[CHNOSZ-commits] r84 - in pkg/CHNOSZ: . data inst man

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

Author: jedick
Date: 2015-05-17 06:44:02 +0200 (Sun, 17 May 2015)
New Revision: 84

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/affinity.Rd
   pkg/CHNOSZ/man/protein.info.Rd
Log:
minor changes to examples


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2015-05-15 09:23:26 UTC (rev 83)
+++ pkg/CHNOSZ/DESCRIPTION	2015-05-17 04:44:02 UTC (rev 84)
@@ -1,6 +1,6 @@
-Date: 2015-05-15
+Date: 2015-05-17
 Package: CHNOSZ
-Version: 1.0.3-21
+Version: 1.0.3-22
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2015-05-15 09:23:26 UTC (rev 83)
+++ pkg/CHNOSZ/data/refs.csv	2015-05-17 04:44:02 UTC (rev 84)
@@ -23,7 +23,6 @@
 DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",http://dx.doi.org/10.1016/0016-7037(95)00403-3
 DRT98,"I. I. Diakonov, K. V. Ragnarsdottir and B. R. Tagirov",1998,"Chem. Geol. 151, 327-347",http://dx.doi.org/10.1016/S0009-2541(98)00088-6
 DS09,"P. Dalla-Betta and M. Schulte",2009,"Int. J. Mol. Sci. 10, 2809-2837",http://dx.doi.org/10.3390/ijms10062809
-DS11,"J. M. Dick and E. L. Shock",2011,"PLoS ONE 6, e22782",http://dx.doi.org/10.1371/journal.pone.0022782
 DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
 DSM+99,"I. I. Diakonov, J. Schott et al.",1999,"Geochim. Cosmochim. Acta 63, 2247-2261",http://dx.doi.org/10.1016/S0016-7037(99)00070-8
 FDK+04,"P. M. B. Fernandes, T. Domitrovic et al.",2004,"FEBS Lett. 556, 153-160",http://dx.doi.org/10.1016/S0014-5793(03)01396-6

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2015-05-15 09:23:26 UTC (rev 83)
+++ pkg/CHNOSZ/inst/NEWS	2015-05-17 04:44:02 UTC (rev 84)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-21 (2015-05-15)
+CHANGES IN CHNOSZ 1.0.3-22 (2015-05-17)
 ---------------------------------------
 
 NEW FEATURES:

Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd	2015-05-15 09:23:26 UTC (rev 83)
+++ pkg/CHNOSZ/man/affinity.Rd	2015-05-17 04:44:02 UTC (rev 84)
@@ -168,7 +168,7 @@
 rxnexpr <- describe.reaction(subcrt("H2O", 1)$reaction, states="all")
 # also in the title is the property with its units
 E.units("J")
-Gexpr <- axis.label("DGr", prefix="k")[[1]]
+Gexpr <- axis.label("DGr", prefix="k")[[2]]
 text(0.5, 0.6, substitute(paste(G~~"for"~~r), list(G=Gexpr, r=rxnexpr)), cex=2)
 text(0.5, 0.2, "after Amend and Shock, 2001 Figure 7", cex=2)
 # now make the plots

Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd	2015-05-15 09:23:26 UTC (rev 83)
+++ pkg/CHNOSZ/man/protein.info.Rd	2015-05-17 04:44:02 UTC (rev 84)
@@ -121,8 +121,7 @@
 log(10) * Astar.residue  # 0.4359, after Eq. 23
 
 \donttest{## using protein.formula: average oxidation state of 
-## carbon of proteins from different organisms
-# after Dick, 2014 (see Supporting Information to make plot with more groups)
+## carbon of proteins from different organisms (Dick, 2014)
 # get amino acid compositions of microbial proteins 
 # generated from the RefSeq database 
 file <- system.file("extdata/refseq/protein_refseq.csv.xz", package="CHNOSZ")
@@ -135,11 +134,11 @@
 # the organism names we search for
 # "" matches all organisms
 terms <- c("Natr", "Halo", "Rhodo", "Acido", "Methylo",
-  "Nitro", "Desulfo", "Chloro", "Geo", "Methano",
+  "Chloro", "Nitro", "Desulfo", "Geo", "Methano",
   "Thermo", "Pyro", "Sulfo", "Buchner", "")
 tps <- thermo$protein$ref[ip]
 plot(0, 0, xlim=c(1, 15), ylim=c(-0.3, -0.05), pch="",
-  ylab="average oxidation state of carbon in proteins",
+  ylab=expression(italic(Z)[C]),
   xlab="", xaxt="n", mar=c(6, 3, 1, 1))
 for(i in 1:length(terms)) {
   it <- grep(terms[i], tps)
@@ -148,8 +147,8 @@
 }
 terms[15] <- paste("all", length(ip))
 axis(1, 1:15, terms, las=2)
-title(main=paste("Average Oxidation State of Carbon:",
-  "Total Protein per taxID in NCBI RefSeq", sep="\n"))
+title(main=paste("Average oxidation state of carbon in proteins",
+  "by taxID in NCBI RefSeq (after Dick, 2014)", sep="\n"))
 }
 }