[CHNOSZ-commits] r194 - in pkg/CHNOSZ: . R demo inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 1 05:46:54 CEST 2017
Author: jedick
Date: 2017-05-01 05:46:53 +0200 (Mon, 01 May 2017)
New Revision: 194
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/basis.R
pkg/CHNOSZ/demo/dehydration.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
minor documentation changes #1
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/DESCRIPTION 2017-05-01 03:46:53 UTC (rev 194)
@@ -1,6 +1,6 @@
-Date: 2017-04-30
+Date: 2017-05-01
Package: CHNOSZ
-Version: 1.0.8-82
+Version: 1.0.8-83
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/R/basis.R 2017-05-01 03:46:53 UTC (rev 194)
@@ -178,7 +178,7 @@
# to load a preset basis definition by keyword
preset.basis <- function(key=NULL) {
# the available keywords
- basis.key <- c("CHNOS", "CHNOS+", "CHNOSe", "CHNOPS+", "MgCHNOPS+", "FeCHNOS", "FeCHNOS+", "QEC")
+ basis.key <- c("CHNOS", "CHNOS+", "CHNOSe", "CHNOPS+", "MgCHNOPS+", "FeCHNOS", "FeCHNOS+", "QEC", "QEC+")
# just list the keywords if none is specified
if(is.null(key)) return(basis.key)
# delete any previous basis definition
@@ -194,6 +194,7 @@
else if(ibase==6) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen")
else if(ibase==7) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen", "H+")
else if(ibase==8) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen")
+ else if(ibase==9) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen", "H+")
# get the preset logact
logact <- preset.logact(species)
# load the species and return the result
Modified: pkg/CHNOSZ/demo/dehydration.R
===================================================================
--- pkg/CHNOSZ/demo/dehydration.R 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/demo/dehydration.R 2017-05-01 03:46:53 UTC (rev 194)
@@ -50,6 +50,8 @@
for(j in 1:2) {
formula <- thermo$obigt$formula[s$reaction$ispecies[j]]
key1 <- thermo$obigt$ref1[s$reaction$ispecies[j]]
+ # remove suffix from the key (e.g. "DLH06 [S15]" --> "DLH06")
+ key1 <- strsplit(key1, " ")[[1]][1]
ikey1 <- which(thermo$refs$key==key1)
URL1 <- thermo$refs$URL[ikey1]
setSVGShapeURL(URL1, target="_blank")
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/inst/NEWS 2017-05-01 03:46:53 UTC (rev 194)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-82 (2017-04-30)
+CHANGES IN CHNOSZ 1.0.8-83 (2017-05-01)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -110,6 +110,8 @@
}
\references{
+ Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{http://dx.doi.org/10.1006/jcht.1997.0192}
+
Schulte, M. D., Shock, E. L. and Wood, R. H. (1995) The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3919--3930. \url{http://dx.doi.org/10.1016/S0016-7037(01)00717-7}
}
@@ -118,7 +120,7 @@
\dontshow{data(thermo)}
## fit experimental heat capacities of CH4
## using revised Helgeson-Kirkham-Flowers equations
-# read the data from Hnedkovsky and Wood, 1997
+# read the data from Hnědkovský and Wood, 1997
f <- system.file("extdata/cpetc/Cp.CH4.HW97.csv", package="CHNOSZ")
d <- read.csv(f)
# have to convert J to cal and MPa to bar
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/add.protein.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -38,7 +38,7 @@
If \code{average} is TRUE the final sum is divided by the number of input compositions.
The name used in the output is taken from the first row of \code{aa} or from \code{protein} and \code{organism} if they are specified.
-Given amino acid composition returned by the \code{*aa} functions described above, \code{add.protein} adds them to \code{thermo$protein} for use by other functions in CHNOSZ.
+Given amino acid compositions returned by the \code{*aa} functions described above, \code{add.protein} adds them to \code{thermo$protein} for use by other functions in CHNOSZ.
The amino acid compositions of proteins in \code{aa} with the same name as one in \code{thermo$protein} are replaced.
The value returned by this function is the rownumbers of \code{thermo$protein} that are added and/or replaced.
}
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/affinity.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -13,7 +13,7 @@
\arguments{
\item{...}{numeric, zero or more named arguments, used to identify the variables of interest in the calculations}
- \item{property}{character, denoting the property to be calculated. Default is \samp{A}, for chemical affinity of formation reactions of species of interest}
+ \item{property}{character, the property to be calculated. Default is \samp{A}, for chemical affinity of formation reactions of species of interest}
\item{sout}{list, output from \code{\link{subcrt}}}
\item{exceed.Ttr}{logical, allow \code{\link{subcrt}} to compute properties for phases beyond their transition temperature?}
\item{return.buffer}{logical. If \code{TRUE}, and a \code{\link{buffer}} has been associated with one or more basis species in the system, return the values of the activities of the basis species calculated using the buffer. Default is \code{FALSE}.}
@@ -36,7 +36,7 @@
If \samp{T}, \samp{P}, and/or \samp{IS} are not among the \code{var}s, their constant values can be supplied in \code{T}, \code{P}, or \code{IS} (in mol kg\eqn{^{-1}}{^-1}).
The units of \samp{T} and \samp{P} are those set by \code{\link{T.units}} and \code{\link{P.units}} (on program start-up these are \eqn{^{\circ}}{°}C and bar, respectively).
-\code{sout}, if provided, replaces the call to \code{\link{subcrt}}, which can greatly speed up the calculations if this intermediate step is stored by other functions (e.g., \code{\link{transfer}}).
+\code{sout}, if provided, replaces the call to \code{\link{subcrt}}, which can greatly speed up the calculations if this intermediate result is stored by other functions (e.g., \code{\link{transfer}}).
\code{exceed.Ttr} is passed to \code{\link{subcrt}} so that the properties of mineral phases beyond their transition temperatures can optionally be calculated.
If one or more buffers are assigned to the definition of \code{\link{basis}} species, the logarithms of activities of these basis species are taken from the buffer (see \code{\link{buffer}}).
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/basis.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -63,6 +63,7 @@
\code{FeCHNOS+} \tab \eqn{\mathrm{Fe_2O_3}}{Fe2O3}, \eqn{\mathrm{CO_2}}{CO2}, \eqn{\mathrm{H_2O}}{H2O},
\eqn{\mathrm{NH_3}}{NH3}, \eqn{\mathrm{H_2S}}{H2S}, \eqn{\mathrm{O_2}}{O2}, \eqn{\mathrm{H^+}}{H+} \cr
\code{QEC} \tab cysteine, glutamic acid, glutamine, \eqn{\mathrm{H_2O}}{H2O}, \eqn{\mathrm{O_2}}{O2} \cr
+ \code{QEC+} \tab cysteine, glutamic acid, glutamine, \eqn{\mathrm{H_2O}}{H2O}, \eqn{\mathrm{O_2}}{O2}, \eqn{\mathrm{H^+}}{H+} \cr
}
}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/diagram.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -2,7 +2,7 @@
\alias{diagram}
\alias{strip}
\alias{find.tp}
-\title{Equilibrium Chemical Activity Diagrams}
+\title{Chemical Activity Diagrams}
\description{
Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis speecies, temperature and/or pressure.
}
@@ -24,7 +24,7 @@
}
\arguments{
- \item{eout}{list, object returned by \code{\link{equilibrate}}} or \code{\link{affinity}}
+ \item{eout}{list, object returned by \code{\link{equilibrate}} or \code{\link{affinity}}}
\item{what}{character, what property to calculate and plot}
\item{alpha}{logical, for speciation diagrams, plot degree of formation instead of activities?}
\item{normalize}{logical, divide chemical affinities by balance coefficients (rescale to whole formulas)?}
@@ -95,7 +95,7 @@
\code{fill.NA} is also used to specify the color outside the water stability limits on Eh-pH or pe-pH diagrams, when \code{limit.water} is TRUE.
Note that the default for \code{fill.NA} is automatically changed to \samp{transparent} when \code{add} is TRUE.
-As of CHNOSZ 1.0.8-11, a new default line-drawing procedure has been implemented.
+In CHNOSZ 1.1.0, a new default line-drawing procedure has been implemented.
This uses \code{\link{contour}} to draw smooth-looking diagonal and curved lines, at the expense of not coinciding exactly with the rectangular grid (which is still used for drawing colors).
\code{lty}, \code{col}, and \code{lwd} can be specified, but limiting the lines via \code{xrange} is not currently supported.
To go back to the old behavior for drawing lines, set \code{dotted} to \samp{0}.
@@ -149,7 +149,7 @@
Then, the species with the highest affinity of formation, after normalization by the balancing coefficients, corresponds to the predominant species in an equilibrium calculation.
The examples below \dQuote{work} because they are relatively simple - the balancing coefficients are unity or all the same value (aqueous aluminum example), or the species are solids with unit activities (the mineral examples).
The examples shown for \code{\link{protein}s} elsewhere also take the balancing coefficients to unity, after normalizing by protein length.
-However, if aqueous species are present with different balancing coefficients, the maximum affinity method is not dependable, as shown in the TCA metabolite example below.
+However, if aqueous species are present with different balancing coefficients, the maximum affinity method may produce unintended results.
}
\seealso{
@@ -257,11 +257,6 @@
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{http://dx.doi.org/10.1111/j.1472-4669.2007.00099.x}
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://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}
-
}
\concept{Primary thermodynamic modeling}
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -28,7 +28,7 @@
}
\details{
-\code{equilibrate} provides an interface to calculate the chemical activities of species in metastable equilibrium, in an open system at constant temperature and pressure and chemical activities of basis species, and with linear balancing constraints on transformations.
+\code{equilibrate} calculates the chemical activities of species in metastable equilibrium, in an open system at constant temperature and pressure and chemical activities of basis species, and with linear balancing constraints on transformations.
It takes as input \code{aout}, the output from \code{\link{affinity}}, which may be calculated from a multidimensional grid of conditions.
The equilibrium chemical activities of species are calculated using either the \code{equil.reaction} or \code{equil.boltzmann} functions, the latter only if the balance is on one mole of species.
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/examples.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -15,8 +15,9 @@
\usage{
examples(do.png = FALSE)
demos(which = c("sources", "protein.equil", "affinity", "NaCl", "density",
- "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic",
- "copper", "solubility", "wjd", "dehydration", "bugstab", "Shh", "activity_ratios"),
+ "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp",
+ "mosaic", "copper", "solubility", "wjd", "dehydration", "bugstab", "Shh",
+ "activity_ratios"),
to.file=FALSE)
}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/man/extdata.Rd 2017-05-01 03:46:53 UTC (rev 194)
@@ -31,7 +31,7 @@
\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{\link{water}} 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 Hnedkovsky and Wood, 1997 and Hnedkovsky et al., 1996. See \code{\link{EOSregress}} for examples that use these files.
+ \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}} for examples that use these files.
\item \code{SC10_Rainbow.csv} Values of temperature (\eqn{^{\circ}}{°}C), pH and logarithms of activity of \eqn{\mathrm{CO_2}}{CO2}, \eqn{\mathrm{H_2}}{H2}, \eqn{\mathrm{NH_4^+}}{NH4+}, \eqn{\mathrm{H_2S}}{H2S} and \eqn{\mathrm{CH_4}}{CH4} for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010.
\item \code{SS98_Fig5a.csv}, \code{SS98_Fig5b.csv} Values of logarithm of fugacity of \eqn{\mathrm{O_2}}{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.
\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.
@@ -129,9 +129,9 @@
HAMAP system. HAMAP FTP directory, \url{ftp://ftp.expasy.org/databases/hamap/}
-Hnedkovsky, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. \emph{J. Chem. Thermodyn.} \bold{28}, 125--142. \url{http://dx.doi.org/10.1006/jcht.1996.0011}
+Hnědkovský, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. \emph{J. Chem. Thermodyn.} \bold{28}, 125--142. \url{http://dx.doi.org/10.1006/jcht.1996.0011}
-Hnedkovsky, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{http://dx.doi.org/10.1006/jcht.1997.0192}
+Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{http://dx.doi.org/10.1006/jcht.1997.0192}
Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. and Frishman, D. (2008) Protein abundance profiling of the \emph{Escherichia coli} cytosol. \emph{BMC Genomics} \bold{9}:102. \url{http://dx.doi.org/10.1186/1471-2164-9-102}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-04-30 07:06:16 UTC (rev 193)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-01 03:46:53 UTC (rev 194)
@@ -1642,7 +1642,7 @@
</p>
We have calculated the distribution of ATP species and average binding number of H<sup>+</sup> and Mg<sup>+2</sup> for given pH, pMg, ionic strength, and temperature.
-Accounting for the distribution of chemical species lends itself to thermodynamic models for reactions between reactants that have multiple ionized and bound states.
+Accounting for the distribution of chemical species lends itself to thermodynamic models for reactions between reactants that have multiple ionized and complexed states.
In contrast, Alberty (2003) and others propose models for biochemical reactions where the ionized and complexed species are combined into a single representation.
Those models invoke Legendre-transformed thermodynamic properties, such as transformed Gibbs energies that are tabulated for specified pH, pMg, and ionic strength.
Although the conceptual pathways are different, the two approaches lead to equivalent results concerning the energetics of the overall reactions and the conditions for equilibrium [@SVI12].
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