[CHNOSZ-commits] r50 - in pkg/CHNOSZ: . R inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 27 01:03:52 CET 2013
Author: jedick
Date: 2013-03-27 01:03:51 +0100 (Wed, 27 Mar 2013)
New Revision: 50
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/wjd.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/vignettes/wjd.Rnw
pkg/CHNOSZ/vignettes/wjd.lyx
Log:
guess() uses "stoich" as default method
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/DESCRIPTION 2013-03-27 00:03:51 UTC (rev 50)
@@ -1,6 +1,6 @@
-Date: 2013-03-24
+Date: 2013-03-27
Package: CHNOSZ
-Version: 0.9-9.10
+Version: 0.9-9.11
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/wjd.R
===================================================================
--- pkg/CHNOSZ/R/wjd.R 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/R/wjd.R 2013-03-27 00:03:51 UTC (rev 50)
@@ -249,7 +249,7 @@
0,0,0,1,2,1,1,0,0,0,
0,0,1,0,0,0,1,1,2,1),ncol=3,
dimnames=list(NULL,c("H","N","O"))),
- B = c(2,1,1), method=c("central", "stoich"), minX=0.001, iguess=1, ic=NULL
+ B = c(2,1,1), method="stoich", minX=0.001, iguess=1, ic=NULL
){
# given the elemental stoichiometries of a set of species (A)
# and the number of moles of elements (B)
@@ -260,7 +260,7 @@
if(all(B==0)) stop("there are zero moles of all elements")
# if method="central" get central solution using limSolve package 20120919
- if("central" %in% method) {
+ if(identical(method, "central")) {
if(!"limSolve" %in% row.names(installed.packages())) {
msgout("guess: skipping 'central' method as limSolve package is not available\n")
} else {
@@ -275,7 +275,7 @@
}
}
- if("stoich" %in% method) {
+ if(identical(method, "stoich")) {
# if method="stoich" use a stoichiometric approach: 20111231 jmd
# - select one of the (many) species combinations (ic) that
# make a square, invertible stoichiometric matrix (the "variable" species)
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/inst/CHECKLIST 2013-03-27 00:03:51 UTC (rev 50)
@@ -38,5 +38,7 @@
- build the package on the source directory:
R CMD build --compact-vignettes chnosz
- (don't use --no-vignettes, that keeps the Rnw files from being copied to inst/doc,
- causing vignettes to disappear from CRAN webpage)
+ don't use --no-vignettes, that keeps the Rnw files from being copied to inst/doc,
+ causing vignettes to disappear from CRAN webpage
+ don't use --compact-vignettes=both, that results in smaller PDFs (using ghostscript),
+ but erases some metadata
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/inst/NEWS 2013-03-27 00:03:51 UTC (rev 50)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 0.9-9.10 (2013-03-24)
+CHANGES IN CHNOSZ 0.9-9.11 (2013-03-26)
---------------------------------------
MAJOR USER-VISIBLE CHANGE:
@@ -73,7 +73,9 @@
- Remove read.supcrt() and write.supcrt().
+- guess() now defaults to "stoich" method, not "central".
+
CHANGES IN CHNOSZ 0.9-9 (2013-01-01)
------------------------------------
Modified: pkg/CHNOSZ/man/wjd.Rd
===================================================================
--- pkg/CHNOSZ/man/wjd.Rd 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/man/wjd.Rd 2013-03-27 00:03:51 UTC (rev 50)
@@ -36,7 +36,7 @@
0,0,0,1,2,1,1,0,0,0,
0,0,1,0,0,0,1,1,2,1),ncol=3,
dimnames=list(NULL,c("H","N","O"))),
- B = c(2,1,1), method=c("central", "stoich"), minX = 0.001, iguess = 1, ic = NULL
+ B = c(2,1,1), method="stoich", minX = 0.001, iguess = 1, ic = NULL
)
run.wjd(ispecies, B = NULL, method = "stoich", Y = run.guess(ispecies, B, method),
P=1, T=25, nlambda=101, imax = 10, Gfrac = 1e-7, tol = 0.01)
Modified: pkg/CHNOSZ/vignettes/wjd.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/wjd.Rnw 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/vignettes/wjd.Rnw 2013-03-27 00:03:51 UTC (rev 50)
@@ -424,14 +424,16 @@
@
-We triggered a single ``not near equilibrium'' message, but overall
-it seems well behaved. And, as expected, it is similar to Fig. 2 of
-\citet{DLE64}, with a major crossing of curves at about 28\% carbon,
-together with an increase in aromatic compounds (e.g. naphthalene,
-anthracene) going toward higher carbon content. Unlike the figure
-in \citet{DLE64}, there appears to be a second major crossing of
-curves at about 43\% carbon, corresponding to a rise in CO. (For a
-higher resolution, try setting \texttt{xCs <- seq(8, 47, 1)}.)
+We triggered some ``not near equilibrium'' messages, but overall
+it seems well behaved (note that using the ``central'' method in
+\texttt{guess()} is one way that leads to fewer of these messages).
+And, as expected, it is similar to Fig. 2 of \citet{DLE64}, with
+a major crossing of curves at about 28\% carbon, together with an
+increase in aromatic compounds (e.g. naphthalene, anthracene) going
+toward higher carbon content. Unlike the figure in \citet{DLE64},
+there appears to be a second major crossing of curves at about 43\%
+carbon, corresponding to a rise in CO. (For a higher resolution, try
+setting \texttt{xCs <- seq(8, 47, 1)}.)
\section{Running Down: Using a Thermodynamic Database}
Modified: pkg/CHNOSZ/vignettes/wjd.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/wjd.lyx 2013-03-24 07:04:53 UTC (rev 49)
+++ pkg/CHNOSZ/vignettes/wjd.lyx 2013-03-27 00:03:51 UTC (rev 50)
@@ -1895,7 +1895,7 @@
\end_layout
\begin_layout Standard
-We triggered a single
+We triggered some
\begin_inset Quotes eld
\end_inset
@@ -1903,7 +1903,19 @@
\begin_inset Quotes erd
\end_inset
- message, but overall it seems well behaved.
+ messages, but overall it seems well behaved (note that using the
+\begin_inset Quotes eld
+\end_inset
+
+central
+\begin_inset Quotes erd
+\end_inset
+
+ method in
+\family typewriter
+guess()
+\family default
+ is one way that leads to fewer of these messages).
And, as expected, it is similar to Fig.
2 of
\begin_inset CommandInset citation
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