[CHNOSZ-commits] r374 - in pkg/CHNOSZ: . man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 27 09:31:43 CET 2019
Author: jedick
Date: 2019-01-27 09:31:35 +0100 (Sun, 27 Jan 2019)
New Revision: 374
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/tests/testthat/test-equilibrate.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
remove broken links to geopig and g3data websites
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/DESCRIPTION 2019-01-27 08:31:35 UTC (rev 374)
@@ -1,7 +1,7 @@
Date: 2019-01-27
Package: CHNOSZ
-Version: 1.1.3-81
-Title: Thermodynamic Calculations and Diagrams for Geo(bio)chemistry
+Version: 1.1.3-82
+Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0687-5890")),
Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/man/data.Rd 2019-01-27 08:31:35 UTC (rev 374)
@@ -243,7 +243,7 @@
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\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
-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/?q=tools}.
+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; moved to http://geopig.asu.edu/?q=tools.
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{https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf}
}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/man/extdata.Rd 2019-01-27 08:31:35 UTC (rev 374)
@@ -39,7 +39,7 @@
\item \code{PM90.csv} Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in \degC is in the first column, and heat capacities of the proteins in J mol\eqn{^{-1}}{^-1} K\eqn{^{-1}}{^-1} in the remaining columns. See \code{\link{ionize.aa}} and the vignette \code{anintro.Rmd} for examples that uses this file.
\item \code{RH95.csv} Heat capacity data for iron taken from Robie and Hemingway, 1995. Temperature in Kelvin is in the first column, heat capacity in J K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1} in the second. See \code{\link{subcrt}} for an example that uses this file.
\item \code{RT71.csv} pH titration measurements for unfolded lysozyme (\samp{LYSC_CHICK}) taken from Roxby and Tanford, 1971. pH is in the first column, net charge in the second. See \code{\link{ionize.aa}} for an example that uses this file.
- \item \code{SOJSH.csv} Experimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. Data were extracted from the figure using g3data (\url{http://www.frantz.fi/software/g3data.php}). See \code{demo("NaCl")} for an example that uses this file.
+ \item \code{SOJSH.csv} Experimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. See \code{demo("NaCl")} for an example that uses this file.
\item \code{Cp.CH4.HW97.csv}, \code{V.CH4.HWM96.csv} Apparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hnědkovský and Wood, 1997 and Hnědkovský et al., 1996. See \code{\link{EOSregress}} and the vignette \code{eos-regress.Rmd} for examples that use these files.
\item \code{SC10_Rainbow.csv} Values of temperature (\degC, pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. See the vignette \code{anintro.Rmd} for an example that uses this file.
\item \code{SS98_Fig5a.csv}, \code{SS98_Fig5b.csv} Values of logarithm of fugacity of \O2 and pH as a function of temperature for mixing of seawater and hydrothermal fluid, digitized from Figs. 5a and b of Shock and Schulte, 1998. See the vignette \code{anintro.Rmd} for an example that uses this file.
Modified: pkg/CHNOSZ/tests/testthat/test-equilibrate.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-equilibrate.R 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/tests/testthat/test-equilibrate.R 2019-01-27 08:31:35 UTC (rev 374)
@@ -62,7 +62,7 @@
# we name them here because S5O6-2 isn't on the plot at logfO2=-30,
# and to get them in order
species.ref <- c("S3O6-2", "S2O6-2", "S2O4-2", "S3-2", "S2-2", "S2O3-2", "HSO3-", "SO2", "HSO4-", "H2S")
- # these values were read from the plot using g3data (http://www.frantz.fi/software/g3data.php)
+ # these values were read from the plot using g3data
loga.ref <- c(-28.82, -24.70, -22.10, -14.19, -12.12, -11.86, -8.40, -7.40, -6.54, -1.95)
# set up the system - see ?diagram for an example showing the entire plot
basis("CHNOS+")
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2019-01-27 08:31:35 UTC (rev 374)
@@ -2057,7 +2057,6 @@
Without additional information, there is often no clear strategy for "fixing" these entries, and they are provided as is.
```{marginfigure}
-See the [Numerical Tools from GEOPIG](http://geopig.asu.edu/?q=tools) for SUPCRT updates (slop files), including corrections that have not yet been ported to CHNOSZ.
```
## Water: SUPCRT92 or IAPWS-95 or DEW
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2019-01-27 06:23:19 UTC (rev 373)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2019-01-27 08:31:35 UTC (rev 374)
@@ -626,9 +626,8 @@
@Misc{SLOP98,
author = {slop98.dat},
title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
- howpublished = {Last updated on 1998-08-20. Accessed on 2017-03-01.},
+ howpublished = {Last updated on 1998-08-20. Accessed from http://geopig.asu.edu/?q=tools on 2017-03-01.},
year = {1998},
- url = {http://geopig.asu.edu/?q=tools},
}
@Article{SH88,
@@ -907,17 +906,15 @@
@Misc{SLOP07,
author = {slop07.dat},
title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
- howpublished = {Last updated on 2008-04-17. Accessed on 2017-03-02.},
+ howpublished = {Last updated on 2008-04-17. Accessed from http://geopig.asu.edu/?q=tools on 2017-03-02.},
year = {2007},
- url = {http://geopig.asu.edu/?q=tools},
}
@Misc{SLOP15,
author = {slop15.dat},
title = {{S}equential-access thermodynamic datafile used by {PROGRAM} supcrt92},
- howpublished = {Last updated on 2015-03-03. Accessed on 2017-03-03.},
+ howpublished = {Last updated on 2015-03-03. Accessed from http://geopig.asu.edu/?q=tools on 2017-03-03.},
year = {2015},
- url = {http://geopig.asu.edu/?q=tools},
}
@Article{MS99,
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