[CHNOSZ-commits] r11 - in pkg: . CHNOSZ CHNOSZ/R CHNOSZ/data CHNOSZ/inst CHNOSZ/inst/doc CHNOSZ/inst/extdata CHNOSZ/inst/extdata/abundance CHNOSZ/inst/extdata/bison CHNOSZ/inst/extdata/cpetc CHNOSZ/inst/extdata/fasta CHNOSZ/inst/extdata/js CHNOSZ/inst/extdata/protein CHNOSZ/inst/extdata/refseq CHNOSZ/inst/extdata/taxonomy CHNOSZ/inst/extdata/thermo CHNOSZ/inst/tests CHNOSZ/man CHNOSZ/src CHNOSZ/tests CHNOSZ/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 21 14:28:22 CEST 2012
Author: jedick
Date: 2012-09-21 14:28:21 +0200 (Fri, 21 Sep 2012)
New Revision: 11
Added:
pkg/CHNOSZ/
pkg/CHNOSZ/.Rinstignore
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/LICENSE
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/
pkg/CHNOSZ/R/EOSregress.R
pkg/CHNOSZ/R/affinity.R
pkg/CHNOSZ/R/anim.R
pkg/CHNOSZ/R/basis.R
pkg/CHNOSZ/R/buffer.R
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/eqdata.R
pkg/CHNOSZ/R/equil.R
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/findit.R
pkg/CHNOSZ/R/hkf.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/ionize.aa.R
pkg/CHNOSZ/R/iprotein.R
pkg/CHNOSZ/R/makeup.R
pkg/CHNOSZ/R/more.aa.R
pkg/CHNOSZ/R/msgout.R
pkg/CHNOSZ/R/protein.info.R
pkg/CHNOSZ/R/read.expr.R
pkg/CHNOSZ/R/revisit.R
pkg/CHNOSZ/R/species.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/swap.basis.R
pkg/CHNOSZ/R/taxonomy.R
pkg/CHNOSZ/R/transfer.R
pkg/CHNOSZ/R/util.affinity.R
pkg/CHNOSZ/R/util.args.R
pkg/CHNOSZ/R/util.array.R
pkg/CHNOSZ/R/util.blast.R
pkg/CHNOSZ/R/util.character.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/R/util.expression.R
pkg/CHNOSZ/R/util.fasta.R
pkg/CHNOSZ/R/util.formula.R
pkg/CHNOSZ/R/util.list.R
pkg/CHNOSZ/R/util.matrix.R
pkg/CHNOSZ/R/util.misc.R
pkg/CHNOSZ/R/util.plot.R
pkg/CHNOSZ/R/util.program.R
pkg/CHNOSZ/R/util.seq.R
pkg/CHNOSZ/R/util.stat.R
pkg/CHNOSZ/R/util.supcrt.R
pkg/CHNOSZ/R/util.units.R
pkg/CHNOSZ/R/water.R
pkg/CHNOSZ/R/wjd.R
pkg/CHNOSZ/R/zzz.R
pkg/CHNOSZ/data/
pkg/CHNOSZ/data/OBIGT.csv
pkg/CHNOSZ/data/buffer.csv
pkg/CHNOSZ/data/element.csv
pkg/CHNOSZ/data/groups.csv
pkg/CHNOSZ/data/opt.csv
pkg/CHNOSZ/data/protein.csv
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/data/thermo.R
pkg/CHNOSZ/data/xxx.R
pkg/CHNOSZ/data/yyy.R
pkg/CHNOSZ/inst/
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/CITATION
pkg/CHNOSZ/inst/FAQ
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/ONEWS
pkg/CHNOSZ/inst/TODO
pkg/CHNOSZ/inst/doc/
pkg/CHNOSZ/inst/doc/anintro.pdf
pkg/CHNOSZ/inst/doc/hs-chemistry.pdf
pkg/CHNOSZ/inst/doc/wjd.pdf
pkg/CHNOSZ/inst/extdata/
pkg/CHNOSZ/inst/extdata/abundance/
pkg/CHNOSZ/inst/extdata/abundance/AA03.csv
pkg/CHNOSZ/inst/extdata/abundance/ISR+08.csv.xz
pkg/CHNOSZ/inst/extdata/abundance/stress.csv
pkg/CHNOSZ/inst/extdata/abundance/yeastgfp.csv.xz
pkg/CHNOSZ/inst/extdata/bison/
pkg/CHNOSZ/inst/extdata/bison/bisonN_vs_refseq49.blastp.xz
pkg/CHNOSZ/inst/extdata/bison/bisonP_vs_refseq49.blastp.xz
pkg/CHNOSZ/inst/extdata/bison/bisonQ_vs_refseq49.blastp.xz
pkg/CHNOSZ/inst/extdata/bison/bisonR_vs_refseq49.blastp.xz
pkg/CHNOSZ/inst/extdata/bison/bisonS_vs_refseq49.blastp.xz
pkg/CHNOSZ/inst/extdata/bison/gi.taxid.txt.xz
pkg/CHNOSZ/inst/extdata/cpetc/
pkg/CHNOSZ/inst/extdata/cpetc/BKM60_Fig7.csv
pkg/CHNOSZ/inst/extdata/cpetc/Cp.CH4.HW97.csv
pkg/CHNOSZ/inst/extdata/cpetc/PM90.csv
pkg/CHNOSZ/inst/extdata/cpetc/RH95.csv
pkg/CHNOSZ/inst/extdata/cpetc/RT71.csv
pkg/CHNOSZ/inst/extdata/cpetc/SC10_Rainbow.csv
pkg/CHNOSZ/inst/extdata/cpetc/SOJSH.csv
pkg/CHNOSZ/inst/extdata/cpetc/V.CH4.HWM96.csv
pkg/CHNOSZ/inst/extdata/fasta/
pkg/CHNOSZ/inst/extdata/fasta/EF-Tu.aln
pkg/CHNOSZ/inst/extdata/fasta/HTCC1062.faa.xz
pkg/CHNOSZ/inst/extdata/js/
pkg/CHNOSZ/inst/extdata/js/sorttable.js
pkg/CHNOSZ/inst/extdata/protein/
pkg/CHNOSZ/inst/extdata/protein/Eco.csv.xz
pkg/CHNOSZ/inst/extdata/protein/Sce.csv.xz
pkg/CHNOSZ/inst/extdata/refseq/
pkg/CHNOSZ/inst/extdata/refseq/README.txt
pkg/CHNOSZ/inst/extdata/refseq/gencat.sh
pkg/CHNOSZ/inst/extdata/refseq/mkfaa.sh
pkg/CHNOSZ/inst/extdata/refseq/protein.refseq.R
pkg/CHNOSZ/inst/extdata/refseq/protein_refseq.csv.xz
pkg/CHNOSZ/inst/extdata/refseq/taxid.names.R
pkg/CHNOSZ/inst/extdata/refseq/taxid_names.csv.xz
pkg/CHNOSZ/inst/extdata/taxonomy/
pkg/CHNOSZ/inst/extdata/taxonomy/names.dmp
pkg/CHNOSZ/inst/extdata/taxonomy/nodes.dmp
pkg/CHNOSZ/inst/extdata/thermo/
pkg/CHNOSZ/inst/extdata/thermo/DLEN67.csv
pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
pkg/CHNOSZ/inst/extdata/thermo/RH98_Table15.csv
pkg/CHNOSZ/inst/extdata/thermo/groups_big.csv
pkg/CHNOSZ/inst/extdata/thermo/groups_small.csv
pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
pkg/CHNOSZ/inst/tests/
pkg/CHNOSZ/inst/tests/test-affinity.R
pkg/CHNOSZ/inst/tests/test-basis.R
pkg/CHNOSZ/inst/tests/test-diagram.R
pkg/CHNOSZ/inst/tests/test-eos.R
pkg/CHNOSZ/inst/tests/test-examples.R
pkg/CHNOSZ/inst/tests/test-findit.R
pkg/CHNOSZ/inst/tests/test-info.R
pkg/CHNOSZ/inst/tests/test-ionize.aa.R
pkg/CHNOSZ/inst/tests/test-ionize.aa_pK.R
pkg/CHNOSZ/inst/tests/test-iprotein.R
pkg/CHNOSZ/inst/tests/test-makeup.R
pkg/CHNOSZ/inst/tests/test-more.aa.R
pkg/CHNOSZ/inst/tests/test-protein.info.R
pkg/CHNOSZ/inst/tests/test-revisit.R
pkg/CHNOSZ/inst/tests/test-species.R
pkg/CHNOSZ/inst/tests/test-subcrt.R
pkg/CHNOSZ/inst/tests/test-swap.basis.R
pkg/CHNOSZ/inst/tests/test-thermo.R
pkg/CHNOSZ/inst/tests/test-util.R
pkg/CHNOSZ/inst/tests/test-util.affinity.R
pkg/CHNOSZ/inst/tests/test-util.data.R
pkg/CHNOSZ/inst/tests/test-wjd.R
pkg/CHNOSZ/inst/tests/test-yeastgfp.R
pkg/CHNOSZ/man/
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/anim.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/eqdata.Rd
pkg/CHNOSZ/man/equil.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/findit.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/iprotein.Rd
pkg/CHNOSZ/man/makeup.Rd
pkg/CHNOSZ/man/more.aa.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/read.expr.Rd
pkg/CHNOSZ/man/revisit.Rd
pkg/CHNOSZ/man/sideeffects.Rd
pkg/CHNOSZ/man/species.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/swap.basis.Rd
pkg/CHNOSZ/man/taxonomy.Rd
pkg/CHNOSZ/man/transfer.Rd
pkg/CHNOSZ/man/util.affinity.Rd
pkg/CHNOSZ/man/util.args.Rd
pkg/CHNOSZ/man/util.array.Rd
pkg/CHNOSZ/man/util.blast.Rd
pkg/CHNOSZ/man/util.character.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.expression.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.list.Rd
pkg/CHNOSZ/man/util.matrix.Rd
pkg/CHNOSZ/man/util.misc.Rd
pkg/CHNOSZ/man/util.plot.Rd
pkg/CHNOSZ/man/util.program.Rd
pkg/CHNOSZ/man/util.seq.Rd
pkg/CHNOSZ/man/util.stat.Rd
pkg/CHNOSZ/man/util.units.Rd
pkg/CHNOSZ/man/water.Rd
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/src/
pkg/CHNOSZ/src/H2O92D.f
pkg/CHNOSZ/tests/
pkg/CHNOSZ/tests/test-all.R
pkg/CHNOSZ/vignettes/
pkg/CHNOSZ/vignettes/anintro.Rnw
pkg/CHNOSZ/vignettes/anintro.lyx
pkg/CHNOSZ/vignettes/chnosz_new.pdf
pkg/CHNOSZ/vignettes/hs-chemistry.Rnw
pkg/CHNOSZ/vignettes/hs-chemistry.lyx
pkg/CHNOSZ/vignettes/vig.bib
pkg/CHNOSZ/vignettes/wjd.Rnw
pkg/CHNOSZ/vignettes/wjd.lyx
Removed:
pkg/.Rinstignore
pkg/DESCRIPTION
pkg/LICENSE
pkg/NAMESPACE
pkg/R/
pkg/data/
pkg/inst/
pkg/man/
pkg/src/
pkg/tests/
pkg/vignettes/
Log:
move files to pkg/CHNOSZ/
Deleted: pkg/.Rinstignore
===================================================================
--- pkg/.Rinstignore 2012-09-20 01:03:23 UTC (rev 10)
+++ pkg/.Rinstignore 2012-09-21 12:28:21 UTC (rev 11)
@@ -1,5 +0,0 @@
-chnosz_new.pdf
-rxn_.*.pdf
-EF-Tu_.*.pdf
-vig.bib
-.*.lyx
Copied: pkg/CHNOSZ/.Rinstignore (from rev 10, pkg/.Rinstignore)
===================================================================
--- pkg/CHNOSZ/.Rinstignore (rev 0)
+++ pkg/CHNOSZ/.Rinstignore 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,5 @@
+chnosz_new.pdf
+rxn_.*.pdf
+EF-Tu_.*.pdf
+vig.bib
+.*.lyx
Copied: pkg/CHNOSZ/DESCRIPTION (from rev 10, pkg/DESCRIPTION)
===================================================================
--- pkg/CHNOSZ/DESCRIPTION (rev 0)
+++ pkg/CHNOSZ/DESCRIPTION 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,20 @@
+Date: 2012-09-20
+Package: CHNOSZ
+Version: 0.9-7.98
+Title: Chemical Thermodynamics and Activity Diagrams
+Author: Jeffrey M. Dick
+Maintainer: Jeffrey M. Dick <jmdick at asu.edu>
+Depends: R (>= 2.10.0), utils
+Suggests: testthat, parallel, limSolve
+Description: This package includes functions and data sets to support chemical thermodynamic
+ modeling in biochemistry and low-temperature geochemistry. The features include calculation
+ of the standard molal thermodynamic properties and chemical affinities of reactions involving
+ minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline
+ and gaseous species; amino acid group additivity for the standard molal thermodynamic
+ properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers
+ equations of state for aqueous species; construction of equilibrium activity diagrams as a
+ function of temperature, pressure, and chemical activities or fugacities of basis species.
+License: GPL (>= 2)
+BuildResaveData: no
+ZipData: no
+URL: http://www.chnosz.net/
Copied: pkg/CHNOSZ/LICENSE (from rev 10, pkg/LICENSE)
===================================================================
--- pkg/CHNOSZ/LICENSE (rev 0)
+++ pkg/CHNOSZ/LICENSE 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,339 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
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+ Everyone is permitted to copy and distribute verbatim copies
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+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
Copied: pkg/CHNOSZ/NAMESPACE (from rev 10, pkg/NAMESPACE)
===================================================================
--- pkg/CHNOSZ/NAMESPACE (rev 0)
+++ pkg/CHNOSZ/NAMESPACE 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,13 @@
+# modified from
+# Default NAMESPACE created by R
+
+# Export all names
+exportPattern(".")
+
+# Import all packages listed as Imports or Depends
+import(
+ utils
+)
+
+# Load shared objects
+useDynLib(CHNOSZ)
Copied: pkg/CHNOSZ/R/EOSregress.R (from rev 10, pkg/R/EOSregress.R)
===================================================================
--- pkg/CHNOSZ/R/EOSregress.R (rev 0)
+++ pkg/CHNOSZ/R/EOSregress.R 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,182 @@
+# CHNOSZ/EOSregress.R
+# model volumes and heat capacities of aqueous species
+# 20091105 first version
+# 20110429 revise and merge with CHNOSZ package
+
+EOSvar <- function(var,T,P) {
+ # get the variables of a term in a regression equation
+ # T (K), P (bar)
+ out <- switch(EXPR = var,
+ "(Intercept)" = rep(1,length(T)),
+ "T" = T,
+ "P" = P,
+ "TTheta" = T-thermo$opt$Theta, # T-Theta
+ "invTTheta" = (T-thermo$opt$Theta)^-1, # 1/(T-Theta)
+ "TTheta2" = (T-thermo$opt$Theta)^2, # (T-Theta)^2
+ "invTTheta2" = (T-thermo$opt$Theta)^-2, # 1/(T-Theta)^2
+ "V" = water(var,T=T,P=P)[,1],
+ "E" = water(var,T=T,P=P)[,1],
+ "kT" = water(var,T=T,P=P)[,1],
+ "alpha" = water(var,T=T,P=P)[,1],
+ "beta" = water(var,T=T,P=P)[,1],
+ "X" = water(var,T=T,P=P)[,1],
+ "Q" = water(var,T=T,P=P)[,1],
+ "TX" = T*water("X",T=T,P=P)[,1],
+ "drho.dT" = -water("rho",T=T,P=P)[,1]*water("E",T=T,P=P)[,1],
+ "V.kT" = water("V",T=T,P=P)[,1]*water("kT",T=T,P=P)[,1],
+ NA
+ )
+ return(out)
+}
+
+EOSlab <- function(var,coeff="") {
+ # make pretty labels for the variables
+ lab <- switch(EXPR = var,
+ "(Intercept)" = substitute(YYY*" ",list(YYY=coeff)),
+ "TTheta" = substitute(YYY%*%(italic(T)-Theta),list(YYY=coeff)),
+ "invTTheta" = substitute(YYY/(italic(T)-Theta),list(YYY=coeff)),
+ "TTheta2" = substitute(YYY%*%(italic(T)-Theta)^2,list(YYY=coeff)),
+ "invTTheta2" = substitute(YYY/(italic(T)-Theta)^2,list(YYY=coeff)),
+ "T" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "P" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "V" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "E" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "X" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "Q" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "TX" = substitute(YYY%*%italic(XXX),list(XXX=var,YYY=coeff)),
+ "kT" = substitute(YYY%*%kappa[italic(T)],list(YYY=coeff)),
+ "alpha" = substitute(YYY%*%alpha,list(YYY=coeff)),
+ "beta" = substitute(YYY%*%beta,list(YYY=coeff)),
+ "drho.dT" = substitute(YYY%*%(d~rho/dT),list(YYY=coeff)),
+ "V.kT" = substitute(YYY%*%V~kappa[italic(T)],list(YYY=coeff)),
+ NA
+ )
+ return(lab)
+}
+
+EOSregress <- function(exptdata,var="",T.max=9999) {
+ # regress exptdata using terms listed in fun
+ # which values to use
+ iT <- which(exptdata$T <= T.max)
+ exptdata <- exptdata[iT,]
+ # temperature and pressure
+ T <- exptdata$T
+ P <- exptdata$P
+ # the third column is the property of interest: Cp or V
+ X <- exptdata[,3]
+ # now build a regression formula
+ if(length(var) == 0) stop("var is missing")
+ fmla <- as.formula(paste("X ~ ",paste(var,collapse="+")))
+ # retrieve the values of the variables
+ for(i in seq_along(var)) assign(var[i],EOSvar(var[i],T=T,P=P))
+ # now regress away!
+ EOSlm <- lm(fmla)
+ return(EOSlm)
+}
+
+EOScalc <- function(coefficients,T,P) {
+ # calculate values of volume
+ # or heat capacity from regression fit
+ X <- 0
+ for(i in 1:length(coefficients)) {
+ coeff.i <- coefficients[[i]]
+ fun.i <- EOSvar(names(coefficients)[i],T,P)
+ X <- X + coeff.i * fun.i
+ }
+ return(X)
+}
+
+EOSplot <- function(exptdata,var=NULL,T.max=9999,T.plot=NULL,
+ P=NULL,fun.legend="topleft",coefficients=NULL) {
+ # plot experimental and modelled volumes and heat capacities
+ # first figure out the property (Cp or V) from the exptdata
+ prop <- colnames(exptdata)[3]
+ # if var is NULL use HKF equations
+ if(is.null(var)) {
+ if(prop=="Cp") var <- c("invTTheta2","TX")
+ if(prop=="V") var <- c("invTTheta","Q")
+ }
+ expt <- exptdata
+ # perform the regression, only using temperatures up to T.max
+ if(is.null(coefficients)) {
+ EOSlm <- EOSregress(expt,var,T.max)
+ coefficients <- EOSlm$coefficients
+ }
+ # only plot points below a certain temperature
+ iexpt <- 1:nrow(expt)
+ if(!is.null(T.plot)) iexpt <- which(expt$T < T.plot)
+ iX <- match(prop,colnames(expt))
+ ylim <- extendrange(expt[iexpt,iX],f=0.1)
+ xlim <- extendrange(expt$T[iexpt],f=0.1)
+ # start plot
+ thermo.plot.new(xlim=xlim,ylim=ylim,xlab=axis.label("T", units="K"),
+ ylab=axis.label(paste(prop,"0",sep="")),yline=2,mar=NULL)
+ # we group the data by pressure ranges;
+ # assume increasing temperatures are in the
+ # same pressure range but a decrease in temperature
+ # signals the next pressure range
+ idrop <- c(1,which(diff(expt$T)<0)+1,length(expt$T)+1)
+ Plab <- character()
+ pch.open <- c(1,0,2)
+ pch.filled <- c(16,15,17)
+ for(i in 1:(length(idrop)-1)) {
+ ip <- idrop[i]:(idrop[i+1]-1)
+ # find the calculated values at these conditions
+ myT <- expt$T[ip]
+ myP <- expt$P[ip]
+ calc.X <- EOScalc(coefficients,myT,myP)
+ expt.X <- expt[ip,iX]
+ # are we within 10% of the values
+ in10 <- which(abs((calc.X-expt.X)/expt.X) < 0.1)
+ pch <- rep(pch.open[i],length(myT))
+ pch[in10] <- pch.filled[i]
+ points(myT,expt[ip,iX],pch=pch)
+ # if we calculate lines at a constant P, do that
+ xs <- seq(xlim[1],xlim[2],length.out=200)
+ if(!is.null(P)) {
+ myT <- xs
+ myP <- P
+ calc.X <- EOScalc(coefficients,myT,myP)
+ }
+ # take out NAs and Infinite values
+ iNA <- is.na(calc.X) | is.infinite(calc.X)
+ xs <- xs[!iNA]
+ calc.X <- calc.X[!iNA]
+ myT <- myT[!iNA]
+ # plot regression line
+ lines(xs,splinefun(myT,calc.X,method="monoH.FC")(xs))
+ Plim <- range(expt$P[ip])
+ Plab <- c(Plab,paste(Plim[1],"-",Plim[2],"bar"))
+ }
+ # make legend
+ if(!is.null(fun.legend)) {
+ coeffs <- as.character(round(as.numeric(coefficients),4))
+ # so that positive ones appear with a plus sign
+ ipos <- which(coeffs >= 0)
+ coeffs[ipos] <- paste("+",coeffs[ipos],sep="")
+ # make labels for the functions
+ fun.lab <- as.expression(lapply(1:length(coeffs),
+ function(x) {EOSlab(names(coefficients)[x],coeffs[x])} ))
+ #fun.lab <- paste(names(coeffs),round(as.numeric(coeffs),4))
+ legend(fun.legend,legend=fun.lab,pt.cex=0.1)
+ }
+ return(invisible(list(xlim=range(expt$T[iexpt]))))
+}
+
+EOScoeffs <- function(species,property) {
+ # get the HKF coefficients for species in the database
+ iis <- info(info(species,"aq"))
+ if(property=="Cp") {
+ out <- iis[,c("c1","c2","omega")]
+ names(out) <- c("(Intercept)","invTTheta2","TX")
+ } else if(property=="V") {
+ iis <- iis[,c("a1","a2","a3","a4","omega")]
+ sigma <- ( iis$a1 + iis$a2 / (2600 + 1) ) * 41.84
+ xi <- ( iis$a3 + iis$a4 / (2600 + 1) ) * 41.84
+ # watch for the negative sign on omega here!
+ out <- data.frame(sigma,xi,-iis$omega)
+ names(out) <- c("(Intercept)","invTTheta","Q")
+ }
+ return(out)
+}
+
Copied: pkg/CHNOSZ/R/affinity.R (from rev 10, pkg/R/affinity.R)
===================================================================
--- pkg/CHNOSZ/R/affinity.R (rev 0)
+++ pkg/CHNOSZ/R/affinity.R 2012-09-21 12:28:21 UTC (rev 11)
@@ -0,0 +1,206 @@
+# CHNOSZ/affinity.R
+# calculate affinities of formation reactions
+
+affinity <- function(...,property=NULL,sout=NULL,exceed.Ttr=FALSE,
+ return.buffer=FALSE,balance="PBB",iprotein=NULL,loga.protein=-3) {
+ # ...: variables over which to calculate
+ # property: what type of energy
+ # (G.basis,G.species,logact.basis,logK,logQ,A)
+ # return.buffer: return buffered activities
+ # balance: balance protein buffers on PBB
+ # exceed.Ttr: extrapolate Gibbs energies
+ # of minerals beyond their T-limits?
+ # sout: provide a previously calculated output from subcrt
+ # iprotein: build these proteins from residues (speed optimization)
+
+ # history: 20061027 jmd version 1
+ # this is where energy.args() used to sit
+ # this is where energy() used to sit
+
+ # the argument list
+ args <- energy.args(list(...))
+ args <- c(args,list(sout=sout,exceed.Ttr=exceed.Ttr))
+
+ # the species we're given
+ mybasis <- thermo$basis
+ myspecies <- thermo$species
+
+ if(!is.null(property)) {
+ # the user just wants an energy property
+ buffer <- FALSE
+ args$what <- property
+ out <- do.call("energy",args)
+ a <- out$a
+ sout <- out$sout
+ } else {
+
+ # affinity calculations
+ property <- args$what
+
+ # iprotein stuff
+ # note that this affinities of the residues are subject
+ # to ionization calculations in energy() so no explicit accounting
+ # is needed here
+ if(!is.null(iprotein)) {
+ # add protein residues to the species list
+ resnames <- c("H2O",aminoacids(3))
+ # residue activities set to zero;
+ # account for protein activities later
+ resprot <- paste(resnames,"RESIDUE",sep="_")
+ species(resprot, 0)
+ ires <- match(resprot, thermo$species$name)
+ }
+
+ # buffer stuff
+ buffer <- FALSE
+ ibufbasis <- which(!can.be.numeric(mybasis$logact))
+ if(!is.null(mybasis) & length(ibufbasis) > 0) {
+ buffer <- TRUE
+ msgout('affinity: loading buffer species\n')
+ if(!is.null(thermo$species)) is.species <- 1:nrow(thermo$species) else is.species <- numeric()
+ is.buffer <- buffer(logK=NULL)
+ is.buff <- numeric()
+ for(i in 1:length(is.buffer)) is.buff <- c(is.buff,as.numeric(is.buffer[[i]]))
+ is.only.buffer <- is.buff[!is.buff %in% is.species]
+ buffers <- names(is.buffer)
+ # reorder the buffers according to thermo$buffers
+ buffers <- buffers[order(match(buffers,thermo$buffers$name))]
+ }
+
+ # here we call 'energy'
+ aa <- do.call("energy",args)
+ a <- aa$a
+ sout <- aa$sout
+
+ # more buffer stuff
+ if(buffer) {
+ args$what <- "logact.basis"
+ args$sout <- sout
+ logact.basis.new <- logact.basis <- do.call("energy",args)$a
+ ibasis.new <- numeric()
+ for(k in 1:length(buffers)) {
+ ibasis <- which(as.character(mybasis$logact)==buffers[k])
+ # calculate the logKs from the affinities
+ logK <- a
+ for(i in 1:length(logK)) {
+ logK[[i]] <- logK[[i]] + thermo$species$logact[i]
+ for(j in 1:length(logact.basis.new)) {
+ logK[[i]] <- logK[[i]] - logact.basis.new[[j]] * thermo$species[i,j]
+ # add ionization correction to proteins
+ #if(i %in% is.buffer & length(grep('_',as.character(thermo$species$name[i])))>0 &
+ # thermo$opt$ionize & rownames(mybasis)[j]=='H+') {
+ # logK[[i]] <- logK[[i]] - logact.basis[[j]] *
+ # as.data.frame(charge[[match(thermo$species$ispecies[i],names(charge))]])
+ #}
+ }
+ }
+ lbn <- buffer(logK=logK,ibasis=ibasis,logact.basis=logact.basis.new,
+ is.buffer=as.numeric(is.buffer[[which(names(is.buffer)==buffers[k])]]),balance=balance)
+ for(j in 1:length(logact.basis.new)) if(j %in% ibasis) logact.basis.new[[j]] <- lbn[[2]][[j]]
+ # calculation of the buffered activities' effect on chemical affinities
+ is.only.buffer.new <- is.only.buffer[is.only.buffer %in% is.buffer[[k]]]
+ for(i in 1:length(a)) {
+ if(i %in% is.only.buffer.new) next
+ for(j in 1:nrow(mybasis)) {
+ # let's only do this for the basis species specified by the user
+ # even if others could be buffered
+ if(!j %in% ibufbasis) next
+ if(!j %in% ibasis) next
+ aa <- a[[i]]
+ a[[i]] <- aa + (logact.basis.new[[j]] - logact.basis[[j]]) * thermo$species[i,j]
+ #if(!identical(a[[i]],aa)) print(paste(i,j))
+ }
+ }
+ if(k==length(buffers) & return.buffer) {
+ logact.basis.new <- lbn[[2]]
+ ibasis.new <- c(ibasis.new,lbn[[1]])
+ } else ibasis.new <- c(ibasis.new,ibasis)
+ }
+ species(is.only.buffer,delete=TRUE)
+ if(length(is.only.buffer) > 0) a <- a[-is.only.buffer]
+ # to return the activities of buffered basis species
+ tb <- logact.basis.new[unique(ibasis.new)]
+ if(!is.null(ncol(tb[[1]]))) {
+ nd <- length(which(dim(tb[[1]]) > 1))
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 11
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