From noreply at r-forge.r-project.org Mon May 1 05:46:54 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 1 May 2017 05:46:54 +0200 (CEST) Subject: [CHNOSZ-commits] r194 - in pkg/CHNOSZ: . R demo inst man vignettes Message-ID: <20170501034654.DE757188AE1@r-forge.r-project.org> 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 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{ + Hn?dkovsk?, 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 Hn?dkovsk? 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 Hn?dkovsk? and Wood, 1997 and Hn?dkovsk? 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} +Hn?dkovsk?, 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} +Hn?dkovsk?, 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 @@

We have calculated the distribution of ATP species and average binding number of H+ and Mg+2 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]. From noreply at r-forge.r-project.org Tue May 2 06:44:02 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 2 May 2017 06:44:02 +0200 (CEST) Subject: [CHNOSZ-commits] r195 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/thermo man Message-ID: <20170502044403.017EA1884CD@r-forge.r-project.org> Author: jedick Date: 2017-05-02 06:44:02 +0200 (Tue, 02 May 2017) New Revision: 195 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/makeup.R pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv pkg/CHNOSZ/man/CHNOSZ-package.Rd pkg/CHNOSZ/man/add.protein.Rd pkg/CHNOSZ/man/basis.Rd pkg/CHNOSZ/man/buffer.Rd pkg/CHNOSZ/man/diagram.Rd pkg/CHNOSZ/man/equilibrate.Rd pkg/CHNOSZ/man/examples.Rd pkg/CHNOSZ/man/extdata.Rd pkg/CHNOSZ/man/findit.Rd pkg/CHNOSZ/man/info.Rd pkg/CHNOSZ/man/makeup.Rd pkg/CHNOSZ/man/more.aa.Rd pkg/CHNOSZ/man/nonideal.Rd pkg/CHNOSZ/man/objective.Rd pkg/CHNOSZ/man/protein.Rd pkg/CHNOSZ/man/read.expr.Rd pkg/CHNOSZ/man/revisit.Rd pkg/CHNOSZ/man/species.Rd pkg/CHNOSZ/man/taxonomy.Rd pkg/CHNOSZ/man/transfer.Rd pkg/CHNOSZ/man/util.array.Rd pkg/CHNOSZ/man/util.blast.Rd pkg/CHNOSZ/man/util.expression.Rd pkg/CHNOSZ/man/util.fasta.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.program.Rd pkg/CHNOSZ/man/util.seq.Rd Log: minor documentation changes #2 Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-01 03:46:53 UTC (rev 194) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-02 04:44:02 UTC (rev 195) @@ -1,6 +1,6 @@ -Date: 2017-05-01 +Date: 2017-05-02 Package: CHNOSZ -Version: 1.0.8-83 +Version: 1.0.8-84 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/makeup.R =================================================================== --- pkg/CHNOSZ/R/makeup.R 2017-05-01 03:46:53 UTC (rev 194) +++ pkg/CHNOSZ/R/makeup.R 2017-05-02 04:44:02 UTC (rev 195) @@ -199,7 +199,7 @@ if(length(iopen) != length(iclose)) stop("formula has unpaired parentheses") # are the parentheses unnested? iparen <- as.numeric(matrix(c(iopen, iclose), nrow=2, byrow=TRUE)) - if(any(diff(iparen) < 0)) stop("formula has nested parentheses") + if(any(diff(iparen) < 0)) stop(paste("formula has nested parentheses: ", formula)) # iend will be the last position including coefficients # (e.g. the position of 2 in (OH)2) iend <- iclose Modified: pkg/CHNOSZ/inst/CHECKLIST =================================================================== --- pkg/CHNOSZ/inst/CHECKLIST 2017-05-01 03:46:53 UTC (rev 194) +++ pkg/CHNOSZ/inst/CHECKLIST 2017-05-02 04:44:02 UTC (rev 195) @@ -11,8 +11,13 @@ - check output of demo("sources") to make sure all data sources are cited -- check output of R CMD Rd2pdf: fix lines truncated by page margins +- recreate extdata/thermo/obigt_check.csv after all data updates: + co <- check.obigt() + write.csv(co, "obigt_check.csv", row.names=FALSE, na="") +- run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/ + and fix any lines truncated by page margins + - run R CMD check using R compiled without long doubles (as in Solaris checks on CRAN) (CFLAGS=-ffloat-store ./configure --disable-long-double) @@ -26,10 +31,6 @@ - update list of documentation topics in examples() with any new ones -- recreate extdata/thermo/obigt_check.csv after all data updates: - co <- check.obigt() - write.csv(co, "obigt_check.csv", row.names=FALSE, na="") - - especially on Windows: - data files are uncompressed on installation? (from BuildResaveData: no) (so that users can copy and modify the thermodynamic database) Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-01 03:46:53 UTC (rev 194) +++ pkg/CHNOSZ/inst/NEWS 2017-05-02 04:44:02 UTC (rev 195) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-83 (2017-05-01) +CHANGES IN CHNOSZ 1.0.8-84 (2017-05-02) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz =================================================================== --- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz 2017-05-01 03:46:53 UTC (rev 194) +++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz 2017-05-02 04:44:02 UTC (rev 195) @@ -1,4 +1,4 @@ -?7zXZ???F!t/??????]7I??b???9??????TB;q?"?q???cL;?"??b???-?y?bZ?/??3O7??????g?H -?_i?~??6?aA ?&6???B~GN77>}?1?[????F?"=??t?aa?s?4?<8a?$A??pf??y?3?{?Lr???bp??DS????6?/S ???Z*Q?|?????;?M?AIC?? 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Ia? ?s3?f?=u???m?*?[?4??????|r??s\???{??????E???HwB??X??Mq???%?y????O????-??j??i?5, +????????W????n??R???V??9}?? =K??lw?????z?f*?W ??? j1????/??>?w??????%?d>qrU???????:?D???=??Nt ++?rQ.??c?5l?/????_Tj}?)?*??#?>??m-_??T?3?0(???_v?q?c? +????x?z?=^??R-Q?????g,k=S??E?O???]?=??&???8g???dY???B}????D v@??E?!??* ?????U??? ?.?? ????2?>??:???[]??^?F????][???A??.~????Qv??????@]*@????lC?i????~r?#?Hy??????V????n?$1?d??hE????J? +??t +6n??5S??????2?@????8#???fy???U??c???=_????????,f>???? r?t???{?}a?@????Z??g0\:!?_jmu????Sm?? +????D????????-?]#????L????B????)???=x'6??[?J$F*:1?a]??????U??]?Rf'????????v??5edr???&?r#{|?);???cDC??0?k?{7>h??.??Qbz? ?%????]o?u?=?J???5??h?????A??????????'?oA?M" ?t?{? -?????;??OU=l???????\fD???m@??? ?@~?????4??B&??g$ -S,????N???g???!4?[??D? --|H?7? ???MMg??!??OB? ?n?????Oke?49?-?"?t}?v?Uil??fKe$ ?f?|)??kz?xpY6K*Y??>?7?X?]R????h?e???????Eme,T????H???]??????@e?B??A?{ -???AeSb~tk??nv??J? ?l=&u=?1E??_??QZ??N?Q?f -v???N?@R????mYVm?X???o\??N???>??I? g??Z?O&?????:?)m?k??[S?2?? -??e?LI?wj?@?k??~?i? ?? -???}??r?????????!:d??????j8o???{? ??"^??%??J?C?_e8kC???-P?\?*i?????????B??A??w@??????5n????Cw???K?{j?J:?uJ;egT?????W??xr??????K????-??f????*aZ?CQ?MmT??!Qu??~?O??i?????? j8??z1?{zY?g????+??G#? -???It?????? -9???D|???Ma??C`N????%?YK??-Q?$??V?UWS7???` -??"?? ???n??h!?%,'????d???e7t??D?(B???o -E:L???????e???i? %:??~-v8?ry??????#?6??WG??F??&7C?&???????Sg???T????B?|?????a[?7/?Q?T?`o[????? -@8??f?????R?????B?Z??V??1D??l??o,:??ju?3?*W? -??%???cj?gM7H? -??g???l??^ -?.??V?PvI?????$)^??U?M?*????h?}n?????? ?f9J?X???h?Y?,;jV?xZ?,??C9?0 ???Xvi???F?G?H????????????s???K?[??@9R??L??? -?T)#???fe?8???r[?U????Ii_C$???b??@?????"???5[??Lm??D$:??0[????!?/:?,??q?A?Lj????$_?B?_O*\kT trI?E??k:j????,?v?c??????F0?>\?S ?9?I?b???l?o?^2?pg?B????X??C?) ?h???D??^?????oh ?W?pW?8j K????P&???H??????hQ*?M?g??L?q -?\??X???)u*????b^Q7???SpQ,8? -?S7?????F?}Cp!???7?X>:x.A???F%??_.? -???[????????x??[??a?-???3@'?g%??x+??NG???/??SjLu?;?5?$?????D??9&????c'!?*? OA??0? -q???x??7??w???? ?????sg]lQ?]O????m???6L ???*Y???????w??????*$???_V?% -?Vw?\}p*?~?;g\??8)??h?2??@#?H???reN?????????e#J]???p?T>??????(Nnc???dR?z!?lR?{?egd????#]?v??)+??0??D????+??l?????\?GK N?g???30pHR[??A?_?9?A&?#8?n?rYikl?S?_V?\?[M?O?I?n*?????|sGA$?tR????!"?)A???j??V5W?CJ??`?6?????dy??20??#?^W??ii@?????x????/??p`?m??;??R?6?,J;B_ at 6MHjo +??H:V?h,;bR?,^?????q??iq?#~?g^?y ?1???r???Iv??????q=?AAUP??`  ??????>B;T\?_?uNw?.z?6 P?/????{?@??u??????9xp?J5?4$?[~^??7?? +?pk.{??|/'?"6?V?P???SG]???K?HFZ@=??eg????5u???0?????? X????s|:])N?????? ?F?~?bR????9???????)?????F.?Ohe?2??z?? ?7 at 6?E?ts +??H??kQ?c?p?[,????? =???n?????l????:?0???????0???ge;o Author: jedick Date: 2017-05-03 04:39:19 +0200 (Wed, 03 May 2017) New Revision: 196 Added: pkg/CHNOSZ/R/palply.R pkg/CHNOSZ/man/palply.Rd Removed: pkg/CHNOSZ/R/util.program.R pkg/CHNOSZ/man/util.program.Rd Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.args.R pkg/CHNOSZ/data/thermo.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/data.Rd pkg/CHNOSZ/man/diagram.Rd pkg/CHNOSZ/man/extdata.Rd pkg/CHNOSZ/man/findit.Rd pkg/CHNOSZ/man/info.Rd pkg/CHNOSZ/man/nonideal.Rd pkg/CHNOSZ/man/read.expr.Rd pkg/CHNOSZ/man/species.Rd pkg/CHNOSZ/man/subcrt.Rd pkg/CHNOSZ/man/transfer.Rd pkg/CHNOSZ/man/util.array.Rd pkg/CHNOSZ/man/util.blast.Rd pkg/CHNOSZ/man/util.expression.Rd pkg/CHNOSZ/man/util.fasta.Rd pkg/CHNOSZ/man/util.misc.Rd pkg/CHNOSZ/man/util.plot.Rd Log: minor documentation changes #3 Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-03 02:39:19 UTC (rev 196) @@ -1,6 +1,6 @@ -Date: 2017-05-02 +Date: 2017-05-03 Package: CHNOSZ -Version: 1.0.8-84 +Version: 1.0.8-85 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Copied: pkg/CHNOSZ/R/palply.R (from rev 195, pkg/CHNOSZ/R/util.program.R) =================================================================== --- pkg/CHNOSZ/R/palply.R (rev 0) +++ pkg/CHNOSZ/R/palply.R 2017-05-03 02:39:19 UTC (rev 196) @@ -0,0 +1,26 @@ +# CHNOSZ/palply.R + +palply <- function(varlist, X, FUN, ...) { + # a wrapper function to run parLapply if length(X) >= thermo$opt$paramin + # and package 'parallel' is available, otherwise run lapply + if(length(X) >= get("thermo")$opt$paramin) { + # Use option mc.cores to choose an appropriate cluster size. + # and set max at 2 for now (per CRAN policies) + nCores <- min(getOption("mc.cores"), 2) + # don't load methods package, to save startup time - ?makeCluster + cl <- parallel::makeCluster(nCores, methods=FALSE) + # export the variables and notify the user + if(! "" %in% varlist) { + parallel::clusterExport(cl, varlist) + message(paste("palply:", caller.name(4), "running", length(X), "calculations on", + nCores, "cores with variable(s)", paste(varlist, collapse=", "))) + } else { + message(paste("palply:", caller.name(4), "running", length(X), "calculations on", + nCores, "cores")) + } + # run the calculations + out <- parallel::parLapply(cl, X, FUN, ...) + parallel::stopCluster(cl) + } else out <- lapply(X, FUN, ...) + return(out) +} Modified: pkg/CHNOSZ/R/util.args.R =================================================================== --- pkg/CHNOSZ/R/util.args.R 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/R/util.args.R 2017-05-03 02:39:19 UTC (rev 196) @@ -1,5 +1,5 @@ # CHNOSZ/util.args.R -# functions to create argument lists +# functions to create argument lists and get name of calling function ### unexported functions ### @@ -72,3 +72,19 @@ } return(state) } + +caller.name <- function(n=2) { + # returns the name of the calling function n frames up + # (n=2: the caller of the function that calls this one) + # or character() if called interactively + if(sys.nframe() < n) name <- character() + else { + sc <- sys.call(-n)[[1]] + name <- try(as.character(sc),silent=TRUE) + # also return character() if the value from sys.call is + # the function itself (why does this sometimes happen, + # e.g. when called from affinity()?) + if(class(name)=="try-error") name <- character() + } + return(name) +} Deleted: pkg/CHNOSZ/R/util.program.R =================================================================== --- pkg/CHNOSZ/R/util.program.R 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/R/util.program.R 2017-05-03 02:39:19 UTC (rev 196) @@ -1,45 +0,0 @@ -# CHNOSZ/util.program.R -# various programming-related functions - -palply <- function(varlist, X, FUN, ...) { - # a wrapper function to run parLapply if length(X) >= thermo$opt$paramin - # and package 'parallel' is available, otherwise run lapply - if(length(X) >= get("thermo")$opt$paramin) { - # Use option mc.cores to choose an appropriate cluster size. - # and set max at 2 for now (per CRAN policies) - nCores <- min(getOption("mc.cores"), 2) - # don't load methods package, to save startup time - ?makeCluster - cl <- parallel::makeCluster(nCores, methods=FALSE) - # export the variables and notify the user - if(! "" %in% varlist) { - parallel::clusterExport(cl, varlist) - message(paste("palply:", caller.name(4), "running", length(X), "calculations on", - nCores, "cores with variable(s)", paste(varlist, collapse=", "))) - } else { - message(paste("palply:", caller.name(4), "running", length(X), "calculations on", - nCores, "cores")) - } - # run the calculations - out <- parallel::parLapply(cl, X, FUN, ...) - parallel::stopCluster(cl) - } else out <- lapply(X, FUN, ...) - return(out) -} - -### unexported functions ### - -caller.name <- function(n=2) { - # returns the name of the calling function n frames up - # (n=2: the caller of the function that calls this one) - # or character() if called interactively - if(sys.nframe() < n) name <- character() - else { - sc <- sys.call(-n)[[1]] - name <- try(as.character(sc),silent=TRUE) - # also return character() if the value from sys.call is - # the function itself (why does this sometimes happen, - # e.g. when called from affinity()?) - if(class(name)=="try-error") name <- character() - } - return(name) -} Modified: pkg/CHNOSZ/data/thermo.R =================================================================== --- pkg/CHNOSZ/data/thermo.R 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/data/thermo.R 2017-05-03 02:39:19 UTC (rev 196) @@ -31,7 +31,6 @@ groups = read.csv("groups.csv", row.names=1, check.names=FALSE), basis = NULL, species = NULL, - Psat = NULL, opar = NULL ) # place it in CHNOSZ environment Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/inst/NEWS 2017-05-03 02:39:19 UTC (rev 196) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-84 (2017-05-02) +CHANGES IN CHNOSZ 1.0.8-85 (2017-05-03) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/man/data.Rd =================================================================== --- pkg/CHNOSZ/man/data.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/data.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -58,7 +58,7 @@ \item \code{thermo$element} Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982. - The standard molal entropy (\eqn{S}(\code{Z})) at 25 \eqn{^{\circ}}{?}C and 1 bar for the element of charge (\code{Z}) was calculated from \eqn{S}(H2,g) + 2\eqn{S}(\code{Z}) = 2\eqn{S}(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. + The standard molal entropy (\eqn{S}(\code{Z})) at 25 \eqn{^{\circ}}{?}C and 1 bar for the \dQuote{element} of charge (\code{Z}) was calculated from \eqn{S}(H2,g) + 2\eqn{S}(\code{Z}) = 2\eqn{S}(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. The mass of \code{Z} is taken to be zero. Accessing this data frame using \code{\link{mass}} or \code{\link{entropy}} will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989. \tabular{lll}{ @@ -83,7 +83,7 @@ } \samp{OrganoBioGeoTherm} is the name of a GUI program to use SUPCRT in Windows, produced in Harold C. Helgeson's Laboratory of Theoretical Geochemistry and Biogeochemistry at the University of California, Berkeley. - The \acronym{OBIGT} database was originally developed for that program, but has been ported to CHNOSZ, with additional modifications. + The \acronym{OBIGT} database was originally developed for that program, and has been ported to CHNOSZ, with additional modifications. There may be an additional meaning for the acronym: \dQuote{One BIG Table} of thermodynamic data. Each entry is referenced to one or two literature sources listed in \code{thermo$refs}. @@ -158,8 +158,8 @@ \code{key} \tab character \tab Source key\cr \code{author} \tab character \tab Author(s)\cr \code{year} \tab character \tab Year\cr - \code{note} \tab character \tab Short description of the compounds or species in this data source\cr \code{citation} \tab character \tab Citation (journal title, volume, and article number or pages; or book or report title)\cr + \code{note} \tab character \tab Short description of the compounds or species in this data source\cr \code{URL} \tab character \tab URL\cr } @@ -208,18 +208,7 @@ \code{name} \tab character \tab Name of species\cr } - \item \code{thermo$water} - The properties calculated with \code{\link{water}} at multiple T, P points (minimum of 26) are stored here so that repeated calculations at the same conditions can be done more quickly. - - \item \code{thermo$Psat} - The values of Psat calculated with \code{water.SUPCRT} at multiple T points (minimum of 26) are stored here. - - \item \code{thermo$water2} - The properties calculated with \code{water.SUPCRT} at multiple T, P points (minimum of 26) are stored here. - - } % end of itemize with long descriptions - } % end of format Modified: pkg/CHNOSZ/man/diagram.Rd =================================================================== --- pkg/CHNOSZ/man/diagram.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/diagram.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -122,7 +122,7 @@ In cases where it applies (see Warning), the maximum affinity method is much faster than an equilibrium calculation. \code{balance} is the option that determines the balancing coefficients (this argument has no effect on the calculations of equilibrium activities.) If \code{what} is the name of a basis species, it refers to option (2) above. -A contour plot is made in the case of 2-D diagrams of the equilibrium activity of a basis species (see \code{\link{demos}("CO2Ac")}, and only the first species of interest is used in the calculation; a warning is produced if there is more than one. +A contour plot is made in the case of 2-D diagrams of the equilibrium activity of a basis species (see the CO2-acetic acid example in \code{\link{buffer}}, and only the first species of interest is used in the calculation; a warning is produced if there is more than one. A different incarnation of 1-D speciation diagrams is provided by \code{strip}. This function generates any number of strip diagrams in a single plot. Modified: pkg/CHNOSZ/man/extdata.Rd =================================================================== --- pkg/CHNOSZ/man/extdata.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/extdata.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -14,8 +14,8 @@ \itemize{ \item \code{TBD+05.csv} lists genes with transcriptomic expression changes in carbon limitation stress response experiments in yeast (Tai et al., 2005). See \code{\link{read.expr}} for an example that uses this file. \item \code{ISR+08.csv} has columns excerpted from Additional File 2 of Ishihama et al. (2008) for protein abundances in \emph{E. coli} cytosol. The columns in this file are ID (Swiss-Prot ID), accession (Swiss-Prot accession), emPAI (exponentially modified protein abundance index), copynumber (emPAI-derived copy number/cell), GRAVY (Kyte-Doolittel), FunCat (FunCat class description), PSORT (PSORT localisation), ribosomal (yes/no). See \code{\link{read.expr}} for an example that uses this file. - \item \code{yeastgfp.csv.xz} Has 28 columns; the names of the first five are \code{yORF}, \code{gene name}, \code{GFP tagged?}, \code{GFP visualized?}, and \code{abundance}. The remaining columns correspond to the 23 subcellular localizations considered in the YeastGFP project (Huh et al., 2003 and Ghaemmaghami et al., 2003) and hold values of either \code{T} or \code{F} for each protein. \samp{yeastgfp.csv} was downloaded on 2007-02-01 from http://yeastgfp.ucsf.edu using the Advanced Search, setting options to download the entire dataset and to include localization table and abundance, sorted by orf number. See \code{\link{yeastgfp}} and \code{\link{demos}("yeastgfp")} for examples that use this file. - \item \code{microbes.csv} has data for microbial occurrence (i.e. relative enrichement) in colorectal cancer and normal tissue. The file is from the Supporting Information of Dick (2016). This file is used by \code{\link{demos}("bugstab")}. + \item \code{yeastgfp.csv.xz} Has 28 columns; the names of the first five are \code{yORF}, \code{gene name}, \code{GFP tagged?}, \code{GFP visualized?}, and \code{abundance}. The remaining columns correspond to the 23 subcellular localizations considered in the YeastGFP project (Huh et al., 2003 and Ghaemmaghami et al., 2003) and hold values of either \code{T} or \code{F} for each protein. \samp{yeastgfp.csv} was downloaded on 2007-02-01 from http://yeastgfp.ucsf.edu using the Advanced Search, setting options to download the entire dataset and to include localization table and abundance, sorted by orf number. See \code{\link{yeastgfp}} and \code{demo("yeastgfp")} for examples that use this file. + \item \code{microbes.csv} has data for microbial occurrence (i.e. relative enrichement) in colorectal cancer and normal tissue. The file is from the Supporting Information of Dick (2016). This file is used by \code{demo("bugstab")}. } Files in \code{bison} contain BLAST results and taxonomic information for an environmental metagenome from the Bison Pool hot spring in Yellowstone National Park: @@ -30,7 +30,7 @@ \item \code{PM90.csv} Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in \eqn{^{\circ}}{?}C 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{\link{demos}("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. 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{Cp.CH4.HW97.csv}, \code{V.CH4.HWM96.csv} Apparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hn?dkovsk? and Wood, 1997 and Hn?dkovsk? 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 (\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. 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 \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. See the vignette \code{anintro.Rmd} for an example that uses this file. @@ -61,7 +61,7 @@ \item \code{microbial.aa.csv} Overall protein compositions of microbial species reported to be positively or negatively enriched in colorectal cancer. This file is taken from Dick, 2016. - It is used by \code{\link{demos}("bugstab")}. + It is used by \code{demo("bugstab")}. } Files in \code{refseq} contain code and results of processing NCBI Reference Sequences (RefSeq) for microbial proteins, using RefSeq release 61 of 2013-09-09: @@ -97,7 +97,7 @@ \item \code{Ste01.csv} and \code{BZA10.csv} contain supplementary thermodynamic data taken from Stefansson (2001) and Bazarkina et al. (2010). They can be added to the database in the current session using \code{\link{add.obigt}}. See \code{\link{add.obigt}} and the vignette \code{eos-regress.Rmd} for examples that use these files. \item \code{obigt_check.csv} contains the results of running \code{\link{check.obigt}} to check the internal consistency of entries in the primary and supplementary databases. \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{\link{demos}("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")} and the vignette \code{wjd.Rmd} for examples that use this file. } Modified: pkg/CHNOSZ/man/findit.Rd =================================================================== --- pkg/CHNOSZ/man/findit.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/findit.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -74,6 +74,6 @@ \code{findit} returns a list having class \code{findit} with elements \code{value} (values of the parameters, and value of the objective function, at each iteration), \code{lolim} (lower limits of the parameters) and \code{hilim} (upper limits of the parameters). } -\seealso{ \code{\link{demos}("findit")} and \code{test-findit.R} for examples. } +\seealso{ \code{demo("findit")} and \code{test-findit.R} for examples. } \concept{Secondary thermodynamic modeling} Modified: pkg/CHNOSZ/man/info.Rd =================================================================== --- pkg/CHNOSZ/man/info.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/info.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -40,16 +40,12 @@ } -\seealso{ \code{\link{thermo}} } +\seealso{ \code{\link{thermo}}, \code{\link{check.obigt}} } \examples{ \dontshow{data(thermo)} ## summary of available data info() -\dontrun{ -## run a consistency check on each species in the database -# (marked dontrun because it takes a while) -info(check=TRUE) } ## species information # search for something named (or whose formula is) "Fe" Modified: pkg/CHNOSZ/man/nonideal.Rd =================================================================== --- pkg/CHNOSZ/man/nonideal.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/nonideal.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -19,7 +19,8 @@ \details{ \code{nonideal} takes a list of dataframes (in \code{proptable}) containing the standard molal properties of the identified \code{species}. -The function bypasses (leaves unchanged) properties of the proton (H+), electron (e-), and all species whose charge (determined by the number of Z in their \code{\link{makeup}}) is equal to zero. +The function bypasses (leaves unchanged) properties of all species whose charge (determined by the number of Z in their \code{\link{makeup}}) is equal to zero. +The proton (H+) and electron (e-) are also bypassed by default; to apply the calculations to H+ and/or e-, change \code{\link{thermo}$opt$ideal.H} or \code{ideal.e} to FALSE. The values of \code{IS} are combined with Alberty's (2003) equation 3.6-1 (extended Debye-H?ckel equation) and its derivatives, to calculate apparent molal properties at the specified ionic strength(s) and temperature(s). The lengths of \code{IS} and \code{T} supplied in the arguments should be equal to the number of rows of each dataframe in \code{proptable}, or one to use single values throughout. The apparent molal properties that can be calculated include \code{G}, \code{H}, \code{S} and \code{Cp}; any columns in the dataframes of \code{proptable} with other names are left untouched. @@ -65,7 +66,7 @@ IS=c(0, 0.1, 0.25), T=25, property="logK") # note that *apparent* values equal *standard* values at IS=0 # reset option to default -thermo$opt$ideal.H <<- FALSE +thermo$opt$ideal.H <<- TRUE ## p. 95: basis and elemental stoichiometries of species # (this example doesn't use activity coefficients) Copied: pkg/CHNOSZ/man/palply.Rd (from rev 195, pkg/CHNOSZ/man/util.program.Rd) =================================================================== --- pkg/CHNOSZ/man/palply.Rd (rev 0) +++ pkg/CHNOSZ/man/palply.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -0,0 +1,32 @@ +\encoding{UTF-8} +\name{palply} +\alias{palply} + +\title{Conditional Parallel Processing} +\description{ + Use multiple processors for large calculations. +} + +\usage{ + palply(varlist, X, FUN, ...) +} + +\arguments{ + \item{...}{equivalent to the same argument in \code{\link[parallel]{parLapply}}} + \item{varlist}{character, names of variables to export using \code{\link[parallel]{clusterExport}}} + \item{X}{vector, argument for \code{\link{lapply}} or \code{parLapply}} + \item{FUN}{function, argument for \code{lapply} or \code{parLapply}} +} + +\details{ +\code{palply} is a wrapper function to run \code{\link[parallel]{parLapply}} if length of \code{X} > \code{\link{thermo}$opt$paramin} and multiple cores are available, otherwise it runs \code{\link{lapply}}. +Note that \code{parLapply} is called with \code{methods} set to FALSE. +If lots of package startup messages are created when running \code{\link[parallel]{makeCluster}} (which is called by \code{palply}), it can probably be stopped by adding a test for \code{\link{interactive}} sessions around any \code{\link{library}} commands in the \code{\link{Rprofile}}. +} + +\seealso{ +\code{\link{read.fasta}}, \code{\link{count.aa}}, \code{\link{affinity}}, \code{\link{equil.boltzmann}} and \code{\link{equil.reaction}} for functions that use \code{palply}. +Tests are in \file{tests/test-util.program.R}, and a \dQuote{real life} example is in \file{demos/density.R}. +} + +\keyword{utilities} Modified: pkg/CHNOSZ/man/read.expr.Rd =================================================================== --- pkg/CHNOSZ/man/read.expr.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/read.expr.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -28,8 +28,8 @@ \code{read.expr} and \code{yeastgfp} read data files stored in \code{\link{extdata}/abundance} to retrieve identities and possibly abundances of proteins in certain conditions. \code{yeastgfp} returns the identities and abundances of proteins with the requested subcellular localization(s) (specified in \code{location}) using data from the YeastGFP project that is stored in \code{\link{extdata}/abundance/yeastgfp.csv.xz}. -The default value of \code{exclusive} (\code{FALSE}) tells the function to grab all proteins that are localized to a compartment even if they are also localized to other compartments. -If \code{exclusive} is \code{TRUE}, only those proteins that are localized exclusively to the requested compartments are identified, unless there are no such proteins, then the non-exclusive localizations are used (applies to the \samp{bud} localization). +If \code{exclusive} is \code{FALSE}, the function grabs all proteins that are localized to a compartment even if they are also localized to other compartments. +If \code{exclusive} is \code{TRUE} (the default), only those proteins that are localized exclusively to the requested compartments are identified, unless there are no such proteins, then the non-exclusive localizations are used (applies to the \samp{bud} localization). \code{read.expr} reads a \code{file} (CSV format) that contains protein sequence names or IDs and protein abundance data. \code{idcol} and \code{abundcol} are either the names of the columns holding the sequence IDs and protein abundances, or numeric values indicating the column numbers where these data are found. @@ -111,8 +111,6 @@ \references{ Boer, V. M., de Winde, J. H., Pronk, J. T. and Piper, M. D. W. (2003) The genome-wide transcriptional responses of \emph{Saccharomyces cerevisiae} grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. \emph{J. Biol. Chem.} \bold{278}, 3265--3274. \url{http://dx.doi.org/10.1074/jbc.M209759200} -Dick, J. M. (2009) Calculation of the relative metastabilities of proteins in subcellular compartments of \emph{Saccharomyces cerevisiae}. \emph{BMC Syst. Biol.} \bold{3}:75. \url{http://dx.doi.org/10.1186/1752-0509-3-75} - 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} 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{http://dx.doi.org/10.1074/jbc.M410573200} Modified: pkg/CHNOSZ/man/species.Rd =================================================================== --- pkg/CHNOSZ/man/species.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/species.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -18,17 +18,27 @@ } \details{ - After defining the \code{\link{basis}} species of your system you can use \code{species} to identify for the program the species of interest. A species is operationally a combination of a \code{name} and \code{state}, which are columns of the thermodynamic database in \code{\link{thermo}$obigt}. The function operates on one or more character values of \code{species}. For each first match of \code{species} (optionally restricted to a \code{state} among \samp{aq}, \samp{cr}, \samp{gas}, \samp{liq}) to the name of a species or a formula or abbreviation in the thermodynamic database, a row is added to \code{thermo$species}. +After defining the \code{\link{basis}} species of your system you can use \code{species} to identify the species of interest. +A species is operationally a combination of a \code{name} and \code{state}, which are columns of the thermodynamic database in \code{\link{thermo}$obigt}. +The function operates on one or more character values of \code{species}. +For each first match of \code{species} (optionally restricted to a \code{state} among \samp{aq}, \samp{cr}, \samp{gas}, \samp{liq}) to the name of a species or a formula or abbreviation in the thermodynamic database, a row is added to \code{thermo$species}. - The data frame in \code{thermo$species} holds the identifying characteristics of the species as well as the stoichiometric reaction coefficients for the formation of each of the species from the basis species, and reference settings for the logarithms of activities or fugacities used in calculations of \code{\link{affinity}}. The default values for logarithms of activities are -3 for aqueous (\samp{aq}) species and 0 for others. +The data frame in \code{thermo$species} holds the identifying characteristics of the species as well as the stoichiometric reaction coefficients for the formation of each of the species from the basis species, the logarithms of activities or fugacities that are used by \code{\link{affinity}}. +The default values for logarithms of activities are -3 for aqueous (\samp{aq}) species and 0 for others. - If \code{state} is \code{NULL} (the default), species in any state can be matched in the thermodynamic database. If there are multiple matches for a species, the one that is in the state given by \code{thermo$opt$state} is chosen, otherwise the matching (or \eqn{n}{n}'th matching duplicate) species is used. Note that the \code{state}s of species representing phases of minerals that undergo phase transitions are coded as \samp{cr1}, \samp{cr2}, \samp{cr3}, \code{...} (phases with increasing temperature). If \code{state} is \samp{cr} when one of these minerals is matched, all the phase species are added. +If \code{state} is \code{NULL} (the default), species in any state can be matched in the thermodynamic database. +If there are multiple matches for a species, the one that is in the state given by \code{thermo$opt$state} is chosen, otherwise the matching (or \eqn{n}{n}'th matching duplicate) species is used. +Note that the \code{state}s of species representing phases of minerals that undergo phase transitions are coded as \samp{cr1}, \samp{cr2}, \samp{cr3}, \code{...} (phases with increasing temperature). +If \code{state} is \samp{cr} when one of these minerals is matched, all the phase species are added. - To modify the logarithms of activities of species (logarithms of fugacities for gases) provide one or more numeric values of \code{species} referring to the rownumbers of the species dataframe, or \code{species} NULL, to modify all currently defined species. The values in \code{state}, if numeric, are interpreted as the logarithms of activities, or if character are interpreted as states to which the species should be changed. If \code{species} is numeric and \code{delete} is \code{TRUE}, the rows representing these species are deleted from the dataframe; if the only argument is \code{delete} and it is \code{TRUE}, all the species are removed. +To modify the logarithms of activities of species (logarithms of fugacities for gases) provide one or more numeric values of \code{species} referring to the rownumbers of the species dataframe, or \code{species} NULL, to modify all currently defined species. +The values in \code{state}, if numeric, are interpreted as the logarithms of activities, or if character are interpreted as states to which the species should be changed. +If \code{species} is numeric and \code{delete} is \code{TRUE}, the rows representing these species are deleted from the dataframe; if the only argument is \code{delete} and it is \code{TRUE}, all the species are removed. } \value{ - With no arguments or when adding species, \code{species} returns the value of \code{thermo$species}, unless \code{index.return} is TRUE, when the function returns the rownumbers of \code{thermo$species} having the new species. With \samp{delete=TRUE}, the value is the definition that existed prior the deletion; with \samp{delete=TRUE} and \samp{species} not NULL, the number of species remaining after the selected ones have been deleted, or \code{NULL} if no species remain. +With no arguments or when adding species, \code{species} returns the value of \code{thermo$species}, unless \code{index.return} is TRUE, when the function returns the rownumbers of \code{thermo$species} having the new species. +With \samp{delete=TRUE}, the value is the definition that existed prior the deletion; with \samp{delete=TRUE} and \samp{species} not NULL, the number of species remaining after the selected ones have been deleted, or \code{NULL} if no species remain. } \seealso{ Modified: pkg/CHNOSZ/man/subcrt.Rd =================================================================== --- pkg/CHNOSZ/man/subcrt.Rd 2017-05-02 04:44:02 UTC (rev 195) +++ pkg/CHNOSZ/man/subcrt.Rd 2017-05-03 02:39:19 UTC (rev 196) @@ -3,7 +3,7 @@ \alias{subcrt} \title{Properties of Species and Reactions} \description{ - Calculate the standard molal thermodynamic properties of one or more species or a reaction between species as a function of temperature and pressure. Import or export thermodynamic data in \acronym{SUPCRT} format. + Calculate the standard molal thermodynamic properties of one or more species or a reaction between species as a function of temperature and pressure. } \usage{ @@ -31,12 +31,14 @@ } \details{ [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 196 From noreply at r-forge.r-project.org Wed May 3 11:45:02 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 3 May 2017 11:45:02 +0200 (CEST) Subject: [CHNOSZ-commits] r197 - in pkg/CHNOSZ: . R inst man vignettes Message-ID: <20170503094502.AE3A21886CC@r-forge.r-project.org> Author: jedick Date: 2017-05-03 11:45:02 +0200 (Wed, 03 May 2017) New Revision: 197 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/basis.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/basis.Rd pkg/CHNOSZ/man/palply.Rd pkg/CHNOSZ/vignettes/anintro.Rmd Log: preset.basis(): add 'QEC4' keyword Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-03 09:45:02 UTC (rev 197) @@ -1,6 +1,6 @@ Date: 2017-05-03 Package: CHNOSZ -Version: 1.0.8-85 +Version: 1.0.8-86 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/basis.R =================================================================== --- pkg/CHNOSZ/R/basis.R 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/R/basis.R 2017-05-03 09:45:02 UTC (rev 197) @@ -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", "QEC+") + basis.key <- c("CHNOS", "CHNOS+", "CHNOSe", "CHNOPS+", "MgCHNOPS+", "FeCHNOS", "FeCHNOS+", "QEC4", "QEC", "QEC+") # just list the keywords if none is specified if(is.null(key)) return(basis.key) # delete any previous basis definition @@ -193,10 +193,12 @@ else if(ibase==5) species <- c("Mg+2", "CO2", "H2O", "NH3", "H3PO4", "H2S", "e-", "H+") 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+") + else if(ibase %in% c(8, 9)) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen") + else if(ibase==10) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen", "H+") # get the preset logact logact <- preset.logact(species) + # for QEC4, we use logact = -4 for the amino acids + if(key=="QEC4") logact[1:3] <- -4 # load the species and return the result return(basis(species, logact)) } Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/inst/NEWS 2017-05-03 09:45:02 UTC (rev 197) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-85 (2017-05-03) +CHANGES IN CHNOSZ 1.0.8-86 (2017-05-03) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/man/basis.Rd =================================================================== --- pkg/CHNOSZ/man/basis.Rd 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/man/basis.Rd 2017-05-03 09:45:02 UTC (rev 197) @@ -29,7 +29,6 @@ Alternatively, the first argument may consist of numeric values indicating the species indices (rownumbers in \code{\link{thermo}$obigt}), but a mixture of character and numeric values will generate an error. The special names \samp{pH}, \samp{pe} and \samp{Eh} can be included in the \code{species} argument; they get translated into the names of the proton (\samp{H+}) and electron (\samp{e-}) as appropriate. - The physical states or logarithms of activities of species in the basis definition can be changed by calling \code{basis} with the formulas of species that are in the basis set, or their species indices. If either of the second or third arguments to \code{basis} is of type character, it refers to the name of a state (if present in \code{thermo$obigt$state}) or to the name of a chemical activity \code{\link{buffer}} (if present in \code{thermo$buffers$name}). If either of these arguments is numeric it specifies the logarithms of activities (or fugacities for gases) of the basis species. @@ -49,7 +48,7 @@ \tabular{ll}{ \code{CHNOS} \tab \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} \cr + \eqn{\mathrm{H_2S}}{H2S}, \eqn{\mathrm{O_2}}{O2} (basis I in Dick, 2016)\cr \code{CHNOS+} \tab \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{CHNOSe} \tab \eqn{\mathrm{CO_2}}{CO2}, \eqn{\mathrm{H_2O}}{H2O}, \eqn{\mathrm{NH_3}}{NH3}, @@ -63,10 +62,12 @@ \eqn{\mathrm{NH_3}}{NH3}, \eqn{\mathrm{H_2S}}{H2S}, \eqn{\mathrm{O_2}}{O2} \cr \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{QEC4} \tab cysteine, glutamic acid, glutamine, \eqn{\mathrm{H_2O}}{H2O}, \eqn{\mathrm{O_2}}{O2} (basis II in Dick, 2016) \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 } +The logarithms of activities of amino acids in the \samp{QEC4} basis are -4; those in \samp{QEC} and \samp{QEC+} are set to approximate concentrations in human plasma (see Dick, 2017). } \value{ @@ -84,6 +85,12 @@ \code{\link{species}} for setting up the formation reactions from basis species. } +\references{ +Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \url{http://dx.doi.org/10.7717/peerj.2238} + +Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{bioRxiv} \url{https://doi.org/10.1101/097667} +} + \examples{ \dontshow{data(thermo)} ## define basis species Modified: pkg/CHNOSZ/man/palply.Rd =================================================================== --- pkg/CHNOSZ/man/palply.Rd 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/man/palply.Rd 2017-05-03 09:45:02 UTC (rev 197) @@ -26,7 +26,7 @@ \seealso{ \code{\link{read.fasta}}, \code{\link{count.aa}}, \code{\link{affinity}}, \code{\link{equil.boltzmann}} and \code{\link{equil.reaction}} for functions that use \code{palply}. -Tests are in \file{tests/test-util.program.R}, and a \dQuote{real life} example is in \file{demos/density.R}. +Tests are in \file{tests/test-util.program.R}, and a \dQuote{real world} example is in \file{demos/density.R}. } \keyword{utilities} Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-03 02:39:19 UTC (rev 196) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-03 09:45:02 UTC (rev 197) @@ -97,7 +97,7 @@ # First steps This document introduces the usage of CHNOSZ, a package for the [R software environment](http://r-project.org). -For more information on R, see "[An Introduction to R](http://cran.r-project.org/manuals.html)" and the [contributed documentation](https://cran.r-project.org/other-docs.html) for R. +For more information on R, see "[An Introduction to R](https://cran.r-project.org/manuals.html)" and the [contributed documentation](https://cran.r-project.org/other-docs.html) for R. CHNOSZ has been developed since 2006 as a tool for thermodynamic calculations in geochemistry and compositional biology. The package provides functions and a thermodynamic database that can be used to calculate the stoichiometric and energetic properties of reactions involving minerals and inorganic and/or organic aqueous species. @@ -1513,7 +1513,7 @@ ## Activity coefficients -`nonideal()` uses the Debye--H?ckel equation, described in Chapter 3 of @Alb03, to calculate activity coefficients of charged species. +`nonideal()` uses the extended Debye--H?ckel equation, described in Chapter 3 of @Alb03, to calculate activity coefficients of charged species. The calculations can be invoked by setting the `IS` argument in `subcrt()` or `affinity()`. The activity coefficients are calculated as a function of ionic strength (*I*), temperature, and charge of each species, without any other species-specific parameters. Due to these assumptions, as well as the limited applicability of the implemented equations to very high *I* and/or *T*, `nonideal()` is presented as an experimental feature. From noreply at r-forge.r-project.org Wed May 3 16:38:51 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 3 May 2017 16:38:51 +0200 (CEST) Subject: [CHNOSZ-commits] r198 - in pkg/CHNOSZ: . R inst man Message-ID: <20170503143851.89DB8188E3D@r-forge.r-project.org> Author: jedick Date: 2017-05-03 16:38:51 +0200 (Wed, 03 May 2017) New Revision: 198 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/util.expression.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/util.expression.Rd Log: syslab(): add 'dash' argument Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-03 09:45:02 UTC (rev 197) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-03 14:38:51 UTC (rev 198) @@ -1,6 +1,6 @@ Date: 2017-05-03 Package: CHNOSZ -Version: 1.0.8-86 +Version: 1.0.8-87 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/util.expression.R =================================================================== --- pkg/CHNOSZ/R/util.expression.R 2017-05-03 09:45:02 UTC (rev 197) +++ pkg/CHNOSZ/R/util.expression.R 2017-05-03 14:38:51 UTC (rev 198) @@ -270,11 +270,11 @@ } # make formatted text for thermodynamic system 20170217 -syslab <- function(system = c("K2O", "Al2O3", "SiO2", "H2O")) { +syslab <- function(system = c("K2O", "Al2O3", "SiO2", "H2O"), dash="\u2013") { for(i in seq_along(system)) { expr <- expr.species(system[i]) # use en dash here - if(i==1) lab <- expr else lab <- substitute(a*"\u2013"*b, list(a=lab, b=expr)) + if(i==1) lab <- expr else lab <- substitute(a*dash*b, list(a=lab, dash=dash, b=expr)) } lab } Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-03 09:45:02 UTC (rev 197) +++ pkg/CHNOSZ/inst/NEWS 2017-05-03 14:38:51 UTC (rev 198) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-86 (2017-05-03) +CHANGES IN CHNOSZ 1.0.8-87 (2017-05-03) --------------------------------------- DOCUMENTATION: Modified: pkg/CHNOSZ/man/util.expression.Rd =================================================================== --- pkg/CHNOSZ/man/util.expression.Rd 2017-05-03 09:45:02 UTC (rev 197) +++ pkg/CHNOSZ/man/util.expression.Rd 2017-05-03 14:38:51 UTC (rev 198) @@ -23,7 +23,7 @@ describe.property(property, value, digits = 1, oneline = FALSE, ret.val = FALSE) describe.reaction(reaction, iname = numeric(), states = NULL) - syslab(system = c("K2O", "Al2O3", "SiO2", "H2O")) + syslab(system = c("K2O", "Al2O3", "SiO2", "H2O"), dash="\u2013") ratlab(ion = "K+") } @@ -46,6 +46,7 @@ \item{iname}{numeric, show names instead of formulas for these species} \item{states}{character, if \samp{all}, show states for all species} \item{system}{character, thermodynamic components} + \item{dash}{character to use for dash between components} \item{ion}{character, an ion} } From noreply at r-forge.r-project.org Thu May 4 05:43:05 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 4 May 2017 05:43:05 +0200 (CEST) Subject: [CHNOSZ-commits] r199 - in pkg/CHNOSZ: . data demo inst inst/extdata/cpetc man man/macros tests/testthat vignettes Message-ID: <20170504034305.44EBF188B04@r-forge.r-project.org> Author: jedick Date: 2017-05-04 05:43:04 +0200 (Thu, 04 May 2017) New Revision: 199 Added: pkg/CHNOSZ/man/macros/ pkg/CHNOSZ/man/macros/macros.Rd Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/data/refs.csv pkg/CHNOSZ/demo/NaCl.R pkg/CHNOSZ/demo/Shh.R pkg/CHNOSZ/demo/activity_ratios.R pkg/CHNOSZ/demo/affinity.R pkg/CHNOSZ/demo/bugstab.R pkg/CHNOSZ/demo/dehydration.R pkg/CHNOSZ/demo/wjd.R pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/extdata/cpetc/rubisco.csv pkg/CHNOSZ/man/CHNOSZ-package.Rd pkg/CHNOSZ/man/EOSregress.Rd pkg/CHNOSZ/man/IAPWS95.Rd pkg/CHNOSZ/man/affinity.Rd pkg/CHNOSZ/man/anim.Rd pkg/CHNOSZ/man/basis.Rd pkg/CHNOSZ/man/data.Rd pkg/CHNOSZ/man/diagram.Rd pkg/CHNOSZ/man/eos.Rd pkg/CHNOSZ/man/equilibrate.Rd pkg/CHNOSZ/man/examples.Rd pkg/CHNOSZ/man/extdata.Rd pkg/CHNOSZ/man/ionize.aa.Rd pkg/CHNOSZ/man/objective.Rd pkg/CHNOSZ/man/protein.info.Rd pkg/CHNOSZ/man/read.expr.Rd pkg/CHNOSZ/man/subcrt.Rd pkg/CHNOSZ/man/transfer.Rd pkg/CHNOSZ/man/util.blast.Rd pkg/CHNOSZ/man/util.data.Rd pkg/CHNOSZ/man/util.formula.Rd pkg/CHNOSZ/man/util.protein.Rd pkg/CHNOSZ/man/util.water.Rd pkg/CHNOSZ/man/water.Rd pkg/CHNOSZ/man/wjd.Rd pkg/CHNOSZ/tests/testthat/test-IAPWS95.R pkg/CHNOSZ/tests/testthat/test-eos.R pkg/CHNOSZ/tests/testthat/test-equilibrate.R pkg/CHNOSZ/tests/testthat/test-ionize.aa.R pkg/CHNOSZ/tests/testthat/test-ionize.aa_pK.R pkg/CHNOSZ/tests/testthat/test-protein.info.R pkg/CHNOSZ/tests/testthat/test-subcrt.R pkg/CHNOSZ/tests/testthat/test-util.data.R pkg/CHNOSZ/tests/testthat/test-water.R pkg/CHNOSZ/tests/testthat/test-wjd.R pkg/CHNOSZ/vignettes/equilibrium.Rnw pkg/CHNOSZ/vignettes/equilibrium.lyx pkg/CHNOSZ/vignettes/hotspring.Rnw pkg/CHNOSZ/vignettes/hotspring.lyx pkg/CHNOSZ/vignettes/rubisco.svg pkg/CHNOSZ/vignettes/wjd.Rnw pkg/CHNOSZ/vignettes/wjd.lyx Log: minor documentation changes #4 Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-03 14:38:51 UTC (rev 198) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-04 03:43:04 UTC (rev 199) @@ -1,6 +1,6 @@ -Date: 2017-05-03 +Date: 2017-05-04 Package: CHNOSZ -Version: 1.0.8-87 +Version: 1.0.8-88 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/data/refs.csv =================================================================== --- pkg/CHNOSZ/data/refs.csv 2017-05-03 14:38:51 UTC (rev 198) +++ pkg/CHNOSZ/data/refs.csv 2017-05-04 03:43:04 UTC (rev 199) @@ -10,95 +10,95 @@ RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452 RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452 RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452 -PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.doi.org/10.1016/0016-7037(82)90056-4 +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",MgSO4,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf -BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2 -Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845 -JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365 -SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",http://dx.doi.org/10.1016/0016-7037(88)90181-0 -SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",http://dx.doi.org/10.1016/0016-7037(89)90341-4 -SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",http://dx.doi.org/10.1016/0016-7037(90)90429-O +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 +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 +SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0 +SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4 +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 Joh92a,"J. W. Johnson",1992,"personal communication","steam, Cp represented by the Maier-Kelley equation", SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "", SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "", SPRONS92.3,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file",""Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."", -Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",http://dx.doi.org/10.1016/0016-7037(92)90392-V -Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",http://dx.doi.org/10.1016/0016-7037(93)90542-5 -Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",http://dx.doi.org/10.1016/0016-7037(93)90542-5 -SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",http://dx.doi.org/10.1016/0016-7037(93)90128-J -SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",http://dx.doi.org/10.1006/icar.1993.1185 -SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,http://dx.doi.org/10.1016/0016-7037(93)90337-V -HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",http://dx.doi.org/10.1016/0016-7037(95)00314-P -PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,http://dx.doi.org/10.1063/1.555964 +Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",https://doi.org/10.1016/0016-7037(92)90392-V +Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5 +Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5 +SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J +SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185 +SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V +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 +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 -SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",http://dx.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 not included in later slop files.",http://dx.doi.org/10.1016/0016-7037(95)00058-8 -Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",http://dx.doi.org/10.2475/ajs.295.5.496 -AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",http://dx.doi.org/10.1039/A608126F -DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",http://dx.doi.org/10.1016/S0016-7037(97)00212-3 -MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO4, NaSO4-, and HCl",http://dx.doi.org/10.1016/S0016-7037(97)00241-X -MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,http://dx.doi.org/10.1016/S0016-7037(97)00241-X -SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",http://dx.doi.org/10.1016/S0016-7037(97)00240-8 -SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,http://dx.doi.org/10.1016/S0016-7037(97)00240-8 -SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",http://dx.doi.org/10.1016/S0016-7037(97)00009-4 -SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","inorganic ions and hydroxide complexes",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 -SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",http://dx.doi.org/10.1016/S0016-7037(96)00339-0 -TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",http://dx.doi.org/10.1016/S1251-8050(97)83981-X -HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 -HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",http://dx.doi.org/10.1016/S0016-7037(97)00219-6 -RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",http://dx.doi.org/10.1016/S0016-7037(97)00345-1 +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 not included in later slop files.",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 +AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F +DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3 +DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3 +DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3 +MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO4, NaSO4-, and HCl",https://doi.org/10.1016/S0016-7037(97)00241-X +MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,https://doi.org/10.1016/S0016-7037(97)00241-X +SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8 +SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8 +SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4 +SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","inorganic ions and hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0 +SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",https://doi.org/10.1016/S0016-7037(96)00339-0 +TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X +HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6 +HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6 +RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1 SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "Gf and Hf from @SS93a TMM"",http://geopig.asu.edu/?q=tools SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools -SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,http://dx.doi.org/10.1016/S0016-7037(98)00049-0 -HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",http://dx.doi.org/10.1016/S0016-7037(99)00276-8 +SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0 +SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0 +SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh+3,https://doi.org/10.1016/S0016-7037(98)00049-0 +HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8 MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221 -PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",http://dx.doi.org/10.1016/S0016-7037(99)00146-5 -SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",http://dx.doi.org/10.2138/rmg.2000.40.9 -AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,http://dx.doi.org/10.1016/S0016-7037(01)00707-4 -AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N2O",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x -AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x -MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",http://dx.doi.org/10.1016/S0883-2927(00)00025-1 -PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",http://dx.doi.org/10.1016/S0016-7037(01)00678-0 -Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",http://dx.doi.org/10.1016/S0016-7037(01)00761-X -SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6",http://dx.doi.org/10.1016/S0016-7037(01)00717-7 -MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",http://dx.doi.org/10.2138/am-2003-5-614 -MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",http://dx.doi.org/10.2138/am-2003-5-613 -MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",http://dx.doi.org/10.1007/s00269-004-0405-z -SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",http://dx.doi.org/10.1016/j.gca.2003.06.001 -HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org/10.1016/j.jct.2005.10.013 -LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",http://dx.doi.org/10.1016/j.gca.2006.04.010 -LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",http://dx.doi.org/10.1016/j.gca.2006.04.010 -LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",http://dx.doi.org/10.1016/j.tca.2006.06.008 -LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",http://dx.doi.org/10.1016/j.tca.2006.06.008 -DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",http://dx.doi.org/10.5194/bg-3-311-2006 -DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",http://dx.doi.org/10.5194/bg-3-311-2006 -MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175 +PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5 +SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9 +AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://doi.org/10.1016/S0016-7037(01)00707-4 +AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N2O",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x +AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x +MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",https://doi.org/10.1016/S0883-2927(00)00025-1 +PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",https://doi.org/10.1016/S0016-7037(01)00678-0 +Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X +SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6",https://doi.org/10.1016/S0016-7037(01)00717-7 +MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614 +MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",https://doi.org/10.2138/am-2003-5-613 +MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z +SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001 +HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013 +LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010 +LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010 +LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",https://doi.org/10.1016/j.tca.2006.06.008 +LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",https://doi.org/10.1016/j.tca.2006.06.008 +DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006 +DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",https://doi.org/10.5194/bg-3-311-2006 +DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",https://doi.org/10.5194/bg-3-311-2006 +MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175 Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain", -MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes",http://dx.doi.org/10.1007/s00254-006-0578-5 +MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363","metal-arsenate and metal-arsenite complexes",https://doi.org/10.1007/s00254-006-0578-5 SLOP07.1,"E. L. Shock et al.",2007,"slop07.dat computer data file","corrected charge of Pu(Oxal)+2",http://geopig.asu.edu/?q=tools SLOP07.2,"E. L. Shock et al.",2007,"slop07.dat computer data file","high-temperature HKF parameters from @AP01",http://geopig.asu.edu/?q=tools Ric08,"L. Richard",2008,"personal communication",alkenes, -GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815","kieserite, starkeyite, hexahydrite, and epsomite",http://dx.doi.org/10.1016/j.gca.2009.08.005 -HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",kerogens,http://dx.doi.org/10.1016/j.gca.2008.03.004 -AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010 -MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",http://dx.doi.org/10.1007/s12665-009-0369-x -Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",http://dx.doi.org/10.1007/s10498-010-9102-3 -RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",http://dx.doi.org/10.1016/j.gca.2011.07.030 -LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",http://dx.doi.org/10.1016/j.gca.2011.11.041 -LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",http://dx.doi.org/10.1016/j.gca.2011.11.041 -LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041 -LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041 -DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",http://dx.doi.org/10.1016/j.gca.2013.08.020 +GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815","kieserite, starkeyite, hexahydrite, and epsomite",https://doi.org/10.1016/j.gca.2009.08.005 +HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",kerogens,https://doi.org/10.1016/j.gca.2008.03.004 +AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260","metal-chromate complexes",https://doi.org/10.1016/j.apgeochem.2009.11.010 +MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",https://doi.org/10.1007/s12665-009-0369-x +Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",https://doi.org/10.1007/s10498-010-9102-3 +RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",https://doi.org/10.1016/j.gca.2011.07.030 +LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",https://doi.org/10.1016/j.gca.2011.11.041 +LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",https://doi.org/10.1016/j.gca.2011.11.041 +LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",https://doi.org/10.1016/j.gca.2011.11.041 +LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",https://doi.org/10.1016/j.gca.2011.11.041 +DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",https://doi.org/10.1016/j.gca.2013.08.020 SLOP15.1,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools SLOP15.2,"E. L. Shock et al.",2015,"slop15.dat computer data file","Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",http://geopig.asu.edu/?q=tools SLOP15.3,"E. L. Shock et al.",2015,"slop15.dat computer data file","formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."",http://geopig.asu.edu/?q=tools @@ -106,8 +106,8 @@ SLOP15.5,"E. L. Shock et al.",2015,"slop15.dat computer data file","n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."",http://geopig.asu.edu/?q=tools SLOP15.6,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools SLOP15.7,"E. L. Shock et al.",2015,"slop15.dat computer data file","hexanol, heptanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to @SH90."",http://geopig.asu.edu/?q=tools -CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",http://dx.doi.org/10.1016/j.gca.2016.08.028 -CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a1--a4 parameters",http://dx.doi.org/10.1016/j.gca.2016.08.028 +CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid cycle metabolites",https://doi.org/10.1016/j.gca.2016.08.028 +CS16.1,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322","citric acid species HKF a1--a4 parameters",https://doi.org/10.1016/j.gca.2016.08.028 CHNOSZ.1,"J. M. Dick",2017,"CHNOSZ package documentation","GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.",http://chnosz.net CHNOSZ.2,"J. M. Dick",2017,"CHNOSZ package documentation","alanate and glycinate: GHS as used by @DLH06",http://chnosz.net CHNOSZ.3,"J. M. Dick",2017,"CHNOSZ package documentation","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net Modified: pkg/CHNOSZ/demo/NaCl.R =================================================================== --- pkg/CHNOSZ/demo/NaCl.R 2017-05-03 14:38:51 UTC (rev 198) +++ pkg/CHNOSZ/demo/NaCl.R 2017-05-04 03:43:04 UTC (rev 199) @@ -3,7 +3,7 @@ ## (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 degrees C and 5 kbar. -## J. Chem. Soc. Faraday Trans. 88, 803-826. http://dx.doi.org/10.1039/FT9928800803 ) +## J. Chem. Soc. Faraday Trans. 88, 803-826. https://doi.org/10.1039/FT9928800803 ) species <- c("NaCl", "Na+", "Cl-") coeffs <- c(-1, 1, 1) # start a new plot and show the experimental logK Modified: pkg/CHNOSZ/demo/Shh.R =================================================================== --- pkg/CHNOSZ/demo/Shh.R 2017-05-03 14:38:51 UTC (rev 198) +++ pkg/CHNOSZ/demo/Shh.R 2017-05-04 03:43:04 UTC (rev 199) @@ -1,5 +1,5 @@ # Compare affinities of Sonic hedgehog and transcription factors involved in dorsal-ventral patterning -# (Dick, 2015. Chemical integration of proteins in signaling and development. http://dx.doi.org/10.1101/015826) +# (Dick, 2015. Chemical integration of proteins in signaling and development. https://doi.org/10.1101/015826) # UniProt names of the proteins pname <- c("SHH", "OLIG2", "NKX22", "FOXA2", "IRX3", "PAX6", "NKX62", "DBX1", Modified: pkg/CHNOSZ/demo/activity_ratios.R =================================================================== --- pkg/CHNOSZ/demo/activity_ratios.R 2017-05-03 14:38:51 UTC (rev 198) +++ pkg/CHNOSZ/demo/activity_ratios.R 2017-05-04 03:43:04 UTC (rev 199) @@ -35,7 +35,7 @@ # with accordingly different axis ranges ## MgO-CaO-SiO2-H2O at 300 degree C and Psat -## Russell et al., 2010 (http://dx.doi.org/10.1111/j.1472-4669.2010.00249.x) +## Russell et al., 2010 (https://doi.org/10.1111/j.1472-4669.2010.00249.x) basis(c("Mg+2", "Ca+2", "SiO2", "H2O", "O2", "H+")) species(c("brucite", "chrysotile", "talc", "tremolite", "diopside", "akermanite")) a <- affinity(SiO2 = c(-10, 0, res), `Ca+2` = c(0, 20, res), T = 300) @@ -45,7 +45,7 @@ ## CaO-MgO-SiO2-H2O and ## CaO-Al2O3-MgO-SiO2-H2O at 300 degree C and 500 bar -## Bach and Klein, 2009 (http://dx.doi.org/10.1016/j.lithos.2008.10.022) +## Bach and Klein, 2009 (https://doi.org/10.1016/j.lithos.2008.10.022) basis(c("Ca+2", "Al+3", "Mg+2", "SiO2", "H2O", "O2", "H+")) species(c("clinochlore,14a", "clinozoisite", "prehnite", "grossular")) a <- affinity(SiO2 = c(-5, 0, res), `Ca+2` = c(6, 11, res), T = 300, P = 500) Modified: pkg/CHNOSZ/demo/affinity.R =================================================================== [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 199 From noreply at r-forge.r-project.org Thu May 4 13:28:40 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 4 May 2017 13:28:40 +0200 (CEST) Subject: [CHNOSZ-commits] r200 - in pkg/CHNOSZ: . inst man vignettes Message-ID: <20170504112840.707E1188D1A@r-forge.r-project.org> Author: jedick Date: 2017-05-04 13:28:39 +0200 (Thu, 04 May 2017) New Revision: 200 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/revisit.Rd pkg/CHNOSZ/man/util.misc.Rd pkg/CHNOSZ/man/util.plot.Rd pkg/CHNOSZ/man/wjd.Rd pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/vig.bib Log: minor documentation changes #5 Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-04 11:28:39 UTC (rev 200) @@ -1,24 +1,23 @@ Date: 2017-05-04 Package: CHNOSZ -Version: 1.0.8-88 +Version: 1.0.8-89 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Depends: R (>= 3.1.0) Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice Imports: grDevices, graphics, stats, utils, colorspace -Description: Tools for thermodynamic calculations in compositional biology and - low-temperature geochemistry. Thermodynamic properties are taken from a database - including aqueous species, minerals, and biomolecules, or from amino acid group - additivity for proteins. High-temperature properties are calculated using the - revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions - are provided to define a system using basis species, automatically balance reactions, - calculate the chemical affinities of reactions for selected species, and plot the - results on potential diagrams or equilibrium activity diagrams. Experimental functions - calculate activity coefficients for aqueous species or optimize multiple thermodynamic - variables using an objective function for chemical activities. +Description: An integrated set of tools for thermodynamic calculations in compositional + biology and geochemistry. Thermodynamic properties are taken from a database for minerals + and inorganic and organic aqueous species including biomolecules, or from amino acid + group additivity for proteins. High-temperature properties are calculated using the + revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions are + provided to define a system using basis species, automatically balance reactions, + calculate the chemical affinities of reactions for selected species, and plot the results + on potential diagrams or equilibrium activity diagrams. Experimental features are + available to calculate activity coefficients for aqueous species or for multidimensional + optimization of thermodynamic variables using an objective function. License: GPL (>= 2) BuildResaveData: no -ZipData: no VignetteBuilder: knitr URL: http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/ Modified: pkg/CHNOSZ/inst/CHECKLIST =================================================================== --- pkg/CHNOSZ/inst/CHECKLIST 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/inst/CHECKLIST 2017-05-04 11:28:39 UTC (rev 200) @@ -33,10 +33,7 @@ - update list of documentation topics in examples() with any new ones -- especially on Windows: - - data files are uncompressed on installation? (from BuildResaveData: no) - (so that users can copy and modify the thermodynamic database) - - anim.*() produce pngs / movies (ImageMagick dependency)? +- especially on Windows: anim.*() produce pngs / movies (ImageMagick dependency)? - check for stale URLs in Rd files @@ -52,3 +49,6 @@ - Secondary thermodynamic modeling (less often-used functions e.g. revisit) - Extra thermodynamic modeling (out-of-workflow functions e.g. transfer) - Protein thermodynamic modeling (protein-specific functions e.g. ionize.aa) + +- although Rd files could use the \doi macro, it generates a largish (ca. 265K) + build/partial.rdb file; just use \url for now. Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/inst/NEWS 2017-05-04 11:28:39 UTC (rev 200) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.8-88 (2017-05-04) +CHANGES IN CHNOSZ 1.0.8-89 (2017-05-04) --------------------------------------- DOCUMENTATION: @@ -156,7 +156,7 @@ - Correct charge (-2) of NAD(red)-2 in biotic_aq.csv. Thanks to Peter Canovas. -- Also correct charge (-2) of MgATP-2. +- Correct charge (-2) of MgATP-2. - subcrt() returns `loggam` using the common logarithm; add test-nonideal.R to check for consistency between loggam and logK Modified: pkg/CHNOSZ/man/revisit.Rd =================================================================== --- pkg/CHNOSZ/man/revisit.Rd 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/man/revisit.Rd 2017-05-04 11:28:39 UTC (rev 200) @@ -69,7 +69,7 @@ In this case, plotting is disabled, since the names of the variables are not in the input. \samp{revisit} is a partial anagram of \samp{diversity}, which was the provisional name of the function but was changed in CHNOSZ-0.9. -While the \code{diversity} function (in \pkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list. +While the \code{diversity} function (in \CRANpkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list. The name of the \samp{H} output value is the conventional symbol for the Shannon diversity index, which was the first target statistic to be implemented in \code{revisit}. } Modified: pkg/CHNOSZ/man/util.misc.Rd =================================================================== --- pkg/CHNOSZ/man/util.misc.Rd 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/man/util.misc.Rd 2017-05-04 11:28:39 UTC (rev 200) @@ -41,10 +41,6 @@ If any of those species are proteins, the function gets their lengths using \code{protein.length}. } -\value{ - Numeric returns are made by \code{dPdTtr}, \code{Ttr}, \code{spearman}, \code{mod.obigt} Functions with no (or unspecified) returns are \code{thermo.plot.new}, \code{thermo.postscript}, \code{label.plot} and \code{water.lines}. -} - \examples{\dontshow{data(thermo)} ## properties of phase transitions si <- info("enstatite") Modified: pkg/CHNOSZ/man/util.plot.Rd =================================================================== --- pkg/CHNOSZ/man/util.plot.Rd 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/man/util.plot.Rd 2017-05-04 11:28:39 UTC (rev 200) @@ -11,7 +11,7 @@ \title{Functions to Create and Modify Plots} \description{ - Initialize a new plot window using preset parameters, open a postcript file for plotting, add an axis or title to a plot, generate labels for plot axes and for identification of subplots and physical and chemical conditions, add stability lines for water to a diagram, get colors for set of values. + Initialize a new plot window using preset parameters, add an axis or title to a plot, generate labels for axes and subplots, add stability lines for water, get colors for a set of numeric values. } @@ -94,7 +94,7 @@ The spacing of the last (bottom) line from the edge of the plot is specified by \code{line}. This function exists to facilitate using \code{\link{expression}}s in multiline titles (see \code{\link{revisit}} for an example.) -\code{ZC.col} returns colors from a diverging palette (red - light grey - blue) corresponding to the values in \code{z}. +\code{ZC.col} uses \CRANpkg{colorspace}) to generate colors from a diverging palette (red - light grey - blue) corresponding to the values in \code{z}. Red is associated with lower values of \code{z}. This function is intended to generate colors for distinguishing average oxidation state of carbon \code{\link{ZC}}, but any numeric values can be supplied. Modified: pkg/CHNOSZ/man/wjd.Rd =================================================================== --- pkg/CHNOSZ/man/wjd.Rd 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/man/wjd.Rd 2017-05-04 11:28:39 UTC (rev 200) @@ -95,7 +95,7 @@ Often, when investigating an equilibrium problem, the stoichiometric constraints are expressed most readily in terms of bulk composition -- numbers of moles of each element. \code{guess} is a function to make initial guesses about the numbers of moles of all species in the system subject to the positivity constraints. Its system-specific arguments are the stoichiometric matrix \code{A} (as defined above for \code{wjd}) and the bulk composition vector \code{B}, giving the number of moles of each element, in the same order that the elements appear in \code{A}. -The first \code{method} available in \code{guess} generates the \sQuote{central} solution of the system of linear equations using the \code{\link[limSolve]{xranges}} function from \pkg{limSolve}. The central solution is the mean of ranges of unknowns. The inequality constraint, or minimum number of moles of any species, is given by \code{minX}. +The first \code{method} available in \code{guess} generates the \sQuote{central} solution of the system of linear equations using the \code{\link[limSolve]{xranges}} function from \CRANpkg{limSolve}. The central solution is the mean of ranges of unknowns. The inequality constraint, or minimum number of moles of any species, is given by \code{minX}. The second method for \code{guess} \sQuote{stoich} (and the default for \code{run.guess} and \code{run.wjd}) is to test successive combinations of species whose elemental compositions are linearly independent. The linearly independent combinations tested are all those from \code{\link{invertible.combs}} if \code{ic} is NULL, or only those identified by \code{ic}. Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-04 11:28:39 UTC (rev 200) @@ -1198,7 +1198,7 @@ ``` By projecting the compositions of proteins into the `QEC` set of basis species, *n*̅`r o2` emerges as a strong indicator of oxidation state, while *n*̅`r h2o` is a relatively uncorrelated (i.e. independent) compositional variable. -These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@Dic17]. +These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@Dic17a]. ## Normalization to residues Modified: pkg/CHNOSZ/vignettes/vig.bib =================================================================== --- pkg/CHNOSZ/vignettes/vig.bib 2017-05-04 03:43:04 UTC (rev 199) +++ pkg/CHNOSZ/vignettes/vig.bib 2017-05-04 11:28:39 UTC (rev 200) @@ -638,13 +638,6 @@ number = {UCRL-MA-110662 PT I}, } - at Article{Dic17, - author = {Dick, Jeffrey M.}, - journal = {PeerJ}, - title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress}, - year = {2017}, -} - @Article{SVI12, author = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano}, journal = {PLoS ONE}, From noreply at r-forge.r-project.org Fri May 5 05:37:57 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 5 May 2017 05:37:57 +0200 (CEST) Subject: [CHNOSZ-commits] r201 - in pkg/CHNOSZ: . inst vignettes Message-ID: <20170505033757.2255F18867D@r-forge.r-project.org> Author: jedick Date: 2017-05-05 05:37:56 +0200 (Fri, 05 May 2017) New Revision: 201 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/vignettes/anintro.Rmd pkg/CHNOSZ/vignettes/eos-regress.Rmd pkg/CHNOSZ/vignettes/obigt.Rmd Log: version 1.1.0 submitted to CRAN Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-04 11:28:39 UTC (rev 200) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-05 03:37:56 UTC (rev 201) @@ -1,6 +1,6 @@ Date: 2017-05-04 Package: CHNOSZ -Version: 1.0.8-89 +Version: 1.1.0 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-04 11:28:39 UTC (rev 200) +++ pkg/CHNOSZ/inst/NEWS 2017-05-05 03:37:56 UTC (rev 201) @@ -1,5 +1,5 @@ -CHANGES IN CHNOSZ 1.0.8-89 (2017-05-04) ---------------------------------------- +CHANGES IN CHNOSZ 1.1.0 (2017-05-04) +------------------------------------ DOCUMENTATION: Modified: pkg/CHNOSZ/vignettes/anintro.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-04 11:28:39 UTC (rev 200) +++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-05-05 03:37:56 UTC (rev 201) @@ -22,7 +22,7 @@ link-citations: yes # The custom CSL file gives a build error on R-Forge (20170212): # pandoc-citeproc: error while parsing the XML string -#csl: elementa.csl +csl: elementa.csl --- ```{r options, include=FALSE} Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-05-04 11:28:39 UTC (rev 200) +++ pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-05-05 03:37:56 UTC (rev 201) @@ -21,7 +21,7 @@ \usepackage[utf8]{inputenc} bibliography: vig.bib link-citations: yes -#csl: elementa.csl +csl: elementa.csl --- ```{r width80, include=FALSE} Modified: pkg/CHNOSZ/vignettes/obigt.Rmd =================================================================== --- pkg/CHNOSZ/vignettes/obigt.Rmd 2017-05-04 11:28:39 UTC (rev 200) +++ pkg/CHNOSZ/vignettes/obigt.Rmd 2017-05-05 03:37:56 UTC (rev 201) @@ -17,7 +17,7 @@ @SPRONS92, @SLOP98, @SLOP07, @SLOP15, @CHNOSZ # 20170212: comment the csl line to build package on R-Forge, to avoid # getting an error there (pandoc-citeproc: error while parsing the XML string) -#csl: elementa.csl +csl: elementa.csl --- From noreply at r-forge.r-project.org Wed May 24 18:06:11 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 24 May 2017 18:06:11 +0200 (CEST) Subject: [CHNOSZ-commits] r202 - in pkg/CHNOSZ: . inst Message-ID: <20170524160611.EB6521887F4@r-forge.r-project.org> Author: jedick Date: 2017-05-24 18:06:11 +0200 (Wed, 24 May 2017) New Revision: 202 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS Log: re-build on R-Forge Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2017-05-05 03:37:56 UTC (rev 201) +++ pkg/CHNOSZ/DESCRIPTION 2017-05-24 16:06:11 UTC (rev 202) @@ -1,6 +1,6 @@ -Date: 2017-05-04 +Date: 2017-05-24 Package: CHNOSZ -Version: 1.1.0 +Version: 1.1.0-1 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/inst/CHECKLIST =================================================================== --- pkg/CHNOSZ/inst/CHECKLIST 2017-05-05 03:37:56 UTC (rev 201) +++ pkg/CHNOSZ/inst/CHECKLIST 2017-05-24 16:06:11 UTC (rev 202) @@ -7,6 +7,8 @@ - compile vignettes with release version number and date +- anintro.Rmd: remove "This vignette depends on some features that are available only in the development version of CHNOSZ." + - run examples() and demos() to check their output - check output of demo("sources") to make sure all data sources are cited Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2017-05-05 03:37:56 UTC (rev 201) +++ pkg/CHNOSZ/inst/NEWS 2017-05-24 16:06:11 UTC (rev 202) @@ -1,3 +1,6 @@ +CHANGES IN CHNOSZ 1.1.0-1 (2017-05-24) +-------------------------------------- + CHANGES IN CHNOSZ 1.1.0 (2017-05-04) ------------------------------------