[CHNOSZ-commits] r619 - in pkg/CHNOSZ: . inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 10 08:30:32 CET 2020
Author: jedick
Date: 2020-11-10 08:30:32 +0100 (Tue, 10 Nov 2020)
New Revision: 619
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/man/DEW.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Fix some URLs
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/DESCRIPTION 2020-11-10 07:30:32 UTC (rev 619)
@@ -1,6 +1,6 @@
Date: 2020-11-10
Package: CHNOSZ
-Version: 1.3.6-92
+Version: 1.3.6-93
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/inst/CHECKLIST 2020-11-10 07:30:32 UTC (rev 619)
@@ -55,7 +55,8 @@
- vignettes/OBIGT.bib: check correct year and version for CHNOSZ reference
- Documentation links: after installation, run doc/mklinks.sh
- and put the modified anintro.html and OBIGT.html in the package
+ to add links (to Rd files and vignettes) to anintro.html and
+ OBIGT.html (for the website)
***************
R compatibility
Modified: pkg/CHNOSZ/man/DEW.Rd
===================================================================
--- pkg/CHNOSZ/man/DEW.Rd 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/man/DEW.Rd 2020-11-10 07:30:32 UTC (rev 619)
@@ -26,7 +26,7 @@
\details{
The Deep Earth Water (DEW) model, described by Sverjensky et al., 2014, extends the applicability of the revised HKF equations of state to 60 kbar.
-This implementation of DEW is based on the VBA macro code in the May, 2017 version of the DEW spreadsheet downloaded from \url{http://dewcommunity.org/}.
+This implementation of DEW is based on the VBA macro code in the May, 2017 version of the DEW spreadsheet downloaded from \url{http://www.dewcommunity.org/}.
The spreadsheet provides multiple options for some calculations; here the default equations for density of water (Zhang and Duan, 2005), dielectric constant (Sverjensky et al., 2014) and Gibbs energy of water (integral of volume, equation created by Brandon Harrison) are used.
Comments in the original code indicate that \code{calculateGibbsOfWater} is valid for 100 \le \T \le 1000 \degC and \P \ge 1000 bar.
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/man/examples.Rd 2020-11-10 07:30:32 UTC (rev 619)
@@ -89,7 +89,7 @@
Akinfiev, N. N. and Tagirov, B. R. (2014) Zn in hydrothermal systems: Thermodynamic description of hydroxide, chloride, and hydrosulfide complexes. \emph{Geochem. Int.} \bold{52}, 197--214. \url{https://doi.org/10.1134/S0016702914030021}
-Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. \emph{Geochem. Int.} \bold{39}, 990--1006. \url{https://pleiades.online/cgi-perl/search.pl/?type=abstract&name=geochem&number=10&year=1&page=990}
+Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. \emph{Geochem. Int.} \bold{39}, 990--1006.
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}
Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/man/util.fasta.Rd 2020-11-10 07:30:32 UTC (rev 619)
@@ -48,7 +48,7 @@
\code{start} and/or \code{stop} can be provided to count a fragment of the sequence (extracted using \code{\link{substr}}).
If only one of \code{start} or \code{stop} is present, the other defaults to 1 (\code{start}) or the length of the sequence (\code{stop}).
-\code{uniprot.aa} returns a data frame of amino acid composition, in the format of \code{thermo()$protein}, retrieved from the protein sequence if it is available from UniProt (\url{https://uniprot.org/}).
+\code{uniprot.aa} returns a data frame of amino acid composition, in the format of \code{thermo()$protein}, retrieved from the protein sequence if it is available from UniProt (\url{https://www.uniprot.org/}).
The \code{protein} argument corresponds to the \samp{Entry name} on the UniProt search pages.
}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2020-11-10 07:30:32 UTC (rev 619)
@@ -117,7 +117,7 @@
# Overview
-This vignette was made for version `r sessionInfo()$otherPkgs$CHNOSZ$Version` of CHNOSZ, a package for the [R software environment](http://r-project.org/).
+This vignette was made for version `r sessionInfo()$otherPkgs$CHNOSZ$Version` of CHNOSZ, a package for the [R software environment](http://www.r-project.org/).
For more information on R, see "[An Introduction to R](https://cran.r-project.org/manuals.html)" and the [contributed documentation](https://cran.r-project.org/other-docs.html) for R.
CHNOSZ has been developed since 2006 as a tool for thermodynamic calculations in geochemistry and compositional biology.
@@ -1791,7 +1791,7 @@
-->
* 2012-06-16 Add "More activity diagrams" (section no longer exists).
* 2015-05-14 Add warning about [internal consistency of thermodynamic data](#thermodynamic-database).
-* 2017-02-15 Completely rewritten; switch from Sweave to [knitr](https://yihui.name/knitr/) ([Tufte style](https://rstudio.github.io/tufte/)).
+* 2017-02-15 Completely rewritten; switch from Sweave to [knitr](https://yihui.org/knitr/) ([Tufte style](https://rstudio.github.io/tufte/)).
* 2019-01-24 Add [section on solubility calculations](#complete-equilibrium-solubility).
View the R Markdown source of this document [on R-Forge](https://r-forge.r-project.org/scm/viewvc.php/pkg/CHNOSZ/vignettes/anintro.Rmd?view=markup&root=chnosz) or in R:
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2020-11-10 06:46:25 UTC (rev 618)
+++ pkg/CHNOSZ/vignettes/vig.bib 2020-11-10 07:30:32 UTC (rev 619)
@@ -11,12 +11,12 @@
}
@Book{Alb03,
- author = {Alberty, Robert A.},
- publisher = {Wiley-Interscience},
- title = {{T}hermodynamics of {B}iochemical {R}eactions},
- year = {2003},
- address = {Hoboken, New Jersey},
- url = {http://www.worldcat.org/oclc/51242181},
+ author = {Alberty, Robert A.},
+ publisher = {Wiley-Interscience},
+ title = {{T}hermodynamics of {B}iochemical {R}eactions},
+ year = {2003},
+ address = {Hoboken, New Jersey},
+ url = {https://www.worldcat.org/oclc/51242181},
}
@Article{AH00,
@@ -50,7 +50,7 @@
year = {1984},
address = {Heidelberg},
pages = {397},
- url = {http://www.worldcat.org/oclc/11133620},
+ url = {https://www.worldcat.org/oclc/11133620},
}
@Article{DLE64,
@@ -150,12 +150,12 @@
}
@Book{GC65,
- author = {Garrels, Robert M. and Christ, Charles L.},
- publisher = {Harper \& Row},
- title = {{S}olutions, {M}inerals, and {E}quilibria},
- year = {1965},
- address = {New York},
- url = {http://www.worldcat.org/oclc/517586},
+ author = {Garrels, Robert M. and Christ, Charles L.},
+ publisher = {Harper \& Row},
+ title = {{S}olutions, {M}inerals, and {E}quilibria},
+ year = {1965},
+ address = {New York},
+ url = {https://www.worldcat.org/oclc/517586},
}
@Article{GHB_03,
@@ -169,7 +169,7 @@
doi = {10.1038/nature02046},
}
- at Incollection{Hel70c,
+ at InCollection{Hel70c,
author = {Helgeson, Harold C.},
booktitle = {Fiftieth Anniversary Symposia},
publisher = {Mineralogical Society of America},
@@ -176,21 +176,21 @@
title = {A chemical and thermodynamic model of ore deposition in hydrothermal systems},
year = {1970},
editor = {Morgan, Benjamin A.},
+ pages = {155--186},
+ series = {Mineralogical Society of America, Special Paper},
volume = {3},
- series = {Mineralogical Society of America, Special Paper},
- pages = {155--186},
- url = {http://www.worldcat.org/oclc/583263},
+ url = {https://www.worldcat.org/oclc/583263},
}
@Article{Hel69,
- author = {Helgeson, Harold C.},
- journal = {American Journal of Science},
- title = {{T}hermodynamics of hydrothermal systems at elevated temperatures and pressures},
- year = {1969},
- volume = {267},
- number = {7},
- pages = {729--804},
- doi = {10.2475/ajs.267.7.729},
+ author = {Helgeson, Harold C.},
+ journal = {American Journal of Science},
+ title = {{T}hermodynamics of hydrothermal systems at elevated temperatures and pressures},
+ year = {1969},
+ number = {7},
+ pages = {729--804},
+ volume = {267},
+ doi = {10.2475/ajs.267.7.729},
}
@Article{Hel70a,
@@ -211,7 +211,7 @@
year = {1969},
address = {San Francisco},
pages = {253},
- url = {http://www.worldcat.org/oclc/902423149},
+ url = {https://www.worldcat.org/oclc/902423149},
}
@Article{HDNB78,
@@ -221,7 +221,7 @@
year = {1978},
pages = {1--229},
volume = {278A},
- url = {http://www.worldcat.org/oclc/13594862},
+ url = {https://www.worldcat.org/oclc/13594862},
}
@Article{HKF81,
@@ -295,12 +295,10 @@
journal = {Geochimica et Cosmochimica Acta},
title = {{S}peciation and thermodynamic properties for cobalt chloride complexes in hydrothermal fluids at 35--440 °{C} and 600 bar: {A}n \emph{in-situ} {XAS} study},
year = {2011},
- volume = {75},
number = {5},
pages = {1227--1248},
+ volume = {75},
doi = {10.1016/j.gca.2010.12.002},
- sn = {0016-7037},
- z9 = {2},
}
@Article{MSS13,
@@ -327,14 +325,14 @@
@InProceedings{NPW_79,
author = {Nordstrom, D. K. and Plummer, L. N. and Wigley, T. M. L. and Wolery, T. J. and Ball, J. W. and Jenne, E. A. and Bassett, R. L. and Crerar, D. A. and Florence, T. M. and Fritz, B. and Hoffman, M. and Holdren, G. R., Jr. and Lafon, G. M. and Mattigod, S. V. and McDuff, R. E. and Morel, F. and Reddy, M. M. and Sposito, G. and Thrailkill, J.},
+ booktitle = {Chemical Modeling in Aqueous Systems: Speciation, Sorption, Solubility, and Kinetics},
title = {A comparison of computerized chemical models for equilibrium calculations in aqueous systems},
- booktitle = {Chemical Modeling in Aqueous Systems: Speciation, Sorption, Solubility, and Kinetics},
year = {1979},
editor = {Jenne, E. A.},
- series = {Series 93},
pages = {857--892},
publisher = {American Chemical Society},
- url = {http://www.worldcat.org/oclc/4591313},
+ series = {Series 93},
+ url = {https://www.worldcat.org/oclc/4591313},
}
@Article{Oth76,
@@ -378,7 +376,7 @@
year = {1949},
address = {London},
pages = {136},
- url = {http://www.worldcat.org/oclc/1356445},
+ url = {https://www.worldcat.org/oclc/1356445},
}
@Article{PM90,
@@ -438,14 +436,14 @@
}
@Article{SSW01,
- author = {Schulte, Mitchell D. and Shock, Everett L. and Wood, Robert H.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{T}he temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes},
- year = {2001},
- volume = {65},
- number = {21},
- pages = {3919--3930},
- doi = {10.1016/S0016-7037(01)00717-7},
+ author = {Schulte, Mitchell D. and Shock, Everett L. and Wood, Robert H.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{T}he temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes},
+ year = {2001},
+ number = {21},
+ pages = {3919--3930},
+ volume = {65},
+ doi = {10.1016/S0016-7037(01)00717-7},
}
@Article{See96,
@@ -596,7 +594,7 @@
@Article{WEP_82,
author = {Wagman, Donald D. and Evans, William H. and Parker, Vivian B. and Schumm, Richard H. and Halow, Iva and Bailey, Sylvia M. and Churney, Kenneth L. and Nuttall, Ralph L.},
journal = {Journal of Physical and Chemical Reference Data},
- title = {{T}he {NBS} tables of chemical thermodynamic properties. {S}elected values for inorganic and {C}$_1$ and {C}$_2$ organic substances in {SI} units},
+ title = {{T}he {NBS} tables of chemical thermodynamic properties. {S}elected values for inorganic and {C}\textsubscript{1} and {C}\textsubscript{2} organic substances in {SI} units},
year = {1982},
number = {Suppl. 2},
pages = {1--392},
@@ -644,7 +642,7 @@
year = {1989},
address = {New York},
pages = {271},
- url = {http://www.worldcat.org/oclc/18559968},
+ url = {https://www.worldcat.org/oclc/18559968},
}
@Article{HW97,
@@ -894,12 +892,10 @@
pages = {56--72},
volume = {3},
doi = {10.1186/1467-4866-3-56},
- sn = {1467-4866},
- z9 = {6},
}
@Article{BBR77,
- author = {Barton, Jr., Paul B., and Bethke, Phillip M. and Roedder, Edwin},
+ author = {Barton, Jr., Paul B. and Bethke, Phillip M. and Roedder, Edwin},
journal = {Economic Geology},
title = {Environment of ore deposition in the {C}reede mining district, {S}an {J}uan {M}ountains, {C}olorado: {P}art {III}. {P}rogress toward interpretation of the chemistry of the ore-forming fluid for the {OH} {V}ein},
year = {1977},
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