From noreply at r-forge.r-project.org  Mon Jul  1 17:20:52 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  1 Jul 2013 17:20:52 +0200 (CEST)
Subject: [CHNOSZ-commits] r54 - in pkg/CHNOSZ: . R inst man vignettes
Message-ID: <20130701152052.710F818596D@r-forge.r-project.org>

Author: jedick
Date: 2013-07-01 17:20:52 +0200 (Mon, 01 Jul 2013)
New Revision: 54

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/more.aa.R
   pkg/CHNOSZ/R/util.list.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/util.expression.Rd
   pkg/CHNOSZ/vignettes/wjd.Rnw
   pkg/CHNOSZ/vignettes/wjd.lyx
Log:
remove inconsolata.sty from wjd.Rnw


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/DESCRIPTION	2013-07-01 15:20:52 UTC (rev 54)
@@ -1,6 +1,6 @@
-Date: 2013-06-02
+Date: 2013-07-01
 Package: CHNOSZ
-Version: 1.0.0-2
+Version: 1.0.0-3
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey M. Dick
 Maintainer: Jeffrey M. Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/more.aa.R
===================================================================
--- pkg/CHNOSZ/R/more.aa.R	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/R/more.aa.R	2013-07-01 15:20:52 UTC (rev 54)
@@ -1,6 +1,5 @@
 # CHNOSZ/more.aa.R
-# get amino acid compositions of proteins from 
-# model organisms really exciting!
+# get amino acid compositions of proteins from model organisms
 # (Eco.csv or Sce.csv)
 
 more.aa <- function(protein=NULL, organism) {
@@ -16,17 +15,13 @@
     msgout("more.aa: ", datapath, " has data for ", nrow(mydata), " proteins\n")
     return(invisible())
   }
-  if(organism=="Sce") {
-    # which columns to search for matches
-    searchcols <- c("OLN", "OLN")
-    # which columns have the amino acids in the order of thermo$protein 
-    iaa <- c(1,5,4,7,14,8,9,10,12,11,13,3,15,6,2,16,17,20,18,19) + 2
-  } else if(organism=="Eco") {
-    # which columns to search for matches
-    searchcols <- c("protein", "abbrv")
-    # which columns have the amino acids in the order of thermo$protein 
-    iaa <- 1:20 + 5
-  }
+  # which columns to search for matches
+  # include "OLN" (Sce.csv dated 2008-08-04)
+  # and "ORF" (Sce.csv dated 2013-06-04)
+  if(organism=="Sce") searchcols <- c("OLN", "ORF", "SGDID")
+  else if(organism=="Eco") searchcols <- c("protein", "abbrv")
+  # which columns have the amino acids, in the order of thermo$protein 
+  iaa <- match(toupper(aminoacids(3)), toupper(colnames(mydata)))
   # iterate over a list
   waslist <- TRUE
   out <- list()
@@ -36,11 +31,13 @@
   }
   for(i in 1:length(protein)) {
     # find the matches
-    icols <- match(searchcols, colnames(mydata))
-    imatch <- match(protein[[i]], mydata[, icols[1]])
-    imatch2 <- match(protein[[i]], mydata[, icols[2]])
-    # use not-NA matches for "abbrv" in Eco.csv
-    imatch[!is.na(imatch2)] <- imatch2[!is.na(imatch2)]
+    imatch <- rep(NA, length(protein[[i]]))
+    for(cname in searchcols) {
+      icol <- match(cname, colnames(mydata))
+      if(is.na(icol)) next
+      iimatch <- match(protein[[i]], mydata[, icol])
+      imatch[!is.na(iimatch)] <- iimatch[!is.na(iimatch)]
+    }
     # report and remember the unsuccessful matches
     if(all(is.na(imatch))) stop("no proteins found!")
     inotmatch <- which(is.na(imatch)) 

Modified: pkg/CHNOSZ/R/util.list.R
===================================================================
--- pkg/CHNOSZ/R/util.list.R	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/R/util.list.R	2013-07-01 15:20:52 UTC (rev 54)
@@ -4,6 +4,7 @@
 which.pmax <- function (elts, na.rm = FALSE, pmin=FALSE) {
   # adapted from R's pmax. elts is a list of numeric vectors
   if(!is.numeric(elts[[1]])[1]) {
+    if(is.data.frame(elts[[1]])) elts[[1]] <- as.matrix(elts[[1]])
     if(is.list(elts[[1]])) elts[[1]] <- elts[[1]][[1]]
     else elts[[1]] <- as.numeric(elts[[1]])
   }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/inst/NEWS	2013-07-01 15:20:52 UTC (rev 54)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.0-2 (2013-06-02)
+CHANGES IN CHNOSZ 1.0.0-3 (2013-07-01)
 --------------------------------------
 
 - Fix IAPWS-95 calculations for subcrt(): in water.IAPWS95(), rename

Modified: pkg/CHNOSZ/man/util.expression.Rd
===================================================================
--- pkg/CHNOSZ/man/util.expression.Rd	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/man/util.expression.Rd	2013-07-01 15:20:52 UTC (rev 54)
@@ -15,7 +15,8 @@
   expr.property(property)
   expr.units(property, prefix = "", per = "mol")
   axis.label(label, units = NULL, basis = get("thermo")$basis, prefix = "")
-  describe.basis(basis = get("thermo")$basis, ibasis = 1:nrow(basis), digits = 1, oneline = FALSE)
+  describe.basis(basis = get("thermo")$basis, ibasis = 1:nrow(basis), digits = 1,
+    oneline = FALSE)
   describe.property(property, value, digits = 1, oneline = FALSE, ret.val = FALSE)
   describe.reaction(reaction, iname = numeric(), states = NULL)
 }

Modified: pkg/CHNOSZ/vignettes/wjd.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/wjd.Rnw	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/vignettes/wjd.Rnw	2013-07-01 15:20:52 UTC (rev 54)
@@ -1,12 +1,13 @@
-%% LyX 2.0.5 created this file.  For more info, see http://www.lyx.org/.
+%% LyX 2.0.6 created this file.  For more info, see http://www.lyx.org/.
 %% Do not edit unless you really know what you are doing.
-\documentclass[noae,round]{article}
+\documentclass[english,noae,round]{article}
 \usepackage{mathpazo}
 \usepackage[T1]{fontenc}
 \usepackage[latin9]{inputenc}
 \usepackage[letterpaper]{geometry}
 \geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
 \usepackage{color}
+\usepackage{babel}
 \usepackage[authoryear]{natbib}
 \usepackage[unicode=true,
  bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
@@ -29,9 +30,6 @@
 % so DOIs in bibliography show up as hyperlinks
 \newcommand*{\doi}[1]{\href{http://dx.doi.org/#1}{doi: #1}}
 
-% for monospaced fonts
-\usepackage{inconsolata}
-
 \makeatother
 
 \begin{document}

Modified: pkg/CHNOSZ/vignettes/wjd.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/wjd.lyx	2013-06-02 05:15:42 UTC (rev 53)
+++ pkg/CHNOSZ/vignettes/wjd.lyx	2013-07-01 15:20:52 UTC (rev 54)
@@ -8,9 +8,6 @@
 
 % so DOIs in bibliography show up as hyperlinks
 \newcommand*{\doi}[1]{\href{http://dx.doi.org/#1}{doi: #1}}
-
-% for monospaced fonts
-\usepackage{inconsolata}
 \end_preamble
 \options round
 \use_default_options true


From noreply at r-forge.r-project.org  Thu Jul  4 18:15:01 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  4 Jul 2013 18:15:01 +0200 (CEST)
Subject: [CHNOSZ-commits] r55 - in pkg/CHNOSZ: . inst
Message-ID: <20130704161501.B3185184644@r-forge.r-project.org>

Author: jedick
Date: 2013-07-04 18:15:01 +0200 (Thu, 04 Jul 2013)
New Revision: 55

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
Log:
prepare version 1.0.1 for release on CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2013-07-01 15:20:52 UTC (rev 54)
+++ pkg/CHNOSZ/DESCRIPTION	2013-07-04 16:15:01 UTC (rev 55)
@@ -1,6 +1,6 @@
-Date: 2013-07-01
+Date: 2013-07-04
 Package: CHNOSZ
-Version: 1.0.0-3
+Version: 1.0.1
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey M. Dick
 Maintainer: Jeffrey M. Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2013-07-01 15:20:52 UTC (rev 54)
+++ pkg/CHNOSZ/inst/NEWS	2013-07-04 16:15:01 UTC (rev 55)
@@ -1,9 +1,9 @@
-CHANGES IN CHNOSZ 1.0.0-3 (2013-07-01)
---------------------------------------
+CHANGES IN CHNOSZ 1.0.1 (2013-07-04)
+------------------------------------
 
-- Fix IAPWS-95 calculations for subcrt(): in water.IAPWS95(), rename
-  internal function from 'epsilon' to 'diel'; in water(), return
-  upper-case versions of names of properties.
+- Allow IAPWS-95 calculations to be used in subcrt(): in 
+  water.IAPWS95(), rename internal function from 'epsilon' to 'diel';
+  in water(), return upper-case versions of names of properties.
 
 - rho.IAPWS95() has modified search interval to give results at
   T < 250 K and P < 300 bar. Thanks to Marc Neveu.