[CHNOSZ-commits] r54 - in pkg/CHNOSZ: . R inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 1 17:20:52 CEST 2013
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
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