DEW17.19,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","HCl: Regression of Ruaya & Seward (1987) & Tagirov et al. (1997) with new full correlations",http://www.dewcommunity.org
-DEW17.20,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","HSiO3-: Revised late Oct. (2014) to fit Baes and Mesmer (1977) along Psat. and high pressure logK's from fitting Kessel et al. (2005) eclogite solubility measurements.",http://www.dewcommunity.org
-DEW17.21,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","HSO3-: revised using published estimated V and pred. a1 from new correlation",http://www.dewcommunity.org
-DEW17.22,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","isobutane: G, H, S, Cp, V from Shock & Helgeson (1990); a1 estimated with Sverjensky et al. (2014); c2 estimated with a new hydrocarbon correlation.",http://www.dewcommunity.org
-DEW17.23,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","KCl: May, 2017 Fitted to logKs from Oelkers & Helgeson (1988) + retrieved logKs from Hemley experiments at 1.0 kb using the HCl referred to above",http://www.dewcommunity.org
-DEW17.25,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","KSO4-: Revised G, S and Cp to fit Noyes et al. (1906) & Sharygin et al. (2006) with a1 of the complex equal to the sum of the a1 values of the ions",http://www.dewcommunity.org
-DEW17.26,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Mg(HCO3)+: Fit to Stefansson et al. (2014) & Siebert & Hostetler (1977); plus revised V increased so that a1 of the complex is the sum of the a1 values of the ions",http://www.dewcommunity.org
-DEW17.27,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgCO3: Sverjensky et al. (1997) revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions; and Cp revised using isocoulombic reln with CaCO3,aq; also omega is set to +0.3 as for all neutral metal complexes.",http://www.dewcommunity.org
-DEW17.28,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgOH+: Revised by Dimitri, March, 2015",http://www.dewcommunity.org
-DEW17.29,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgSO4: S, Cp, V, omega from fit to Akilan et al. (2006a) and Frantz et al. (1994)",http://www.dewcommunity.org
-DEW17.30,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaCO3-: Fit to Stefansson et al. (2013; 80 to 200 C) & Garrels et al., (1961; at 25 C) to get G, S and Cp;  with a1 pred. from the sum of the ions and used to predict the volume",http://www.dewcommunity.org
-DEW17.31,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaHCO3: Fit to Stefansson et al. (2013; 80 to 200 C) & Nakayama (1971; at 25 C) to get G, S and Cp;  with V, a1, and omega from fitting high PT Raman data (Facq et al., 2015)",http://www.dewcommunity.org
-DEW17.32,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaOH: Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume",http://www.dewcommunity.org
-DEW17.33,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","OH-: August 16th, 2013 fit to Bandura & Lvov (2005)",http://www.dewcommunity.org
-DEW17.34,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propane: Shock & Helgeson (1990) with new a1-a4 based on revised correlation to predict a1 in Sverjensky et al. (2013)",http://www.dewcommunity.org
-DEW17.36,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","S3-: Regression of data from Pokrovski & Dubessy (2015), Guggenheim (1971); Feb. 2015",http://www.dewcommunity.org
-DEW17.38,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","SO2: Shock et al. (1989) with revised a1 predicted as a complex from delVn",http://www.dewcommunity.org
-DEW17.39,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","toluene: Plyasunov & Shock (2001) with new a1 to a4 predicted with revised a1 consistent with Sverjensky et al. (2013)",http://www.dewcommunity.org
-DEW17.40,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","urea: Revised Feb. 2015 by Dimitri: c1, c2, and omega from PS01 based on Stokes (1967) data; V from Cabani et al. (1981) with a1-a4 predicted.",http://www.dewcommunity.org
 DEW17.101,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","methane: revised with new predicted a1 for complex species",http://www.dewcommunity.org
 DEW17.102,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgCl<sup>+</sup>: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions",http://www.dewcommunity.org
 DEW17.103,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaCl: revised with new predicted a1 for complex species",http://www.dewcommunity.org

Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R	2017-11-09 07:43:29 UTC (rev 282)
+++ pkg/CHNOSZ/demo/sources.R	2017-11-09 11:47:07 UTC (rev 283)
@@ -3,10 +3,18 @@
 ref.source <- thermo$refs$key
 # sources in the primary thermodynamic database
 # we omit the [S92] in "HDNB78 [S92]" etc.
-os1 <- gsub("\ .*", "", thermo$obigt$ref1)
-os2 <- gsub("\ .*", "", thermo$obigt$ref2)
+tdata <- get("thermo")$obigt
+ps1 <- gsub("\ .*", "", tdata$ref1)
+ps2 <- gsub("\ .*", "", tdata$ref2)
+# sources in the optional datafiles
+tdata <- read.csv(system.file("extdata/OBIGT/DEW_aq.csv", package="CHNOSZ"), as.is=TRUE)
+os1 <- gsub("\ .*", "", tdata$ref1)
+os2 <- gsub("\ .*", "", tdata$ref2)
+tdata <- read.csv(system.file("extdata/OBIGT/SUPCRTBL.csv", package="CHNOSZ"), as.is=TRUE)
+os3 <- gsub("\ .*", "", tdata$ref1)
+os4 <- gsub("\ .*", "", tdata$ref2)
 # all of the thermodynamic data sources - some of them might be NA
-obigt.source <- unique(c(os1,os2))
+obigt.source <- unique(c(ps1, ps2, os1, os2, os3, os4))
 obigt.source <- obigt.source[!is.na(obigt.source)]
 # these all produce character(0) if the sources are all accounted for
 print("missing these sources for thermodynamic properties:")

More information about the CHNOSZ-commits mailing list