[CHNOSZ-commits] r565 - in pkg/CHNOSZ: . R demo inst inst/extdata/OBIGT man man/macros vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jul 16 07:47:38 CEST 2020
Author: jedick
Date: 2020-07-16 07:47:38 +0200 (Thu, 16 Jul 2020)
New Revision: 565
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/saturation.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/duplex.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/macros/macros.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/man/solubility.Rd
pkg/CHNOSZ/man/thermo.Rd
pkg/CHNOSZ/vignettes/mklinks.sh
Log:
Add Rd viglink macro to link to vignettes
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-16 05:47:38 UTC (rev 565)
@@ -1,6 +1,6 @@
Date: 2020-07-16
Package: CHNOSZ
-Version: 1.3.6-38
+Version: 1.3.6-39
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/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/R/examples.R 2020-07-16 05:47:38 UTC (rev 565)
@@ -10,8 +10,11 @@
"util.fasta", "util.formula", "util.matrix", "util.misc", "util.seq", "util.units",
"util.water", "taxonomy", "info", "retrieve", "add.OBIGT", "protein.info",
"hkf", "water", "IAPWS95", "subcrt", "berman",
- "makeup", "basis", "swap.basis", "species", "affinity", "solubility", "equilibrate",
- "diagram", "buffer", "nonideal", "NaCl", "add.protein", "protein", "ionize.aa",
+ "makeup", "basis", "swap.basis", "species", "affinity",
+ "solubility", "equilibrate",
+ "diagram", "mosaic", "duplex",
+ "buffer", "nonideal", "NaCl",
+ "add.protein", "protein", "ionize.aa",
"objective", "revisit", "EOSregress", "wjd")
plot.it <- FALSE
if(is.character(save.png))
Modified: pkg/CHNOSZ/demo/saturation.R
===================================================================
--- pkg/CHNOSZ/demo/saturation.R 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/demo/saturation.R 2020-07-16 05:47:38 UTC (rev 565)
@@ -16,7 +16,7 @@
## Helgeson et al., 1969, p. 136 (http://www.worldcat.org/oclc/902423149)
## Bowers et al., 1984, p. 246 (http://www.worldcat.org/oclc/224591948)
par(cex = 1.4)
-basis(c("H2O", "carbon dioxide", "Ca+2", "Mg+2", "SiO2", "O2", "H+"))
+basis(c("SiO2", "Ca+2", "Mg+2", "carbon dioxide", "H2O", "O2", "H+"))
species(c("quartz", "talc", "chrysotile", "forsterite", "tremolite",
"diopside", "wollastonite", "monticellite", "merwinite"))
# calculate the chemical affinities of formation reactions
@@ -33,5 +33,5 @@
# add title and legend
title(main = syslab(c("H2O", "CO2", "CaO", "MgO", "SiO2")))
dprop <- describe.property(c("T", "P"), c(300, 1000))
-dbasis <- describe.basis(ibasis = 2)
+dbasis <- describe.basis(ibasis = 4)
legend("bottomright", c(dprop, dbasis), bty = "n", cex = 0.9)
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -93,6 +93,9 @@
now in the \samp{bison.Rmd} vignette in the \pkg{JMDplots} package
(\url{https://github.com/jedick/JMDplots}).
+ \item Add \samp{viglink} Rd macro so HTML versions of Rd files can link
+ to vignettes.
+
}
}
@@ -155,13 +158,8 @@
\item TODO: make separate directories for default and optional data files
- \item TODO: demo/saturation.R: put Al+3 first in basis definition (it's
- confusing to have H2O first when the reactions are balanced on Al)
-
\item TODO: diagram(): make error or warning for NA values of affinity
- \item TODO: use https in refs.csv
-
\item TODO: move protein.equil() example (previously in equilibrium.Rnw) to JMDplots.
\item TODO: change add.obigt --> add.OBIGT on website (Fe-O-H-S example) when package is submitted to CRAN.
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2020-07-16 05:47:38 UTC (rev 565)
@@ -1,25 +1,25 @@
key,author,year,citation,note,URL
-Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",http://www.worldcat.org/oclc/693388901
-Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",http://www.worldcat.org/oclc/693388901
-Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",http://www.worldcat.org/oclc/693388901
-Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,http://www.worldcat.org/oclc/14154245
-PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",http://www.worldcat.org/oclc/14154292
-BK73,"I. Barin and O. Knacke",1973,"Thermochemical Properties of Inorganic Substances","scheelite Cp",http://www.worldcat.org/oclc/695258
+Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",https://www.worldcat.org/oclc/693388901
+Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",https://www.worldcat.org/oclc/693388901
+Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901
+Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245
+PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292
+BK73,"I. Barin and O. Knacke",1973,"Thermochemical Properties of Inorganic Substances","scheelite Cp",https://www.worldcat.org/oclc/695258
NRK74,"G. B. Naumov, B. N. Ryzhenko and I. L. Khodakovskii",1974,"Handbook of Thermodynamic Data, U. S. Geological Survey, Water Resources Division",arsenopyrite,https://trove.nla.gov.au/work/22192707
-HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",http://www.worldcat.org/oclc/13594862
-HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",http://www.worldcat.org/oclc/13594862
-HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",http://www.worldcat.org/oclc/13594862
-RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,http://pubs.er.usgs.gov/publication/b1452
-RHF78.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","halloysite",http://pubs.er.usgs.gov/publication/b1452
-RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
-RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",http://pubs.er.usgs.gov/publication/b1452
-RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",http://pubs.er.usgs.gov/publication/b1452
+HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",https://www.worldcat.org/oclc/13594862
+HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",https://www.worldcat.org/oclc/13594862
+HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862
+RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://pubs.er.usgs.gov/publication/b1452
+RHF78.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","halloysite",https://pubs.er.usgs.gov/publication/b1452
+RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://pubs.er.usgs.gov/publication/b1452
+RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://pubs.er.usgs.gov/publication/b1452
+RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://pubs.er.usgs.gov/publication/b1452
PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO<sub>4</sub>,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
-HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,http://www.worldcat.org/oclc/858456124
+HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,https://www.worldcat.org/oclc/858456124
Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X
@@ -38,7 +38,7 @@
Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.",
OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-Hückel extended term parameter (<i>b</i><sub>$\gamma$</sub>)",https://doi.org/10.1016/0016-7037(90)90368-U
SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
-HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,http://pubs.er.usgs.gov/publication/70016664
+HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.er.usgs.gov/publication/70016664
SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
@@ -60,13 +60,13 @@
HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",http://pubs.er.usgs.gov/publication/b2131
-RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",http://pubs.er.usgs.gov/publication/b2131
-RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",http://pubs.er.usgs.gov/publication/b2131
-RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, pyrope (G and H not in SUPCRT92)",http://pubs.er.usgs.gov/publication/b2131
-RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",http://pubs.er.usgs.gov/publication/b2131
-RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",http://pubs.er.usgs.gov/publication/b2131
-RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",http://pubs.er.usgs.gov/publication/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://pubs.er.usgs.gov/publication/b2131
+RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://pubs.er.usgs.gov/publication/b2131
+RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://pubs.er.usgs.gov/publication/b2131
+RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, pyrope (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
+RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
+RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://pubs.er.usgs.gov/publication/b2131
+RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species.",https://doi.org/10.1016/0016-7037(95)00058-8
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -11,7 +11,7 @@
\section{Warm Tips}{
\itemize{
\item To view the manual, run \code{help.start()} then select \sQuote{Packages} and \sQuote{CHNOSZ}. Examples in the function help pages can be run by pasting the code block into the \R console.
- \item Be sure to check out the vignette titled \emph{An Introduction to CHNOSZ}, which is available by following the link in \code{help.start} to \sQuote{User guides, package vignettes and other documentation}.
+ \item Also check out the vignette \viglink{anintro} (\emph{An Introduction to CHNOSZ}).
\item Run the command \code{\link{examples}()} to run all of the examples provided in CHNOSZ. This should take about a minute.
}
}
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -107,7 +107,7 @@
}
\seealso{
-The vignette \emph{Regressing thermodynamic data} has more references and examples, including an iterative method to retrieve \code{omega.PrTr}.
+The vignette \viglink{eos-regress} has more references and examples, including an iterative method to retrieve \code{omega.PrTr}.
}
\references{
Modified: pkg/CHNOSZ/man/duplex.Rd
===================================================================
--- pkg/CHNOSZ/man/duplex.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/duplex.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -31,10 +31,11 @@
}
\seealso{
-A longer example is in the vignette \samp{multi-metal.Rmd}.
+A longer example is in the vignette \viglink{multi-metal}.
}
\examples{
+def.par <- par(no.readonly = TRUE)
layout(matrix(c(1, 1, 2, 2, 0, 3, 3, 0), nrow = 4))
# Define basis species with Fe and Cu
basis(c("Fe+2", "Cu+", "hydrogen sulfide", "oxygen", "H2O", "H+"))
@@ -53,6 +54,7 @@
db <- describe.basis(ibasis = 3)
leg <- lex(lTP(400, 2000), db)
legend("bottomleft", legend = leg, bty = "n")
+par(def.par)
}
\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -104,7 +104,7 @@
\code{\link{diagram}} has examples of using \code{equilibrate} to make equilibrium activity diagrams. \code{\link{revisit}} can be used to perform further analysis of the equilibrium activities.
\code{\link{palply}} is used by both \code{equil.reaction} and \code{equil.boltzmann} to parallelize intensive parts of the calculations.
-See the vignette \code{multi-metal.Rmd} for an example of balancing on two elements (N in the basis species, C in the formed species).
+See the vignette \viglink{multi-metal} for an example of balancing on two elements (N in the basis species, C in the formed species).
}
\value{
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/extdata.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -36,13 +36,13 @@
Files in \code{cpetc} contain experimental and calculated thermodynamic and environmental data:
\itemize{
- \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 use this file.
+ \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 \viglink{anintro} for examples that use 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{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.
- \item \code{rubisco.csv} UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See the vignette \code{anintro.Rmd} 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 \viglink{eos-regress} 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 \viglink{anintro} 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 \viglink{anintro} for an example that uses this file.
+ \item \code{rubisco.csv} UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See the vignette \viglink{anintro} for an example that uses this file.
\item \code{bluered.txt} Blue - light grey - red color palette, computed using \CRANpkg{colorspace}\code{::diverge_hcl(1000,} \code{c = 100, l = c(50, 90), power = 1)}. This is used by \code{\link{ZC.col}}.
\item \code{AD03_Fig1?.csv} Experimental data points digitized from Figure 1 of Akinfiev and Diamond, 2003, used in \code{demo("AkDi")}.
\item \code{TKSS14_Fig2.csv} Experimental data points digitized from Figure 2 of Tutolo et al., 2014, used in \code{demo("aluminum")}.
@@ -52,7 +52,7 @@
Files in \code{protein} contain protein sequences and amino acid compositions for proteins.
\itemize{
\item \code{EF-Tu.aln} consists of aligned sequences (394 amino acids) of elongation factor Tu (EF-Tu). The sequences correspond to those taken from UniProtKB for ECOLI (\emph{Escherichia coli}), THETH (\emph{Thermus thermophilus}) and THEMA (\emph{Thermotoga maritima}), and reconstructed ancestral sequences taken from Gaucher et al., 2003 (maximum likelihood bacterial stem and mesophilic bacterial stem, and alternative bacterial stem). See \code{\link{read.fasta}} for an example that uses this file.
- \item \code{rubisco.fasta} Sequences of Rubisco obtained from UniProt (see Dick, 2014). See the vignette \code{anintro.Rmd} for an example that uses this file.
+ \item \code{rubisco.fasta} Sequences of Rubisco obtained from UniProt (see Dick, 2014). See the vignette \viglink{anintro} for an example that uses this file.
\item \code{POLG.csv}
Amino acid compositions of a few proteins used for some tests and examples.
These are various subunits of the Poliovirus type 1 polyprotein (POLG_POL1M in UniProt).
@@ -96,7 +96,7 @@
\item \code{BZA10.csv} contains supplementary thermodynamic data taken from Bazarkina et al. (2010). The data can be added to the database in the current session using \code{\link{add.OBIGT}}. See \code{\link{add.OBIGT}} for an example that uses this file.
\item \code{OBIGT_check.csv} contains the results of running \code{\link{check.OBIGT}} to check the internal consistency of entries in the default and optional datafiles.
\item \code{RH98_Table15.csv} Group stoichiometries for high molecular weight crystalline and liquid organic compounds taken from Table 15 of Richard and Helgeson, 1998. The first three columns have the \code{compound} name, \code{formula} and physical \code{state} (\samp{cr} or \samp{liq}). The remaining columns have the numbers of each group in the compound; the names of the groups (columns) correspond to species in \code{\link{thermo}$OBIGT}. The compound named \samp{5a(H),14a(H)-cholestane} in the paper has been changed to \samp{5a(H),14b(H)-cholestane} here to match the group stoichiometry given in the table. See \code{\link{RH2OBIGT}} for a function that uses this file.
- \item \code{DLEN67.csv} Standard Gibbs energies of formation, in kcal/mol, from Dayhoff et al., 1967, for nitrogen (N2) plus 17 compounds shown in Fig. 2 of Dayhoff et al., 1964, at 300, 500, 700 and 1000 K. See \code{demo("wjd")} and the vignette \code{wjd.Rmd} for examples that use this file.
+ \item \code{DLEN67.csv} Standard Gibbs energies of formation, in kcal/mol, from Dayhoff et al., 1967, for nitrogen (N2) plus 17 compounds shown in Fig. 2 of Dayhoff et al., 1964, at 300, 500, 700 and 1000 K. See \code{demo("wjd")} for an example that uses this file.
\item \code{SK95.csv} contains thermodynamic data for alanate, glycinate, and their complexes with metals, taken from Shock and Koretsky (1995) as corrected in slop98.dat. The data are used in the package tests (\code{test-recalculate.R}) to check the recalculated values of G, H, and S in \code{thermo()$OBIGT} using properties for alanate and glycinate from Amend and Helgeson (1997).
\item \code{LA19_test.csv} contains thermodynamic data for dimethylamine and trimethylamine from LaRowe and Amend (2019) in energy units of both J and cal. This file is used in \code{test-util.data.R}) to check the messages produced by \code{\link{checkGHS}} and \code{\link{checkEOS}}.
}
Modified: pkg/CHNOSZ/man/macros/macros.Rd
===================================================================
--- pkg/CHNOSZ/man/macros/macros.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/macros/macros.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -49,3 +49,6 @@
\newcommand{\eacute}{\ifelse{latex}{\out{\'{e}}}{\ifelse{html}{\out{é}}{é}}}
\newcommand{\gamma}{\ifelse{latex}{\eqn{\gamma}}{\ifelse{html}{\out{γ}}{γ}}}
\newcommand{\alpha}{\ifelse{latex}{\eqn{\alpha}}{\ifelse{html}{\out{α}}{α}}}
+
+% links to vignettes 20200716
+\newcommand{\viglink}{\ifelse{html}{\out{<a href="../doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/mosaic.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -67,8 +67,8 @@
\dontshow{reset()}# Fe-minerals and aqueous species in Fe-S-O-H system
# speciate SO4-2, HSO4-, HS-, H2S as a function of Eh and pH
# after Garrels and Christ, 1965 Figure 7.20
-pH <- c(0, 14, 250)
-Eh <- c(-1, 1, 250)
+pH <- c(0, 14)
+Eh <- c(-1, 1)
T <- 25
basis(c("FeO", "SO4-2", "H2O", "H+", "e-"))
basis("SO4-2", -6)
Modified: pkg/CHNOSZ/man/solubility.Rd
===================================================================
--- pkg/CHNOSZ/man/solubility.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/solubility.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -56,7 +56,7 @@
The output of \code{solubility} has the same format as that of \code{equilibrate}, and can be used by \code{\link{diagram}} with \code{type = "loga.balance"} to plot the solubilities, or with \code{type = NULL} to plot the activities of species.
The value of \code{loga.balance} reflects the activity (or molality) of the conserved basis species, i.e. the thing being dissolved.
Use \code{in.terms.of} to express this value in terms of another species.
-For example, the solubility of corundum (Al\s{2}O\s{3}) can be expressed in terms of the moles of Al\S{+3} in solution (see the vignette \code{anintro.Rmd}).
+For example, the solubility of corundum (Al\s{2}O\s{3}) can be expressed in terms of the moles of Al\S{+3} in solution (see the vignette \viglink{anintro}).
}
\section{Warning}{
Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/man/thermo.Rd 2020-07-16 05:47:38 UTC (rev 565)
@@ -99,7 +99,7 @@
Each entry is referenced to one or two literature sources listed in \code{thermo()$refs}.
Use \code{\link{thermo.refs}} to look up the citation information for the references.
- See the vignette \emph{OBIGT thermodynamic database} for a complete description of the sources of data.
+ See the vignette \viglink{OBIGT} for a complete description of the sources of data.
The original \acronym{OBIGT} database was influenced by the \acronym{SUPCRT92} (Johnson et al., 1992) and \acronym{slop98.dat} data files (Shock et al., 1998), and the references in those files are included here.
In order to represent thermodynamic data for minerals with phase transitions, the higher-temperature phases of these minerals are represented as phase species that have states denoted by \samp{cr2}, \samp{cr3}, etc.
Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh 2020-07-16 04:32:38 UTC (rev 564)
+++ pkg/CHNOSZ/vignettes/mklinks.sh 2020-07-16 05:47:38 UTC (rev 565)
@@ -1,8 +1,8 @@
# CHNOSZ/vignettes/mklinks.sh
-# add documentation links to anintro, OBIGT, and equilibrium vignettes
+# add documentation links to vignettes
# 20190125 jmd
-# add links to help topics
+# anintro.html: add links to help topics
# set background-image:none to remove underlines (from bootstrap theme)
sed -i 's/<code>?`CHNOSZ-package`<\/code>/<code><a href="..\/html\/CHNOSZ-package.html" style="background-image:none;">?`CHNOSZ-package`<\/a><\/code>/g' anintro.html
sed -i 's/<code>?basis<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">?basis<\/a><\/code>/g' anintro.html
@@ -21,7 +21,7 @@
sed -i 's/<code>?wjd<\/code>/<code><a href="..\/html\/wjd.html" style="background-image:none;">?wjd<\/a><\/code>/g' anintro.html
sed -i 's/<code>?taxonomy<\/code>/<code><a href="..\/html\/taxonomy.html" style="background-image:none;">?taxonomy<\/a><\/code>/g' anintro.html
-# add links to function names
+# anintro.html: add links to function names
# start at line 120 (below the TOC)
sed -i '120,$s/<code>info()<\/code>/<code><a href="..\/html\/info.html" style="background-image:none;">info()<\/a><\/code>/g' anintro.html
sed -i '120,$s/<code>ZC()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">ZC()<\/a><\/code>/g' anintro.html
@@ -76,7 +76,7 @@
sed -i '120,$s/<code>RH2OBIGT()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">RH2OBIGT()<\/a><\/code>/g' anintro.html
sed -i '120,$s/<code>eqdata()<\/code>/<code><a href="..\/html\/eqdata.html" style="background-image:none;">eqdata()<\/a><\/code>/g' anintro.html
-# functions from R base packages
+# anintro.html: functions from R base packages
sed -i '120,$s/<code>install.packages/<code><a href="..\/..\/utils\/html\/install.packages.html" style="background-image:none;">install.packages<\/a>/g' anintro.html
sed -i '120,$s/<code>library/<code><a href="..\/..\/base\/html\/library.html" style="background-image:none;">library<\/a>/g' anintro.html
sed -i '120,$s/help()/<a href="..\/..\/utils\/html\/help.html" style="background-image:none;">help()<\/a>/g' anintro.html
@@ -107,3 +107,10 @@
sed -i 's/equilibrate()/<a href="..\/html\/equilibrate.html">equilibrate()<\/a>/g' equilibrium.html
sed -i 's/solubility()/<a href="..\/html\/solubility.html">solubility()<\/a>/g' equilibrium.html
sed -i 's/add.OBIGT()/<a href="..\/html\/add.OBIGT.html">add.OBIGT()<\/a>/g' equilibrium.html
+
+# add links to multi-metal.html 20200716
+sed -i 's/duplex()/<a href="..\/html\/duplex.html">duplex()<\/a>/g' multi-metal.html
+sed -i 's/ratlab()/<a href="..\/html\/util.expression.html">ratlab()<\/a>/g' multi-metal.html
+sed -i 's/diagram()/<a href="..\/html\/diagram.html">diagram()<\/a>/g' multi-metal.html
+sed -i 's/mosaic()/<a href="..\/html\/mosaic.html">mosaic()<\/a>/g' multi-metal.html
+sed -i 's/equilibrate()/<a href="..\/html\/equilibrate.html">equilibrate()<\/a>/g' multi-metal.html
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