[CHNOSZ-commits] r265 - in pkg/CHNOSZ: . demo inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 23 17:12:51 CEST 2017
Author: jedick
Date: 2017-10-23 17:12:50 +0200 (Mon, 23 Oct 2017)
New Revision: 265
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/go-IU.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/DEW.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/IAPWS95.Rd
pkg/CHNOSZ/man/add.obigt.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/anim.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/eqdata.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/findit.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/makeup.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/objective.Rd
pkg/CHNOSZ/man/palply.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/revisit.Rd
pkg/CHNOSZ/man/species.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/swap.basis.Rd
pkg/CHNOSZ/man/taxonomy.Rd
pkg/CHNOSZ/man/util.array.Rd
pkg/CHNOSZ/man/util.blast.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.expression.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.list.Rd
pkg/CHNOSZ/man/util.matrix.Rd
pkg/CHNOSZ/man/util.misc.Rd
pkg/CHNOSZ/man/util.plot.Rd
pkg/CHNOSZ/man/util.protein.Rd
pkg/CHNOSZ/man/util.seq.Rd
pkg/CHNOSZ/man/util.test.Rd
pkg/CHNOSZ/man/util.units.Rd
pkg/CHNOSZ/man/util.water.Rd
pkg/CHNOSZ/man/water.Rd
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/man/yeast.Rd
Log:
reorganize concept index entries in Rd files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/DESCRIPTION 2017-10-23 15:12:50 UTC (rev 265)
@@ -1,6 +1,6 @@
-Date: 2017-10-21
+Date: 2017-10-23
Package: CHNOSZ
-Version: 1.1.0-63
+Version: 1.1.0-64
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/demo/go-IU.R 2017-10-23 15:12:50 UTC (rev 265)
@@ -117,7 +117,7 @@
diagram(m$A.species, fill=fill)
dprop <- describe.property(c("T", "P"), c(25, 1))
legend("bottomleft", legend=dprop, bty="n")
-t1 <- quote("As-O-H-S, "~list(sum(S)==10^-3*M, sum(As)==10^-5*M))
+t1 <- quote("As-O-H-S, "~list(Sigma*S==10^-3~M, Sigma*As==10^-5~M))
t2 <- "After Lu and Zhu, 2011 Fig. 2b"
# doi:10.1007/s12665-010-0652-x
mtitle(as.expression(c(t1, t2)), cex=0.95)
@@ -132,7 +132,8 @@
AlF <- c("AlF+2", "AlF2+", "AlF3", "AlF4-")
AlOHF <- c("Al(OH)2F2-", "Al(OH)2F", "AlOHF2")
species(c(AlOH, Al, AlF, AlOHF), "aq")
-a <- affinity(pH=c(0, 10), `F-`=c(-1, -9), T=200)
+res <- 300
+a <- affinity(pH=c(0.5, 6.5, res), `F-`=c(-2, -9, res), T=200)
diagram(a, fill=rev(cm.colors(nrow(species()))))
dprop <- describe.property(c("T", "P"), c(200, "Psat"))
legend("topright", legend=dprop, bty="n")
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/inst/NEWS 2017-10-23 15:12:50 UTC (rev 265)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-61 (2017-10-20)
+CHANGES IN CHNOSZ 1.1.0-64 (2017-10-23)
---------------------------------------
MAJOR CHANGES:
@@ -164,6 +164,10 @@
- Remove extdata/OBIGT/CHNOSZ_aq.csv and move the entry for
pseudo-H4SiO4 to inorganic_aq.csv.
+- Reorganize concept index entries in Rd files: Main workflow, Extended
+ workflow, Thermodynamic data, Thermodynamic calculations, Water
+ properties, Protein properties, Other tools, Utility functions.
+
CHANGES IN CHNOSZ 1.1.0 (2017-05-04)
------------------------------------
@@ -508,7 +512,8 @@
species. See also new 'mosaic.R' demo.
- Add thermo$opt$varP option for subcrt() to calculate Gibbs energies
- of gases using a variable-pressure standard state.
+ of gases using a variable-pressure standard state. Thanks to Kirt
+ Robinson for the submitting the problem that led to this change.
- Add 'solubility.R' demo, and add calcite solubility plot to
anintro.Rnw.
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -11,12 +11,20 @@
\section{Getting Help}{
The major features of the package are outlined in the Overview given below, with links to specific help topics.
See the vignette \emph{An Introduction to CHNOSZ} (\code{anintro.Rmd}) for more in-depth example of the usage the functions.
-The help pages have been given either keywords or \dQuote{concept index entries} which are visible to \code{\link{help.search}} (aka \code{??}).
-Use \code{??primary} to browse the most commonly used functions and \code{??secondary} to see other high-level, but less often-used functions.
-\code{??protein} shows functions for working with proteins, and \code{??extra} lists functions with extra functionality (beyond the main workflow).
-For help on the thermodynamic database, use \code{??"thermodynamic data"}.
-Finally, \code{??utilities} (one of the standard \R keywords) can be used to locate utility functions in the package; these include useful tools for modifying the database, converting units, reading protein sequence files, parsing chemical formulas, etc.
+Each help page (other than this one) has been given one of the following \dQuote{concept index entries}:
+\itemize{
+ \item Main workflow: \code{\link{info}}, \code{\link{subcrt}}, \code{\link{basis}}, \code{\link{species}}, \code{\link{affinity}}, \code{\link{equilibrate}}, \code{\link{diagram}}
+ \item Extended workflow: \code{\link{swap.basis}}, \code{\link{buffer}}, \code{\link{mosaic}}, \code{\link{objective}}, \code{\link{revisit}}, \code{\link{findit}}, \code{\link{anim}}, \code{\link{EOSregress}}, \code{\link{wjd}}
+ \item Thermodynamic data: \code{\link{data}}, \code{\link{extdata}}, \code{\link{add.obigt}}, \code{\link{util.data}}
+ \item Thermodynamic calculations: \code{\link{util.formula}}, \code{\link{makeup}}, \code{\link{util.units}}, \code{\link{eos}}, \code{\link{berman}}, \code{\link{nonideal}}, \code{\link{util.misc}}
+ \item Water properties: \code{\link{water}}, \code{\link{util.water}}, \code{\link{DEW}}, \code{\link{IAPWS95}}
+ \item Protein properties: \code{\link{protein}}, \code{\link{protein.info}}, \code{\link{add.protein}}, \code{\link{util.fasta}}, \code{\link{util.protein}}, \code{\link{util.seq}}, \code{\link{ionize.aa}}, \code{\link{yeast}}
+ \item Other tools: \code{\link{examples}}, \code{\link{eqdata}}, \code{\link{taxonomy}}, \code{\link{util.blast}}
+ \item Utility functions: \code{\link{util.expression}}, \code{\link{util.plot}}, \code{\link{util.array}}, \code{\link{util.matrix}}, \code{\link{util.list}}, \code{\link{util.test}}, \code{\link{palply}}
}
+These concept entries are visible to \code{\link{help.search}} (aka \code{??}).
+For example, help pages related to thermodynamic data can be listed using \code{??"thermodynamic data"}.
+}
\section{Warning}{
All thermodynamic data and examples are provided on an as-is basis.
Modified: pkg/CHNOSZ/man/DEW.Rd
===================================================================
--- pkg/CHNOSZ/man/DEW.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/DEW.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -56,4 +56,4 @@
Zhang, Z. and Duan, Z. (2005) Prediction of the \emph{PVT} properties of water over wide range of temperatures and pressures from molecular dynamics simulation. \emph{Phys. Earth Planet. Inter.} \bold{149}, 335--354. \url{https://doi.org/10.1016/j.pepi.2004.11.003}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Water properties}
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -190,4 +190,4 @@
# not consistent with the high-T heat capacities
}
-\concept{Extra thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/IAPWS95.Rd
===================================================================
--- pkg/CHNOSZ/man/IAPWS95.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/IAPWS95.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -46,4 +46,4 @@
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{https://doi.org/10.1063/1.1461829}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Water properties}
Modified: pkg/CHNOSZ/man/add.obigt.Rd
===================================================================
--- pkg/CHNOSZ/man/add.obigt.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/add.obigt.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -114,3 +114,5 @@
Sverjensky, D. A., Shock, E. L., and Helgeson, H. C. (1997) Prediction of the thermodynamic properties of aqueous metal complexes to 1000 °C and 5 kbar. \emph{Geochim. Cosmochim. Acta} \bold{61}, 1359--1412. \url{https://doi.org/10.1016/S0016-7037(97)00009-4}
}
+
+\concept{Thermodynamic data}
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/add.protein.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -66,4 +66,4 @@
\code{\link{protein}} for examples of affinity calculations and diagrams.
}
-\concept{Protein thermodynamic modeling}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/affinity.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -96,4 +96,4 @@
Helgeson, H. C., Richard, L, McKenzie, W. F., Norton, D. L. and Schmitt, A. (2009) A chemical and thermodynamic model of oil generation in hydrocarbon source rocks. \emph{Geochim. Cosmochim. Acta} \bold{73}, 594--695. \url{https://doi.org/10.1016/j.gca.2008.03.004}
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/anim.Rd
===================================================================
--- pkg/CHNOSZ/man/anim.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/anim.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -60,4 +60,4 @@
Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \url{https://doi.org/10.1371/journal.pone.0022782}
}
-\concept{Extra thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/basis.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -110,4 +110,4 @@
basis("CO2", "gas")
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/berman.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -109,4 +109,4 @@
Sverjensky, D. A., Hemley, J. J. and D'Angelo, W. M. (1991) Thermodynamic assessment of hydrothermal alkali feldspar-mica-aluminosilicate equilibria. \emph{Geochim. Cosmochim. Acta} \bold{55}, 989-1004. \url{https://doi.org/10.1016/0016-7037(91)90157-Z}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/buffer.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -165,4 +165,4 @@
Garrels, R. M. (1960) \emph{Mineral Equilibria}. Harper & Brothers, New York, 254 p. \url{http://www.worldcat.org/oclc/552690}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/diagram.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -264,4 +264,4 @@
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{https://doi.org/10.1127/0935-1221/2006/0018-0175}
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/eos.Rd
===================================================================
--- pkg/CHNOSZ/man/eos.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/eos.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -1,5 +1,6 @@
\encoding{UTF-8}
\name{eos}
+\alias{eos}
\alias{hkf}
\alias{cgl}
\title{Equations of State}
@@ -101,4 +102,4 @@
}
-\concept{Secondary thermodynamic modeling}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/eqdata.Rd
===================================================================
--- pkg/CHNOSZ/man/eqdata.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/eqdata.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -53,4 +53,4 @@
eqdata("rainbow2.6o",c("h+","sio2,aq","h2,aq"),"log act") }
}
-\concept{Extra thermodynamic modeling}
+\concept{Other tools}
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -124,4 +124,4 @@
Dick, J. M. (2008) Calculation of the relative metastabilities of proteins using the CHNOSZ software package. \emph{Geochem. Trans.} \bold{9}:10. \url{https://doi.org/10.1186/1467-4866-9-10}
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/examples.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -116,4 +116,4 @@
}
-\concept{Extra thermodynamic modeling}
+\concept{Other tools}
Modified: pkg/CHNOSZ/man/findit.Rd
===================================================================
--- pkg/CHNOSZ/man/findit.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/findit.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -76,4 +76,4 @@
\seealso{ \code{demo("findit")} and \code{test-findit.R} for examples. }
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/info.Rd
===================================================================
--- pkg/CHNOSZ/man/info.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/info.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -79,4 +79,4 @@
info(" H2O")
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/ionize.aa.Rd
===================================================================
--- pkg/CHNOSZ/man/ionize.aa.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/ionize.aa.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -94,4 +94,4 @@
Privalov, P. L. and Makhatadze, G. I. (1990) Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. \emph{J. Mol. Biol.} \bold{213}, 385--391. \url{https://doi.org/10.1016/S0022-2836(05)80198-6}
}
-\concept{Protein thermodynamic modeling}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/makeup.Rd
===================================================================
--- pkg/CHNOSZ/man/makeup.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/makeup.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -84,4 +84,4 @@
\seealso{ \code{\link{mass}}, \code{\link{entropy}}, \code{\link{basis}}, \code{\link{i2A}} }
-\concept{Secondary thermodynamic modeling}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/mosaic.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -79,4 +79,4 @@
Garrels, R. M. and Christ, C. L. (1965) \emph{Solutions, Minerals, and Equilibria}, Harper & Row, New York, 450 p. \url{http://www.worldcat.org/oclc/517586}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/nonideal.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -175,4 +175,4 @@
Manning, C. E., Shock, E. L. and Sverjensky, D. A. (2013) The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints. \emph{Rev. Mineral. Geochem.} \bold{75}, 109--148. \url{https://doi.org/10.2138/rmg.2013.75.5}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/objective.Rd
===================================================================
--- pkg/CHNOSZ/man/objective.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/objective.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -137,4 +137,4 @@
}
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/palply.Rd
===================================================================
--- pkg/CHNOSZ/man/palply.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/palply.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -29,4 +29,4 @@
Tests are in \file{tests/test-util.program.R}, and a \dQuote{real world} example is in \file{demos/density.R}.
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/protein.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/protein.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -76,4 +76,4 @@
title(main="Bovine proteins, GSH/GSSG redox buffer")
}
-\concept{Protein thermodynamic modeling}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/protein.info.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -188,4 +188,4 @@
Dick, J. M. (2014) Average oxidation state of carbon in proteins. \emph{J. R. Soc. Interface} \bold{11}, 20131095. \url{https://doi.org/10.1098/rsif.2013.1095}
}
-\concept{Protein thermodynamic modeling}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/revisit.Rd
===================================================================
--- pkg/CHNOSZ/man/revisit.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/revisit.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -151,4 +151,4 @@
par(opar)
}
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/species.Rd
===================================================================
--- pkg/CHNOSZ/man/species.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/species.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -70,4 +70,4 @@
species() # NULL
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/subcrt.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -280,6 +280,30 @@
Na <- expr.species("Na+")
degC <- expr.units("T")
title(main=substitute(H2O~and~Na~to~-20~degC, list(H2O=H2O, Na=Na, degC=degC)))
+
+## Calculations using a variable-pressure standard state
+thermo$opt$varP <<- TRUE
+# Calculate the boiling point of n-octane at 2 and 20 bar
+# We need exceed.Ttr=TRUE because the liquid is metastable
+# at high temperatures (also, the gas is metastable at low
+# temperatures, but that doesn't produce NA in the output)
+sout2 <- subcrt(rep("n-octane", 2), c("liq", "gas"),
+ c(-1, 1), T=seq(-50, 300, 0.1), P=2, exceed.Ttr=TRUE)$out
+sout20 <- subcrt(rep("n-octane", 2), c("liq", "gas"),
+ c(-1, 1), T=seq(-50, 300, 0.1), P=20, exceed.Ttr=TRUE)$out
+# find T with the Gibbs energy of reaction that is closest to zero
+Tvap2 <- sout2$T[which.min(abs(sout2$G))]
+Tvap20 <- sout20$T[which.min(abs(sout20$G))]
+# the boiling point increases with pressure
+stopifnot(Tvap20 > Tvap2)
+# more precisely, the calculated boiling points should be near the
+# empirical values (digitized from Fig. 1 of Helgeson et al., 1998)
+Tvap_2bar <- 156
+Tvap_20bar <- 276
+stopifnot(abs(Tvap2 - Tvap_2bar) < 6)
+stopifnot(abs(Tvap20 - Tvap_20bar) < 25)
+# those comparisons would fail if varP were FALSE (the default)
+thermo$opt$varP <<- FALSE
}
\references{
@@ -287,6 +311,8 @@
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. \emph{Comp. Geosci.} \bold{18}, 899--947. \url{https://doi.org/10.1016/0098-3004(92)90029-Q}
+ Helgeson, H. C., Owens, C. E., Knox, A. M. and Richard, L. (1998) Calculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures. \emph{Geochim. Cosmochim. Acta} \bold{62}, 985--1081. \url{https://doi.org/10.1016/S0016-7037(97)00219-6}
+
LaRowe, D. E. and Helgeson, H. C. (2007) Quantifying the energetics of metabolic reactions in diverse biogeochemical systems: electron flow and ATP synthesis. \emph{Geobiology} \bold{5}, 153--168. \url{https://doi.org/10.1111/j.1472-4669.2007.00099.x}
Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. \emph{Orig. Life Evol. Biosph.} \bold{25}, 161--173. \url{https://doi.org/10.1007/BF01581580}
@@ -294,4 +320,4 @@
Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \url{https://doi.org/10.1039/FT9928800803}
}
-\concept{Primary thermodynamic modeling}
+\concept{Main workflow}
Modified: pkg/CHNOSZ/man/swap.basis.Rd
===================================================================
--- pkg/CHNOSZ/man/swap.basis.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/swap.basis.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -92,4 +92,4 @@
stopifnot(all.equal(a1$values, a3$values))
}
-\concept{Secondary thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/taxonomy.Rd
===================================================================
--- pkg/CHNOSZ/man/taxonomy.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/taxonomy.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -91,4 +91,4 @@
sciname(id8,names=names)
}
-\concept{Extra thermodynamic modeling}
+\concept{Other tools}
Modified: pkg/CHNOSZ/man/util.array.Rd
===================================================================
--- pkg/CHNOSZ/man/util.array.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.array.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -87,4 +87,4 @@
stopifnot(all.equal(a1$values,a3$values))
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.blast.Rd
===================================================================
--- pkg/CHNOSZ/man/util.blast.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.blast.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -114,4 +114,4 @@
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. \emph{Nucleic Acids Res.} \bold{25}, 3389--3402. \url{https://doi.org/doi:10.1093/nar/25.17.3389}
}
-\keyword{utilities}
+\concept{Other tools}
Modified: pkg/CHNOSZ/man/util.data.Rd
===================================================================
--- pkg/CHNOSZ/man/util.data.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.data.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -86,4 +86,4 @@
Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. \emph{Geochim. Cosmochim. Acta} \bold{62}, 3591--3636. \url{https://doi.org/10.1016/S0016-7037(97)00345-1}
}
-\keyword{utilities}
+\concept{Thermodynamic data}
Modified: pkg/CHNOSZ/man/util.expression.Rd
===================================================================
--- pkg/CHNOSZ/man/util.expression.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.expression.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -156,4 +156,4 @@
text(3, 4.75, describe.reaction(reaction, iname=1:4))
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.fasta.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -100,4 +100,4 @@
}
}
-\keyword{utilities}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/util.formula.Rd
===================================================================
--- pkg/CHNOSZ/man/util.formula.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.formula.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -112,4 +112,4 @@
Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \url{https://doi.org/10.1371/journal.pone.0022782}
}
-\keyword{utilities}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/util.list.Rd
===================================================================
--- pkg/CHNOSZ/man/util.list.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.list.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -23,4 +23,4 @@
If \code{na.rm} is \code{TRUE}, values of \code{NA} are removed; if \code{pmin} is \code{TRUE} the function finds locations of the minimum values instead.
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.matrix.Rd
===================================================================
--- pkg/CHNOSZ/man/util.matrix.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.matrix.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -42,4 +42,4 @@
stopifnot(tail(names(sc), 2)==c("C", "M"))
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.misc.Rd
===================================================================
--- pkg/CHNOSZ/man/util.misc.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.misc.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -90,4 +90,4 @@
stopifnot(isTRUE(all.equal(sum(10^loga * length),1)))
}
-\keyword{utilities}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/util.plot.Rd
===================================================================
--- pkg/CHNOSZ/man/util.plot.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.plot.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -93,4 +93,4 @@
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/util.protein.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.protein.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -1,5 +1,6 @@
\encoding{UTF-8}
\name{util.protein}
+\alias{util.protein}
\alias{group.formulas}
\alias{MP90.cp}
\title{Functions for Proteins (Other Calculations)}
@@ -33,4 +34,4 @@
Makhatadze, G. I. and Privalov, P. L. (1990) Heat capacity of proteins. 1. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect \emph{J. Mol. Biol.} \bold{213}, 375--384. \url{https://doi.org/10.1016/S0022-2836(05)80197-4}
}
-\concept{utilities}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/util.seq.Rd
===================================================================
--- pkg/CHNOSZ/man/util.seq.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.seq.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -51,4 +51,4 @@
nucleic.formula(RNA.comp) # C40H42N32O11
}
-\keyword{utilities}
+\concept{Protein properties}
Modified: pkg/CHNOSZ/man/util.test.Rd
===================================================================
--- pkg/CHNOSZ/man/util.test.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.test.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -28,4 +28,4 @@
The function uses \code{\link[testthat]{expect}} to generate an expectation in the \CRANpkg{testthat} framework.
}
-\keyword{utilities}
+\concept{Utility functions}
Modified: pkg/CHNOSZ/man/util.units.Rd
===================================================================
--- pkg/CHNOSZ/man/util.units.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.units.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -77,4 +77,4 @@
T.units("C")
}
-\keyword{utilities}
+\concept{Thermodynamic calculations}
Modified: pkg/CHNOSZ/man/util.water.Rd
===================================================================
--- pkg/CHNOSZ/man/util.water.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/util.water.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -78,4 +78,4 @@
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{https://doi.org/10.1063/1.1461829}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Water properties}
Modified: pkg/CHNOSZ/man/water.Rd
===================================================================
--- pkg/CHNOSZ/man/water.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/water.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -177,4 +177,4 @@
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{https://doi.org/10.1063/1.1461829}
}
-\concept{Secondary thermodynamic modeling}
+\concept{Water properties}
Modified: pkg/CHNOSZ/man/wjd.Rd
===================================================================
--- pkg/CHNOSZ/man/wjd.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/wjd.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -176,4 +176,4 @@
White, W. B., Johnson, S. M. and Dantzig, G. B. (1958) Chemical equilibrium in complex mixtures. \emph{J. Chem. Phys.} \bold{28}, 751--755. \url{https://doi.org/10.1063/1.1744264}
}
-\concept{Extra thermodynamic modeling}
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/man/yeast.Rd
===================================================================
--- pkg/CHNOSZ/man/yeast.Rd 2017-10-21 15:34:45 UTC (rev 264)
+++ pkg/CHNOSZ/man/yeast.Rd 2017-10-23 15:12:50 UTC (rev 265)
@@ -1,5 +1,6 @@
\encoding{UTF-8}
\name{yeast}
+\alias{yeast}
\alias{yeast.aa}
\alias{yeastgfp}
\title{Composition, Localization, and Abundances of Proteins in Yeast}
@@ -105,4 +106,4 @@
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J.-M. and Pronk, J. T. (2005) Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in \emph{Saccharomyces cerevisiae}. \emph{J. Biol. Chem.} \bold{280}, 437--447. \url{https://doi.org/10.1074/jbc.M410573200}
}
-\concept{Protein thermodynamic modeling}
+\concept{Protein properties}
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