[CHNOSZ-commits] r64 - in pkg/CHNOSZ: . R inst man

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

Author: jedick
Date: 2014-01-30 17:20:32 +0100 (Thu, 30 Jan 2014)
New Revision: 64

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/affinity.R
   pkg/CHNOSZ/R/util.affinity.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/equilibrate.Rd
Log:
energy(): add missing 'IS' argument in call to subcrt()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2014-01-30 14:40:30 UTC (rev 63)
+++ pkg/CHNOSZ/DESCRIPTION	2014-01-30 16:20:32 UTC (rev 64)
@@ -1,6 +1,6 @@
 Date: 2014-01-30
 Package: CHNOSZ
-Version: 1.0.3-1
+Version: 1.0.3-2
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R	2014-01-30 14:40:30 UTC (rev 63)
+++ pkg/CHNOSZ/R/affinity.R	2014-01-30 16:20:32 UTC (rev 64)
@@ -213,7 +213,7 @@
     else if(length(Eharg) == 2) Ehvals <- seq(Eharg[1], Eharg[2], length.out=128)
     vals[[iEh]] <- Ehvals
   }
-  # get pe and pH and Eh
+  # get pe and pH
   ipe <- match("pe", names(args.orig))
   if(!is.na(ipe)) {
     ie <- match("e-", names(args$lims))

Modified: pkg/CHNOSZ/R/util.affinity.R
===================================================================
--- pkg/CHNOSZ/R/util.affinity.R	2014-01-30 14:40:30 UTC (rev 63)
+++ pkg/CHNOSZ/R/util.affinity.R	2014-01-30 16:20:32 UTC (rev 64)
@@ -119,7 +119,7 @@
       species <- c(mybasis$ispecies,myspecies$ispecies)
       if("T" %in% vars) T <- vals[[which(vars=="T")]]
       if("P" %in% vars) P <- vals[[which(vars=="P")]]
-      s.args <- list(species=species,property=property,T=T,P=P,grid=grid,convert=FALSE,exceed.Ttr=exceed.Ttr)
+      s.args <- list(species=species,property=property,T=T,P=P,IS=IS,grid=grid,convert=FALSE,exceed.Ttr=exceed.Ttr)
       if("IS" %in% vars) {
         IS <- vals[[which(vars=="IS")]]
         # do the calculation in parts: basis species (IS=0)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2014-01-30 14:40:30 UTC (rev 63)
+++ pkg/CHNOSZ/inst/NEWS	2014-01-30 16:20:32 UTC (rev 64)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-1 (2014-01-30)
+CHANGES IN CHNOSZ 1.0.3-2 (2014-01-30)
 --------------------------------------
 
 - Add files with average amino acid compositions of proteins from Bison
@@ -8,6 +8,9 @@
 - Convert hotspring.Rnw to use knitr, and add example calculations of
   relative abundances of microbial phyla from Dick and Shock, 2013.
 
+- In energy(), add missing 'IS' argument in call to subcrt(). Thanks to
+  Grayson Boyer for the bug report.
+
 CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd	2014-01-30 14:40:30 UTC (rev 63)
+++ pkg/CHNOSZ/man/equilibrate.Rd	2014-01-30 16:20:32 UTC (rev 64)
@@ -85,7 +85,7 @@
 }
 
 \value{
-\code{equil.reaction} and \code{equil.boltzman} each return a list with dimensions and length equal to those of \code{Astar}, giving the \code{\link{log10}} of the equilibrium activities of the species of interest.
+\code{equil.reaction} and \code{equil.boltzmann} each return a list with dimensions and length equal to those of \code{Astar}, giving the \code{\link{log10}} of the equilibrium activities of the species of interest.
 \code{equilibrate} returns a list, containing first the values in \code{aout}, to which are appended \code{m.balance} (the balancing coefficients if \code{normalize} is TRUE, a vector of \samp{1}s otherwise), \code{n.balance} (the balancing coefficients if \code{normalize} is FALSE, a vector of \samp{1}s otherwise) and \code{loga.equil} (the calculated equilibrium activities of the species).
 \code{balance} returns a list containing the balancing coefficients (\code{n}) and a textual description (\code{description}).
 }