[CHNOSZ-commits] r46 - in pkg/CHNOSZ: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 11 02:31:14 CET 2013
Author: jedick
Date: 2013-03-11 02:31:14 +0100 (Mon, 11 Mar 2013)
New Revision: 46
Removed:
pkg/CHNOSZ/LICENSE
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/EOSregress.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/EOSregress.Rd
Log:
EOSlab() gets label from attribute of user-defined function
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/DESCRIPTION 2013-03-11 01:31:14 UTC (rev 46)
@@ -1,6 +1,6 @@
-Date: 2013-02-13
+Date: 2013-03-11
Package: CHNOSZ
-Version: 0.9-9.6
+Version: 0.9-9.7
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick <jmdick at asu.edu>
Deleted: pkg/CHNOSZ/LICENSE
===================================================================
--- pkg/CHNOSZ/LICENSE 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/LICENSE 2013-03-11 01:31:14 UTC (rev 46)
@@ -1,339 +0,0 @@
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Modified: pkg/CHNOSZ/R/EOSregress.R
===================================================================
--- pkg/CHNOSZ/R/EOSregress.R 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/R/EOSregress.R 2013-03-11 01:31:14 UTC (rev 46)
@@ -35,7 +35,7 @@
return(out)
}
-EOSlab <- function(var,coeff="") {
+EOSlab <- function(var, coeff="") {
# make pretty labels for the variables
lab <- switch(EXPR = var,
# these are regression variables listed in EOSregress.Rd
@@ -46,19 +46,34 @@
"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)),
+ "invPPsi" = substitute(YYY/(italic(P)+Psi),list(YYY=coeff)),
+ "invPPsiTTheta" = substitute(YYY/((italic(P)+Psi)(italic(T)-Theta)), list(YYY=coeff)),
"TXBorn" = substitute(YYY%*%italic(TX), list(YYY=coeff)),
"drho.dT" = substitute(YYY%*%(d~rho/dT), list(YYY=coeff)),
"V.kT" = substitute(YYY%*%V~kappa[italic(T)], list(YYY=coeff)),
- # the rest are properties of water listed in water.Rd
- "V" = substitute(YYY%*%italic(V), list(YYY=coeff)),
- "E" = substitute(YYY%*%italic(E), list(YYY=coeff)),
+ # these are non-single-letter properties of water as listed in water.Rd
"kT" = substitute(YYY%*%kappa[italic(T)], list(YYY=coeff)),
"alpha" = substitute(YYY%*%alpha, list(YYY=coeff)),
"beta" = substitute(YYY%*%beta, list(YYY=coeff)),
+ "diel" = substitute(YYY%*%epsilon, list(YYY=coeff)),
+ "rho" = substitute(YYY%*%rho, list(YYY=coeff)),
+ "NBorn" = substitute(YYY%*%italic(N), list(YYY=coeff)),
+ "QBorn" = substitute(YYY%*%italic(Q), list(YYY=coeff)),
"XBorn" = substitute(YYY%*%italic(X), list(YYY=coeff)),
- "QBorn" = substitute(YYY%*%italic(Q), list(YYY=coeff)),
- # fallback, use the name of the variable (may be the name of a user-defined function)
- substitute(YYY%*%italic(XXX), list(YYY=coeff, XXX=var))
+ "YBorn" = substitute(YYY%*%italic(Y), list(YYY=coeff)),
+ "ZBorn" = substitute(YYY%*%italic(Z), list(YYY=coeff)),
+ (
+ # if var is a function, does have an attribute named "label"?
+ if(exists(var)) {
+ if(is.function(get(var))) {
+ if(!is.null(attr(get(var), "label"))) {
+ return(substitute(YYY*XXX, list(YYY=coeff, XXX=attr(get(var), "label"))))
+ # fallback, use the name of the variable
+ # (e.g. for a property of water such as A, G, S, U, H, or name of a user-defined function)
+ } else substitute(YYY%*%italic(XXX), list(YYY=coeff, XXX=var))
+ } else substitute(YYY%*%italic(XXX), list(YYY=coeff, XXX=var))
+ } else substitute(YYY%*%italic(XXX), list(YYY=coeff, XXX=var))
+ )
)
return(lab)
}
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/R/util.data.R 2013-03-11 01:31:14 UTC (rev 46)
@@ -79,14 +79,15 @@
if(length(iold) > 0) {
# loop over species
for(i in 1:length(iold)) {
- # the old values
+ # the old values and the state
oldprop <- thermo$obigt[ispecies[iold[i]], icol]
+ state <- thermo$obigt$state[ispecies[iold[i]]]
# tell user if they're the same, otherwise update the data entry
if(isTRUE(all.equal(oldprop, args[iold[i], ], check.attributes=FALSE)))
- msgout("mod.obigt: no change for ", args$name[iold[i]], "(", args$state[iold[i]], ")\n")
+ msgout("mod.obigt: no change for ", args$name[iold[i]], "(", state, ")\n")
else {
thermo$obigt[ispecies[iold[i]], icol] <<- args[iold[i], ]
- msgout("mod.obigt: updated ", args$name[iold[i]], "(", args$state[iold[i]], ")\n")
+ msgout("mod.obigt: updated ", args$name[iold[i]], "(", state, ")\n")
}
}
}
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/inst/CHECKLIST 2013-03-11 01:31:14 UTC (rev 46)
@@ -29,3 +29,5 @@
- ensure all Rd files have \keyword{...}
- test read.supcrt(), write.supcrt() on e.g. slop98.dat
+
+- update .Rinstignore with any new/deleted files
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/inst/NEWS 2013-03-11 01:31:14 UTC (rev 46)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 0.9-9.6 (2013-02-13)
+CHANGES IN CHNOSZ 0.9-9.7 (2013-03-11)
--------------------------------------
- Fix calculation of free energy derivative in wjd().
@@ -54,7 +54,10 @@
- [temporary] Deactivate code using 'central' method in guess()
(wjd.Rnw) as limSolve package on not available on R-Forge for windows.
+- EOSlab() gets label from attribute (if present) of user-defined
+ function.
+
CHANGES IN CHNOSZ 0.9-9 (2013-01-01)
------------------------------------
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2013-03-04 13:16:28 UTC (rev 45)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2013-03-11 01:31:14 UTC (rev 46)
@@ -67,7 +67,9 @@
The point symbols are filled circles where the calculated value is within 10\% of the experimental value; open circles otherwise.
\code{EOSlab} produces labels for the variables listed above that can be used \code{\link{as.expression}}s in plots.
-The value of \code{coeff} is prefixed (using \code{\link{substitute}}) to the name of the variable.
+The value of \code{coeff} is prefixed to the name of the variable (using \code{\link{substitute}}, with a multiplication symbol).
+For the properties listed in the table above, and selected properties listed in \code{\link{water}}, the label is formatted using \code{\link{plotmath}} expressions (e.g., with italicized symbols and Greek letters).
+If \code{var} is a user-defined function, the function can be given a \samp{label} attribute to provide \code{\link{plotmath}}-style formatting; in this case the appropriate multiplication or division symbol should be specified (see example below).
\code{EOScoeffs} retrieves coefficients in the Helgeson-Kirkham-Flowers equations from the thermodynamic database (\code{\link{thermo}$obigt}) for the given aqueous \code{species}.
If the \code{property} is \samp{Cp}, the resulting data frame has column names of \samp{(Intercept)}, \samp{invTTheta2} and \samp{TX}, respectively holding the coefficients \eqn{c_1}{c1}, \eqn{c_2}{c2} and \eqn{\omega}{omega} in the equation \eqn{Cp^\circ = c_1 + c_2/(T-\Theta)^2 + {\omega}TX}{Cp = c1 + c2/(T-Theta)^2 + omega*TX}.
@@ -123,16 +125,20 @@
EOSplot(d, coefficients=CH4coeffs, T.plot=600)
title("Cp from EOS parameters in database")
-# following from above, with user-defined variables
+# continuing from above, with user-defined variables
invTTTheta3 <- function(T, P) (2*T)/(T-T*thermo$opt$Theta)^3
invTX <- function(T, P) 1/T*water("XBorn", T=T, P=P)[,1]
+# print the calculated values of invTTTheta3
EOSvar("invTTTheta3", d$T, d$P)
+# use invTTTheta and invTX in a regression
var <- c("invTTTheta3", "invTX")
EOSregress(d, var)
-# the plot is commented for this toy example
+# give them a "label" attribute for use in the legend
+attr(invTTTheta3, "label") <- quote(phantom()\%*\%2*italic(T)/(italic(T)-italic(T)*Theta)^3)
+attr(invTX, "label") <- quote(phantom()/italic(T*X))
+# uncomment the following to make the plot
#EOSplot(d, var)
-
## model experimental volumes of CH4
## using HKF equation and an exploratory one
f <- system.file("extdata/cpetc/V.CH4.HWM96.csv", package="CHNOSZ")
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