[CHNOSZ-commits] r315 - in pkg/CHNOSZ: . inst

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2018-04-11 16:43:37 +0200 (Wed, 11 Apr 2018)
New Revision: 315

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/CITATION
Log:
update DESCRIPTION and CITATION


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2018-04-08 12:30:45 UTC (rev 314)
+++ pkg/CHNOSZ/DESCRIPTION	2018-04-11 14:43:37 UTC (rev 315)
@@ -1,6 +1,6 @@
-Date: 2018-04-08
+Date: 2018-04-11
 Package: CHNOSZ
-Version: 1.1.3-22
+Version: 1.1.3-23
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -14,15 +14,20 @@
 Depends: R (>= 3.1.0)
 Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
 Imports: grDevices, graphics, stats, utils
-Description: An integrated set of tools for thermodynamic calculations in geochemistry and
-  compositional biology. Thermodynamic properties are taken from a database for minerals
-  and inorganic and organic aqueous species including biomolecules, or from amino acid
-  group additivity for proteins. High-temperature properties are calculated using the
-  revised Helgeson-Kirkham-Flowers equations of state for aqueous species, and activity
-  coefficients can be calculated for specified ionic strength. Functions are
-  provided to define a system using basis species, automatically balance reactions,
-  calculate the chemical affinities of formation reactions for selected species, calculate
-  equilibrium activities, and plot the results on chemical activity diagrams.
+Description: An integrated set of tools for thermodynamic calculations in geochemistry and compositional
+  biology. Thermodynamic properties are taken from a database for minerals and inorganic and
+  organic aqueous species including biomolecules, or from amino acid group additivity for proteins
+  (Dick et al., 2006 <doi:10.5194/bg-3-311-2006>). High-temperature properties are calculated
+  using the Berman-Brown (1985) <doi:10.1007/BF00379451> equations for minerals and the
+  revised Helgeson-Kirkham-Flowers (1981) <doi:10.2475/ajs.281.10.1249> equations of state for
+  aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model
+  (Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the
+  extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>)
+  to calculate standard-state properties and activity coefficients for given ionic strength at high
+  pressure (to 60 kb). Functions are provided to define a system using basis species, automatically
+  balance reactions, calculate the chemical affinities of formation reactions for selected species,
+  calculate equilibrium activities, and plot the results on chemical activity diagrams.
+Encoding: UTF-8
 License: GPL (>= 2)
 BuildResaveData: no
 VignetteBuilder: knitr

Modified: pkg/CHNOSZ/inst/CITATION
===================================================================
--- pkg/CHNOSZ/inst/CITATION	2018-04-08 12:30:45 UTC (rev 314)
+++ pkg/CHNOSZ/inst/CITATION	2018-04-11 14:43:37 UTC (rev 315)
@@ -1,6 +1,4 @@
-citHeader("To cite CHNOSZ in publications use:")
-
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
          title = "Calculation of the relative metastabilities of proteins using the CHNOSZ software package",
          author = person(given = c("Jeffrey", "M."), family = "Dick", email="jmdick at asu.edu"),
          journal = "Geochemical Transactions",
@@ -8,12 +6,5 @@
          volume = "9",
          number = "10",
          pages = "",
-	 month = "October",
          doi = "10.1186/1467-4866-9-10",
-         textVersion =   
-         paste("Dick, J. M. (2008). ",
-               "Calculation of the relative metastabilities of proteins using the CHNOSZ software package. ",
-               "Geochemical Transactions, Vol. 9 Art. 10.",sep="")
 	 )
-
-citFooter("See",sQuote("citation()"),"for citing R itself.")