[CHNOSZ-commits] r77 - in pkg/CHNOSZ: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 6 02:54:24 CET 2015
Author: jedick
Date: 2015-03-06 02:54:23 +0100 (Fri, 06 Mar 2015)
New Revision: 77
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/water.Rd
Log:
fix some URLs in Rd files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/DESCRIPTION 2015-03-06 01:54:23 UTC (rev 77)
@@ -1,19 +1,19 @@
-Date: 2015-03-01
+Date: 2015-03-06
Package: CHNOSZ
-Version: 1.0.3-14
+Version: 1.0.3-15
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Depends: R (>= 2.12.0)
Suggests: limSolve, parallel, testthat, knitr
-Description: A set of functions and data sets to support chemical thermodynamic
- modeling in biochemistry and low-temperature geochemistry. The features include calculation
- of the standard molal thermodynamic properties and chemical affinities of reactions involving
- minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline
- and gaseous species; amino acid group additivity for the standard molal thermodynamic
- properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers
- equations of state for aqueous species; construction of equilibrium activity diagrams as a
- function of temperature, pressure, and chemical activities or fugacities of basis species.
+Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
+ and low-temperature geochemistry. The features include calculation of the standard molal
+ thermodynamic properties and chemical affinities of reactions involving minerals and/or
+ biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
+ species; amino acid group additivity for the standard molal thermodynamic properties of
+ neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
+ for aqueous species; construction of equilibrium activity diagrams as a function of
+ temperature, pressure, and chemical activities or fugacities of basis species.
License: GPL (>= 2)
BuildResaveData: no
ZipData: no
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/inst/NEWS 2015-03-06 01:54:23 UTC (rev 77)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-14 (2015-03-01)
+CHANGES IN CHNOSZ 1.0.3-15 (2015-03-06)
---------------------------------------
- Add files with average amino acid compositions of proteins from Bison
Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/man/data.Rd 2015-03-06 01:54:23 UTC (rev 77)
@@ -241,7 +241,7 @@
Shock, E. L. et al. {1998} \emph{SLOP98.dat} (computer data file). http://geopig.asu.edu/supcrt92_data/slop98.dat, accessed on 2005-11-05. Current location: \url{http://geopig.asu.edu/sites/default/files/slop98.dat}.
- Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L. (1982) The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C\eqn{_1}{1} and C\eqn{_2}{2} organic substances in SI units. \emph{J. Phys. Chem. Ref. Data} \bold{11} (supp. 2), 1--392. \url{http://www.nist.gov/srd/PDFfiles/jpcrdS2Vol11.pdf}
+ Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L. (1982) The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C\eqn{_1}{1} and C\eqn{_2}{2} organic substances in SI units. \emph{J. Phys. Chem. Ref. Data} \bold{11} (supp. 2), 1--392. \url{http://www.nist.gov/data/PDFfiles/jpcrdS2Vol11.pdf}
}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/man/diagram.Rd 2015-03-06 01:54:23 UTC (rev 77)
@@ -316,7 +316,7 @@
Majzlan, J., Navrotsky, A., McClesky, R. B. and Alpers, C. N. (2006) Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe2(SO4)3(H2O)5. \emph{Eur. J. Mineral.} \bold{18}, 175--186. \url{http://dx.doi.org/10.1127/0935-1221/2006/0018-0175}
- Seewald, J. S. (1997) Mineral redox buffers and the stability of organic compounds under hydrothermal conditions. \emph{Mat. Res. Soc. Symp. Proc.} \bold{432}, 317--331. \url{http://lucy.mrs.org/meetings/spring96/Program/S.S96.html}
+ Seewald, J. S. (1997) Mineral redox buffers and the stability of organic compounds under hydrothermal conditions. \emph{Mat. Res. Soc. Symp. Proc.} \bold{432}, 317--331. \url{http://dx.doi.org/10.1557/PROC-432-317}
Seewald, J. S. (2001) Aqueous geochemistry of low molecular weight hydrocarbons at elevated temperatures and pressures: Constraints from mineral buffered laboratory experiments \emph{Geochim. Cosmochim. Acta} \bold{65}, 1641--1664. \url{http://dx.doi.org/10.1016/S0016-7037(01)00544-0}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/man/extdata.Rd 2015-03-06 01:54:23 UTC (rev 77)
@@ -53,7 +53,7 @@
\item \code{Eco.csv.xz}
Amino acid compositions of 4407 proteins in \emph{Escherichia coli} strain K12.
Format is the one used \code{\link{thermo}$protein}, with columns \samp{protein} holding the gene name, \samp{organism} set to \samp{ECOLI}, and \code{abbrv} holding the UniProt ID.
- The source of data is the file \samp{ECOLI.fas} downloaded from the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes system) FTP site (Gattiker et al., 2003) (\url{ftp://ftp.expasy.org/databases/hamap/complete_proteomes/fasta/bacteria}) on 2010-09-25.
+ The source of data is the file \samp{ECOLI.fas} downloaded from the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes system) FTP site (Gattiker et al., 2003) on 2010-09-25 (old URL: \code{ftp://ftp.expasy.org/databases/hamap/complete_proteomes/fasta/bacteria}) .
}
@@ -109,11 +109,11 @@
Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A. (2003) Automatic annotation of microbial proteomes in Swiss-Prot. \emph{Comput. Biol. Chem.} \bold{27}, 49--58. \url{http://dx.doi.org/10.1016/S1476-9271(02)00094-4}
- Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. \emph{Nature} \bold{425}(6955), 285--288. \url{http://dx.doi.org/10.1038/nature01977}
+ Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. \emph{Nature} \bold{425}(6955), 285--288. \code{http://dx.doi.org/10.1038/nature01977}
- Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. \emph{Nature} \bold{425}(6959), 737--741. \url{http://dx.doi.org/10.1038/nature02046}
+ Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. \emph{Nature} \bold{425}(6959), 737--741. \code{http://dx.doi.org/10.1038/nature02046}
- Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. \emph{Nature} \bold{425}(6959), 686--691. \url{http://dx.doi.org/10.1038/nature02026}
+ Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. \emph{Nature} \bold{425}(6959), 686--691. \code{http://dx.doi.org/10.1038/nature02026}
HAMAP system. HAMAP FTP directory, \url{ftp://ftp.expasy.org/databases/hamap/}
Modified: pkg/CHNOSZ/man/water.Rd
===================================================================
--- pkg/CHNOSZ/man/water.Rd 2015-03-01 17:01:52 UTC (rev 76)
+++ pkg/CHNOSZ/man/water.Rd 2015-03-06 01:54:23 UTC (rev 77)
@@ -159,7 +159,7 @@
\references{
- Archer, D. G. and Wang, P. M. (1990) The dielectric constant of water and Debye-Huckel limiting law slopes. \emph{J. Phys. Chem. Ref. Data} \bold{19}, 371--411. \url{http://www.nist.gov/srd/PDFfiles/jpcrd383.pdf}
+ Archer, D. G. and Wang, P. M. (1990) The dielectric constant of water and Debye-Huckel limiting law slopes. \emph{J. Phys. Chem. Ref. Data} \bold{19}, 371--411. \url{http://www.nist.gov/data/PDFfiles/jpcrd383.pdf}
Haar, L., Gallagher, J. S. and Kell, G. S. (1984) \emph{NBS/NRC Steam Tables}. Hemisphere, Washington, D. C., 320 p. \url{http://www.worldcat.org/oclc/301304139}
@@ -169,7 +169,7 @@
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\eqn{^{\circ}}{°}C. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{http://dx.doi.org/10.1016/0098-3004(92)90029-Q}
- Levelt-Sengers, J. M. H., Kamgarparsi, B., Balfour, F. W. and Sengers, J. V. (1983) Thermodynamic properties of steam in the critical region. \emph{J. Phys. Chem. Ref. Data} \bold{12}, 1--28. \url{http://www.nist.gov/srd/PDFfiles/jpcrd214.pdf}
+ Levelt-Sengers, J. M. H., Kamgarparsi, B., Balfour, F. W. and Sengers, J. V. (1983) Thermodynamic properties of steam in the critical region. \emph{J. Phys. Chem. Ref. Data} \bold{12}, 1--28. \url{http://www.nist.gov/data/PDFfiles/jpcrd214.pdf}
Wagner, W. and Pruss, A. (2002) The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J. Phys. Chem. Ref. Data} \bold{31}, 387--535. \url{http://dx.doi.org/10.1063/1.1461829}
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