[CHNOSZ-commits] r102 - in pkg/CHNOSZ: . demo inst vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2015-11-19 17:53:20 +0100 (Thu, 19 Nov 2015)
New Revision: 102

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/yeastgfp.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/equilibrium.Rnw
   pkg/CHNOSZ/vignettes/equilibrium.lyx
Log:
prepare version 1.0.7 for submission to CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2015-11-19 13:15:23 UTC (rev 101)
+++ pkg/CHNOSZ/DESCRIPTION	2015-11-19 16:53:20 UTC (rev 102)
@@ -1,6 +1,6 @@
 Date: 2015-11-19
 Package: CHNOSZ
-Version: 1.0.6-6
+Version: 1.0.7
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R	2015-11-19 13:15:23 UTC (rev 101)
+++ pkg/CHNOSZ/demo/yeastgfp.R	2015-11-19 16:53:20 UTC (rev 102)
@@ -39,7 +39,7 @@
 for(i in 1:length(nloc)) {
   diagram(a, normalize=TRUE, names=names[inames], groups=as.list(inames),
     fill=fill[inames], cex.axis=0.75, cex.names=1)
-  label.plot(letters[i])
+  label.plot(letters[i], xfrac=0.95, yfrac=0.9, paren=TRUE, italic=TRUE)
   title(main=paste(length(inames), "locations"))
   # take out the stable species
   inames <- inames[-(1:nloc[i])]

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2015-11-19 13:15:23 UTC (rev 101)
+++ pkg/CHNOSZ/inst/NEWS	2015-11-19 16:53:20 UTC (rev 102)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.6-6 (2015-11-19)
+CHANGES IN CHNOSZ 1.0.7 (2015-11-19)
 --------------------------------------
 
 - Add functions usrfig() (get figure limits in user coordinates) and

Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rnw	2015-11-19 13:15:23 UTC (rev 101)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rnw	2015-11-19 16:53:20 UTC (rev 102)
@@ -236,7 +236,8 @@
 species(aminoacids(""))[1:5, ]
 @
 
-Code for figures. Function names are keyed to the subfigures.
+Code for making the diagrams. Function names refer to the subfigure
+labels.
 
 <<AAfigures>>=
 res <- 200
@@ -608,7 +609,7 @@
 basis(c("Cu+2", "H2O", "H+", "e-"))
 species(c("Cu+2", "copper", "cuprite", "tenorite"))
 for(loga in c(-1, 0, -2, -3)) {
-  species(c("Cu+2"), loga) 
+  species("Cu+2", loga) 
   a <- affinity(pH=c(1.6, 7.6, 400), Eh=c(-0.2, 1, 400))
   if(loga==-1) d <- diagram(a)
   else d <- diagram(a, add=TRUE, names=NULL)

Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.lyx	2015-11-19 13:15:23 UTC (rev 101)
+++ pkg/CHNOSZ/vignettes/equilibrium.lyx	2015-11-19 16:53:20 UTC (rev 102)
@@ -842,8 +842,8 @@
 \end_layout
 
 \begin_layout Standard
-Code for figures.
- Function names are keyed to the subfigures.
+Code for making the diagrams.
+ Function names refer to the subfigure labels.
 \end_layout
 
 \begin_layout Standard
@@ -2619,7 +2619,7 @@
 
 \begin_layout Plain Layout
 
-  species(c("Cu+2"), loga) 
+  species("Cu+2", loga) 
 \end_layout
 
 \begin_layout Plain Layout