From noreply at r-forge.r-project.org  Sun Jan  1 11:48:02 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  1 Jan 2017 11:48:02 +0100 (CET)
Subject: [CHNOSZ-commits] r119 - in pkg/CHNOSZ: . R demo inst
	inst/extdata/abundance inst/extdata/protein man
Message-ID: <20170101104802.BB041187A7C@r-forge.r-project.org>

Author: jedick
Date: 2017-01-01 11:48:01 +0100 (Sun, 01 Jan 2017)
New Revision: 119

Added:
   pkg/CHNOSZ/demo/bugstab.R
   pkg/CHNOSZ/inst/extdata/abundance/microbes.csv
   pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/examples.R
   pkg/CHNOSZ/demo/00Index
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/man/extdata.Rd
Log:
add demo bugstab.R


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-01 10:48:01 UTC (rev 119)
@@ -1,6 +1,6 @@
-Date: 2016-12-21
+Date: 2017-01-01
 Package: CHNOSZ
-Version: 1.0.8-6
+Version: 1.0.8-7
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R	2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/R/examples.R	2017-01-01 10:48:01 UTC (rev 119)
@@ -32,7 +32,7 @@
 demos <- function(which=c("sources", "NaCl", "density", 
   "nucleobase", "ORP", "revisit", "findit",
   "ionize", "buffer", "yeastgfp", "mosaic",
-  "copper", "solubility", "wjd", "dehydration"), to.file=FALSE) {
+  "copper", "solubility", "wjd", "dehydration", "bugstab"), to.file=FALSE) {
   # run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
   for(i in 1:length(which)) {
     # say something so the user sees where we are
@@ -41,7 +41,10 @@
       msgout("demos: skipping dehydration demo as to.file is FALSE\n")
       next 
     } else msgout(paste("demos: running '", which[i], "'\n", sep=""))
-    if(to.file & !which[i]=="dehydration") png(paste(which[i],"%d.png",sep=""),width=500,height=500,pointsize=12)
+    if(to.file & !which[i]=="dehydration") {
+      if(which[i]=="bugstab") png(paste(which[i], "%d.png", sep=""), width=700, height=500, pointsize=12)
+      else png(paste(which[i], "%d.png", sep=""), width=500, height=500, pointsize=12)
+    }
     out <- demo(which[i], package="CHNOSZ", character.only=TRUE, echo=FALSE, ask=FALSE)
     if(to.file & !which[i]=="dehydration") dev.off()
   }

Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index	2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/demo/00Index	2017-01-01 10:48:01 UTC (rev 119)
@@ -13,3 +13,4 @@
 solubility      solubility of calcite or CO2(gas) as a function of pH
 wjd             run.wjd() with proteins: cell periphery of yeast
 dehydration     log K of dehydration reactions; SVG file contains tooltips and links
+bugstab         formation potential of microbial proteins in colorectal cancer

Added: pkg/CHNOSZ/demo/bugstab.R
===================================================================
--- pkg/CHNOSZ/demo/bugstab.R	                        (rev 0)
+++ pkg/CHNOSZ/demo/bugstab.R	2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,67 @@
+# formation potential of microbial proteins in colorectal cancer
+# based on "bugstab" function in Supporting Information of Dick, 2016
+# (http://dx.doi.org/10.7717/peerj.2238)
+
+# resolution for plots
+res <- 500
+# basis can be "AA" or "CHNOS"
+basis <- "AA"
+layout(cbind(matrix(sapply(list(c(1, 2), c(3, 4)), function(x) rep(rep(x, each=3), 3)), nrow=6, byrow=TRUE),
+             matrix(rep(c(0, 5, 5, 5, 5, 0), each=4), nrow=6, byrow=TRUE)))
+par(mar=c(3.3, 3.3, 1.5, 1.5), mgp=c(2.1, 0.7, 0), xaxs="i", yaxs="i", las=1, cex=0.9)
+# read bioproject ids, species names
+mfile <- system.file("extdata/abundance/microbes.csv", package="CHNOSZ")
+bugs <- read.csv(mfile, as.is=TRUE)
+# where to keep the locations of healthy zones
+healthbugs <- list()
+if(basis=="CHNOS") {
+  O2 <- c(-85, -65, res)
+  H2O <- c(-15, 5, res)
+} else {
+  O2 <- c(-75, -55, res)
+  H2O <- c(-10, 10, res)
+}
+# the datasets that are considered
+datasets <- c("WCQ+12", "ZTV+14", "CTB+14", "FLJ+15")
+# colors
+blue <- "#4A6FE3"
+lightblue <- "#9DA8E2"
+neutral <- "#E2E2E2"
+lightred <- "#E495A5"
+red <- "#D33F6A"
+# labels
+logfO2lab <- expression(log*italic("f")[O[2]*group("(", italic("g"), ")")])
+logaH2Olab <- expression(log*italic("a")[H[2]*O*group("(", italic("liq"), ")")])
+for(i in 1:4) {
+  ibug <- bugs$study==datasets[i] & (is.na(bugs$logodds) | abs(bugs$logodds) > 0.15)
+  # get amino acid compositions
+  aafile <- system.file("extdata/protein/microbial.aa.csv", package="CHNOSZ")
+  microbial.aa <- read.csv(aafile, stringsAsFactors=FALSE)
+  aa <- microbial.aa[match(bugs$bioproject[ibug], microbial.aa$organism), ]
+  ip <- add.protein(aa)
+  # set up system, calculate relative stabilities
+  col <- ifelse(bugs$upcan[ibug], lightred, lightblue)
+  basis(basis)
+  a <- affinity(O2=O2, H2O=H2O, iprotein=ip, T=37)
+  names <- bugs$abbrv[ibug]
+  d <- CHNOSZ::diagram(a, names=names, fill=col, as.residue=TRUE, tplot=FALSE, xlab=logfO2lab, ylab=logaH2Olab)
+  if(i==1) title(main="fecal 16S rRNA", cex.main=1)
+  if(i==2) title(main="fecal metagenome (ZTV+14)", cex.main=1)
+  if(i==3) title(main="co-abundance groups", cex.main=1)
+  if(i==4) title(main="fecal metagenome (FLJ+15)", cex.main=1)
+  box()
+  label.figure(LETTERS[i], yfrac=0.96, paren=FALSE, font=2, cex=1)
+  # store locations of healthy bug zones
+  p <- d$predominant
+  p[p %in% which(bugs$upcan[ibug])] <- 0
+  p[p != 0] <- 1
+  healthbugs[[i]] <- p
+}
+# now show the healthy zones
+xs <- seq(O2[1], O2[2], length.out=O2[3])
+ys <- seq(H2O[1], H2O[2], length.out=H2O[3])
+hhh <- healthbugs[[1]] + healthbugs[[2]] + healthbugs[[3]] + healthbugs[[4]]
+image(xs, ys, hhh, col=c(red, lightred, neutral, lightblue, blue), useRaster=TRUE, xlab=logfO2lab, ylab=logaH2Olab)
+title(main="cumulative stability count")
+box()
+label.figure("E", yfrac=0.96, paren=FALSE, font=2, cex=1)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2016-12-21 11:10:04 UTC (rev 118)
+++ pkg/CHNOSZ/inst/NEWS	2017-01-01 10:48:01 UTC (rev 119)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-6 (2016-12-21)
+CHANGES IN CHNOSZ 1.0.8-7 (2017-01-01)
 --------------------------------------
 
 - Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -22,6 +22,8 @@
   (citric acid cycle metabolites; thioester species have been kept) and
   from Dick et al., 2006 (methionine and [Met]).
 
+- Add demo bugstab.R.
+
 CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
 ------------------------------------
 

Added: pkg/CHNOSZ/inst/extdata/abundance/microbes.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/abundance/microbes.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/abundance/microbes.csv	2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,75 @@
+species,abbrv,bioproject,study,upcan,abundance,logodds,dx,dy,ZC,nH2O
+"B. vulgatus",Bvu,PRJNA13378,WCQ+12,FALSE,21.49,NA,-0.01,-0.005,-0.1625,-0.8003
+"B. uniformis",Bun,PRJNA18195,WCQ+12,FALSE,21.49,NA,0.007,0,-0.1622,-0.7996
+"R. intestinalis",Rin,PRJNA30005,WCQ+12,FALSE,3.59,NA,-0.01,-0.005,-0.1637,-0.7583
+"A. indistinctus",Ain,PRJNA46373,WCQ+12,FALSE,1.11,NA,0.002,0,-0.1545,-0.7725
+"E. rectale",Ere,PRJNA29071,WCQ+12,FALSE,0.52,NA,-0.007,0,-0.1676,-0.75
+"P. excrementihominis",Pex,PRJNA48497,WCQ+12,FALSE,0.44,NA,0,0,-0.1743,-0.7269
+"P. gingivalis",Pgi,PRJNA48,WCQ+12,TRUE,1.74,NA,-0.01,-0.005,-0.1613,-0.7683
+"E. coli",Eco,PRJNA47121,WCQ+12,TRUE,2.45,NA,0,0,-0.1588,-0.7491
+"E. faecalis",Efa,PRJNA57669,WCQ+12,TRUE,2.4,NA,-0.01,-0.005,-0.1887,-0.7337
+"S. infantarius",Sin,PRJNA20527,WCQ+12,TRUE,1.19,NA,-0.002,0,-0.1854,-0.7303
+"P. stomatis",Pst,PRJNA34073,WCQ+12,TRUE,0.59,NA,0,0,-0.1914,-0.7052
+"B. fragilis",Bfr,PRJNA58195,WCQ+12,TRUE,NA,NA,0,0,-0.1685,-0.7903
+"B. longum",Blo,PRJNA57939,CTB+14,FALSE,NA,NA,0,0,-0.1226,-0.7404
+"F. prausnitzii",Fpr,PRJNA39151,CTB+14,FALSE,NA,NA,0,0,-0.1535,-0.7434
+"F. nucleatum",Fnu,PRJNA49043,CTB+14,TRUE,NA,NA,0,0,-0.2242,-0.7062
+"P. copri",Pco,PRJNA30025,CTB+14,TRUE,NA,NA,0,0,-0.1619,-0.7884
+Coprobacillus,Csp,PRJNA32495,CTB+14,TRUE,NA,NA,0,0,-0.1958,-0.7464
+"F. nucleatum subsp. vincentii",Fnv,PRJNA1419,ZTV+14,TRUE,NA,1.39,0,-0.01,-0.2202,-0.7123
+"F. nucleatum subsp. animalis",Fna,PRJNA32501,ZTV+14,TRUE,NA,0.66,0,0,-0.2232,-0.7083
+"P. stomatis",Pst,PRJNA34073,ZTV+14,TRUE,NA,0.56,-0.004,0,-0.1914,-0.7052
+"P. asaccharolytica",Pas,PRJNA51745,ZTV+14,TRUE,NA,0.38,0,-0.01,-0.1559,-0.7547
+"C. symbiosum",Csy,PRJNA18183,ZTV+14,TRUE,NA,0.34,0.01,-0.006,-0.1719,-0.7393
+"C. hylemonae",Chy,PRJNA30369,ZTV+14,TRUE,NA,0.18,0,0,-0.1676,-0.7341
+"L. salivarius",Lsa,PRJNA31503,ZTV+14,TRUE,NA,0.16,0,0,-0.1896,-0.7298
+"C. scindens",Csc,PRJNA18175,ZTV+14,FALSE,NA,-0.16,0.008,-0.01,-0.1713,-0.741
+"E. eligens",Eel,PRJNA29073,ZTV+14,FALSE,NA,-0.16,-0.008,-0.002,-0.1725,-0.7363
+"M. stadtmanae",Mst,PRJNA15579,ZTV+14,FALSE,NA,-0.18,0,0,-0.1832,-0.7028
+"P. succinatutens",Psu,PRJNA48505,ZTV+14,FALSE,NA,-0.23,0,0,-0.1811,-0.7188
+Ruminococcus,Rsp,PRJNA18179,ZTV+14,FALSE,NA,-0.3,0,-0.01,-0.1733,-0.7467
+"S. salivarius",Ssa,PRJNA34091,ZTV+14,FALSE,NA,-0.54,-0.01,-0.005,-0.1751,-0.74
+"Acidaminococcus intestini DSM 21505",Ain,PRJNA188796,FLJ+15,TRUE,NA,NA,NA,NA,-0.1749,-0.7285
+"Alistipes finegoldii DSM 17242",Afi,PRJNA40775,FLJ+15,TRUE,NA,NA,NA,NA,-0.1427,-0.7847
+"Alistipes onderdonkii WAL 8169 = DSM 19147",Aon,PRJNA174975,FLJ+15,TRUE,NA,NA,NA,NA,-0.1398,-0.7934
+"Alistipes putredinis DSM 17216",Apu,PRJNA19655,FLJ+15,TRUE,NA,NA,NA,NA,-0.1533,-0.7724
+"Bacteroides caccae MR1_13",Bca,PRJNA212635,FLJ+15,TRUE,NA,NA,NA,NA,-0.1683,-0.7914
+"Bacteroides dorei DSM 17855",Bdo,PRJNA27831,FLJ+15,TRUE,NA,NA,-0.01,-0.005,-0.1633,-0.8005
+"Bacteroides eggerthii DSM 20697",Beg,PRJNA27827,FLJ+15,TRUE,NA,NA,NA,NA,-0.1647,-0.7924
+"Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223",Bma,PRJNA169707,FLJ+15,TRUE,NA,NA,NA,NA,-0.1657,-0.7873
+"Bacteroides ovatus strain:KLE1656",Bov,PRJNA257718,FLJ+15,TRUE,NA,NA,0.01,-0.005,-0.1613,-0.8002
+"Bacteroides sp. 1_1_30",B30,PRJNA41955,FLJ+15,TRUE,NA,NA,NA,NA,-0.1614,-0.7975
+"Bacteroides sp. 4_1_36",B36,PRJNA39357,FLJ+15,TRUE,NA,NA,NA,NA,-0.1606,-0.7975
+"Bacteroides vulgatus ATCC 8482",Bvu,PRJNA13378,FLJ+15,TRUE,NA,NA,NA,NA,-0.1625,-0.8003
+"Bacteroides xylanisolvens XB1A",Bxy,PRJNA197168,FLJ+15,TRUE,NA,NA,NA,NA,-0.1625,-0.7973
+"Bilophila wadsworthia ATCC 49260",Bwa,PRJNA223063,FLJ+15,TRUE,NA,NA,NA,NA,-0.1586,-0.7368
+"Burkholderiales bacterium 1_1_47",Bba,PRJNA41965,FLJ+15,TRUE,NA,NA,NA,NA,-0.1738,-0.728
+"butyrate-producing bacterium SS3/4",But,PRJNA197159,FLJ+15,TRUE,NA,NA,0,0,-0.1656,-0.7385
+"Clostridium asparagiforme DSM 15981",Cas,PRJNA29263,FLJ+15,TRUE,NA,NA,0,-0.01,-0.1562,-0.7537
+"Clostridium bolteae WAL-14578",Cbo,PRJNA46383,FLJ+15,TRUE,NA,NA,NA,NA,-0.1599,-0.7509
+"Clostridium hathewayi DSM 13479",Cha,PRJNA30755,FLJ+15,TRUE,NA,NA,NA,NA,-0.1643,-0.7658
+"Clostridium symbiosum ATCC 14940",Csy,PRJNA18183,FLJ+15,TRUE,NA,NA,NA,NA,-0.1719,-0.7393
+"Dialister invisus DSM 15470",Din,PRJNA33143,FLJ+15,TRUE,NA,NA,NA,NA,-0.1727,-0.7398
+"Escherichia coli NC101",Eco,PRJNA47121,FLJ+15,TRUE,NA,NA,NA,NA,-0.1588,-0.7491
+"Fusobacterium sp. oral taxon 370 str. F0437",Fsp,PRJNA50399,FLJ+15,TRUE,NA,NA,0,0,-0.2211,-0.7127
+"Gemella morbillorum CC57F",Gmo,PRJNA71551,FLJ+15,TRUE,NA,NA,NA,NA,-0.2132,-0.7123
+"Lachnospiraceae bacterium 3_1_46FAA",L46,PRJNA40027,FLJ+15,TRUE,NA,NA,NA,NA,-0.1665,-0.7388
+"Lachnospiraceae bacterium 3_1_57FAA_CT1",L57,PRJNA39383,FLJ+15,TRUE,NA,NA,0,0,-0.166,-0.7807
+"Lachnospiraceae bacterium 7_1_58FAA",L58,PRJNA39397,FLJ+15,TRUE,NA,NA,NA,NA,-0.1416,-0.7557
+"Odoribacter splanchnicus DSM 20712",Osp,PRJNA43469,FLJ+15,TRUE,NA,NA,NA,NA,-0.1719,-0.7892
+"Parabacteroides distasonis ATCC 8503",Pdi,PRJNA13485,FLJ+15,TRUE,NA,NA,NA,NA,-0.1693,-0.7889
+"Parabacteroides merdae ATCC 43184",Pme,PRJNA18193,FLJ+15,TRUE,NA,NA,NA,NA,-0.1683,-0.7898
+"Paraprevotella clara YIT 11840",Pcl,PRJNA48501,FLJ+15,TRUE,NA,NA,0,-0.012,-0.1474,-0.8098
+"Parvimonas micra ATCC 33270",Pmi,PRJNA18169,FLJ+15,TRUE,NA,NA,NA,NA,-0.2178,-0.7185
+"Peptostreptococcus stomatis DSM 17678",Pst,PRJNA34073,FLJ+15,TRUE,NA,NA,0,0,-0.1914,-0.7052
+"Porphyromonas somerae DSM 23386",Pso,PRJNA165425,FLJ+15,TRUE,NA,NA,NA,NA,-0.1652,-0.7671
+"Prevotella copri DSM 18205",Pco,PRJNA30025,FLJ+15,TRUE,NA,NA,NA,NA,-0.1619,-0.7884
+"Ruminococcaceae bacterium D16",Rba,PRJNA42541,FLJ+15,TRUE,NA,NA,0.01,-0.005,-0.1557,-0.7426
+"Sutterella wadsworthensis HGA0223",Swa,PRJNA169488,FLJ+15,TRUE,NA,NA,NA,NA,-0.1575,-0.7254
+"Veillonella atypica UC1_FAA_A",Vat,PRJNA212673,FLJ+15,TRUE,NA,NA,NA,NA,-0.1724,-0.7348
+"Actinomyces viscosus C505",Avi,PRJNA38743,FLJ+15,FALSE,NA,NA,0,0,-0.1168,-0.6981
+"Bifidobacterium animalis subsp. lactis AD011",Ban,PRJNA19423,FLJ+15,FALSE,NA,NA,0,0,-0.118,-0.7549
+"Clostridium sp. SS2/1",Csp,PRJNA18201,FLJ+15,FALSE,NA,NA,0.002,-0.012,-0.1861,-0.7338
+"Ruminococcus sp. 5_1_39BFAA",Rsp,PRJNA32503,FLJ+15,FALSE,NA,NA,0,0,-0.1675,-0.7499
+"Streptococcus mutans",Smu,PRJNA13225,FLJ+15,FALSE,NA,NA,-0.004,0,-0.1934,-0.7359
+"Streptococcus thermophilus",Sth,PRJNA13799,FLJ+15,FALSE,NA,NA,0,0,-0.1854,-0.732

Added: pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/microbial.aa.csv	2017-01-01 10:48:01 UTC (rev 119)
@@ -0,0 +1,69 @@
+protein,organism,ref,abbrv,chains,Ala,Cys,Asp,Glu,Phe,Gly,His,Ile,Lys,Leu,Met,Asn,Pro,Gln,Arg,Ser,Thr,Val,Trp,Tyr
+mean,PRJNA13225,NA,NA,1,22.0408163265306,1.68673469387755,16.7071428571429,18.8836734693878,14.0489795918367,18.5051020408163,5.78112244897959,22.8658163265306,21.9331632653061,29.9397959183673,7.16428571428572,14.3311224489796,9.32448979591837,12.0540816326531,11.5459183673469,18.5683673469388,16.5933673469388,19.4790816326531,2.57704081632653,11.3882653061225
+mean,PRJNA13378,NA,NA,1,25.6036900369003,4.84969249692498,20.3945879458796,24.7416974169742,17.0792127921279,25.5567035670357,7.4029520295203,25.7269372693727,25.4361623616236,33.7136531365314,10.5645756457565,19.5377613776139,13.9052890528905,12.7448954489544,17.5675276752767,22.4142681426814,20.7950799507996,23.5758917589175,5.00123001230015,16.9778597785979
+mean,PRJNA13485,NA,NA,1,26.0537662337662,4.43012987012987,20.8332467532467,24.4075324675324,17.518961038961,25.718961038961,6.78051948051948,26.1615584415584,24.1888311688311,35.0501298701298,10.2651948051948,18.6194805194805,14.6511688311688,12.3592207792208,17.9098701298701,23.6522077922078,20.6431168831169,24.4311688311688,4.65142857142856,16.6955844155844
+mean,PRJNA13799,NA,NA,1,20.9127031908489,1.53100541842264,16.3756773028296,19.151715833835,12.8121613485852,18.4455147501505,5.30042143287177,20.6387718242023,19.1896447922938,27.6616496086695,7,12.7814569536424,9.12703190848886,10.524984948826,11.4954846478025,17.3257074051776,15.8609271523179,19.9554485249849,2.32510535821794,10.4274533413606
+mean,PRJNA1419,NA,NA,1,14.272,2.13066666666667,14.608,21.2093333333334,12.9333333333333,16.7755555555556,3.18933333333334,26.4719999999999,27.2102222222223,24.5857777777777,6.37333333333333,17.2204444444444,6.82933333333332,5.88399999999999,8.85822222222225,15.824,13.0933333333334,15.9266666666666,1.77422222222222,11.936
+mean,PRJNA15579,NA,NA,1,16.6505867014342,3.78031290743155,19.5834419817471,21.8826597131682,11.480443285528,19.0977835723598,5.45436766623207,33.1981747066493,26.27444589309,26.9393741851369,7.32855280312908,24.1786179921773,10.1975228161669,8.32268578878747,9.73272490221643,20.1675358539765,21.6988265971317,20.2979139504563,1.77835723598436,13.9406779661017
+mean,PRJNA165425,NA,NA,1,25.6383207750269,3.20452099031216,19.1103336921421,26.272874058127,14.6130247578041,25.3573735199139,7.43702906350914,23.4720129171152,22.1167922497309,36.3304628632939,9.33907427341227,15.2238966630786,14.6286329386437,13.694833153929,18.3509149623251,22.9305705059204,19.7395048439182,23.7922497308934,4.14693218514532,15.2039827771798
+mean,PRJNA169488,NA,NA,1,40.9726368159204,4.13723051409618,18.3793532338308,21.4195688225539,14.301824212272,27.1762023217247,6.51492537313433,18.7039800995025,16.1455223880597,35.2927031509121,8.893864013267,10.8370646766169,16.6504975124378,11.0841625207297,21.4825870646766,21.0290215588723,19.297263681592,25.3897180762852,4.71641791044776,8.46227197346601
+mean,PRJNA169707,NA,NA,1,24.8824163969795,4.54422869471413,19.4867853290183,24.1957928802589,15.925836030205,23.7036138079828,6.8435814455232,24.8357605177993,24.7667206040993,32.1639697950378,9.98975188781014,18.1637001078749,13.0687702265372,12.2545846817691,16.4983818770226,21.11380798274,19.7918015102481,22.5404530744337,4.38754045307443,15.8149946062568
+mean,PRJNA174975,NA,NA,1,33.798286090969,4.59129861568886,20.9881344759393,22.8058668424522,15.5527356624918,28.3388266315095,6.51549110085696,20.9545154911008,17.5840474620962,32.3576137112722,9.45352669742914,14.5906394199077,15.2007251153592,11.387936717205,22.9119973632169,20.5959129861569,21.1064601186553,25.2788398154252,4.90079103493739,15.2943309162821
+mean,PRJNA18169,NA,NA,1,14.7210965435042,3.14481525625745,17.3224076281287,23.5488676996424,15.9201430274136,18.2061978545888,3.67997616209774,29.3569725864124,30.3802145411204,27.3843861740167,7.37067938021454,19.6174016686531,7.51132300357569,6.28665077473183,10.0625744934446,19.2514898688915,14.5023837902265,19.6066746126341,1.9362336114422,12.6573301549464
+mean,PRJNA18175,NA,NA,1,20.7852315394243,4.21426783479349,15.3411764705882,21.2443053817272,10.8272841051314,19.8002503128911,4.87133917396746,20.4105131414268,19.2187734668335,24.2190237797247,8.91914893617022,11.0685857321652,9.17421777221527,8.93391739674594,12.9862327909887,15.2250312891114,14.1624530663329,18.3344180225282,2.51163954943679,11.2352941176471
+mean,PRJNA18179,NA,NA,1,19.6966521850243,4.18936877076412,14.416304625607,22.3163812931255,11.3074367492972,19.0337337081523,4.87733197035523,19.9207768975211,19.884998722208,24.6746741630462,8.7868642984922,11.5502172246358,8.77689752108356,10.0981344237158,12.4444160490672,15.4099156657296,14.7794531050345,18.7937643751597,2.68387426526962,11.3559928443649
+mean,PRJNA18183,NA,NA,1,23.1068702290076,4.45580554439534,15.0176777822418,21.4521896343913,12.107472880675,22.392527119325,4.71313780634793,20.7567296102853,17.9439533949377,26.5359582161511,9.29188429087987,11.4777018883086,10.4244676576938,8.77340297308157,14.3182000803535,16.9887505022097,15.1488549618321,19.3475291281639,2.66834069907593,11.2089192446766
+mean,PRJNA18193,NA,NA,1,21.4787864963504,3.74817518248175,16.944799270073,19.9450273722628,14.4270072992701,21.1142791970803,5.65396897810219,21.035355839416,20.3599452554744,28.1270529197081,8.47217153284673,15.2338047445256,11.8398722627737,10.2294708029197,14.6475821167884,18.5647810218978,16.8496806569343,20.0335310218978,3.82709854014599,13.4206204379562
+mean,PRJNA18195,NA,NA,1,22.7550932875831,4.1559082135964,17.0581170920008,20.3622131674887,14.5496461505469,21.9221531203088,6.19601115161913,20.6041175209093,20.0068625348488,28.7469440274501,8.96161269568946,15.3892343984559,11.9182929444564,10.7014797340768,15.1520480377439,18.7973407677461,17.4550718421617,20.5382800772035,4.14346986918294,14.0160840660519
+mean,PRJNA18201,NA,NA,1,19.7837069782128,4.11398800126302,17.0606251973476,22.0779917903379,12.353646984528,20.0274707925481,5.51215661509315,24.022102936533,25.1594568992738,25.3009156930849,9.67035048942217,13.4840543100726,8.93337543416483,9.98231765077361,11.6769813703821,16.6832964951058,16.1834543732239,19.9538995895169,2.43542784970003,12.6450899905273
+mean,PRJNA188796,NA,NA,1,27.4694505494505,3.90373626373626,16.9920879120879,19.9547252747253,12.5802197802198,24.3010989010989,6.73846153846154,19.5446153846154,19.6228571428572,30.0843956043956,9.59692307692308,10.556043956044,12.5665934065934,9.39252747252747,15.5854945054945,17.2114285714286,17.4892307692308,21.9762637362637,2.9389010989011,10.5327472527473
+mean,PRJNA19423,NA,NA,1,37.9142670157068,3.6053664921466,23.0130890052356,21.6302356020942,12.348167539267,27.6236910994764,8.59489528795812,19.1708115183246,12.9155759162304,31.2840314136126,10.1086387434555,12.3965968586387,16.6753926701571,13.0013089005236,22.0130890052356,20.7284031413613,20.8527486910995,27.6969895287958,4.71989528795812,9.64267015706807
+mean,PRJNA19655,NA,NA,1,23.0047410649161,3.74507658643326,15.4959883296864,18.8778264040846,12.2687819110139,19.7396061269147,4.87490882567469,18.0525164113786,15.27352297593,25.0295404814004,7.17906637490883,11.2407002188184,11.2053245805981,8.99161196207148,17.0568927789934,16.0853391684901,15.6622902990518,18.6520787746171,3.10612691466084,10.9055433989788
+mean,PRJNA197159,NA,NA,1,23.3324423655195,4.17641162712997,16.1660541262947,21.5599732709656,11.5910457734714,21.6204477113264,5.01002338790511,19.6184430337454,19.2746408286001,25.0831941196124,9.26227865018376,11.729368526562,9.9605746742399,8.41129301703976,13.1319746074173,16.2034747744738,15.8606749081189,19.8703641830939,2.6321416638824,11.0350818576679
+mean,PRJNA197168,NA,NA,1,25.0603585205355,4.41093714545042,20.2473337871568,24.2167007034264,16.5200816882233,24.7077376900386,6.55139550714771,25.3253914227365,24.714091218516,32.4878602223735,9.96687088722487,19.2407533469481,13.5883821193556,12.669616519174,16.2645790787384,22.5203085999546,20.7585659178579,22.9897889720898,4.87542545949627,16.8123439981847
+mean,PRJNA20527,NA,NA,1,21.351048269137,1.6611409068747,16.526084836665,18.8347147732813,12.5841053144807,17.900048756704,5.2457337883959,20.4310092637738,19.7591418820088,27.008288639688,7.1496830814237,13.0360799609946,8.65870307167235,10.1452949780595,10.7469527059971,17.1131155533886,16.0141394441736,19.8035104826914,2.33788395904437,10.4275962944905
+mean,PRJNA212635,NA,NA,1,26.2762969332187,4.6262539409573,20.8601318429349,25.4800802522213,17.6864431069074,25.9492691315563,6.94640298079679,27.2032100888507,26.1126397248495,34.8096875895672,10.3983949555747,20.1338492404701,14.445113212955,13.2662654055603,17.3098308971052,23.4130123244482,21.5333906563485,24.633992548008,4.93035253654343,17.3195758096876
+mean,PRJNA212673,NA,NA,1,25.3055091819699,3.27935447968836,18.5386755703951,20.4691151919866,12.2487479131886,23.2309404563161,7.22426265998886,24.328324986088,19.1452420701169,28.5982192543127,9.52643294379519,13.9855314412911,11.841958820256,10.8436282693378,13.9265442404006,18.1107401224263,18.4056761268781,24.0372843628269,3.00556483027266,11.8219254312743
+mean,PRJNA223063,NA,NA,1,33.3793103448275,4.83926147162638,16.7705674721694,20.1830029866957,13.0323106163454,26.9940266087429,6.5164268259571,17.1306000543035,13.8400760249796,34.2112408362748,9.0529459679609,9.70730382840075,16.5495519956557,9.94759706760792,20.2468096660331,18.4713548737442,16.8050502307901,23.0494162367634,4.12163996741787,8.55063806679337
+mean,PRJNA257718,NA,NA,1,25.0828220858896,4.40720858895705,20.3046395705522,24.0761119631902,16.6715874233129,25.0124616564417,6.58454754601227,25.4158358895705,24.8778757668712,32.5776457055215,10.0427530674847,19.7302530674847,13.6144555214724,12.8293711656442,16.354486196319,22.8843941717791,21.1209739263804,23.1708205521472,5.03604294478528,17.0901073619632
+mean,PRJNA27827,NA,NA,1,24.6030719482619,4.39450282942603,18.589329021827,22.2403664780383,15.6725949878739,23.6009161950957,6.5313931554837,23.3777957423875,22.4653732147669,31.0215575316626,9.53570466181622,17.3190514686068,12.8978711937483,11.5295068714632,16.2842899488009,20.2872541094045,19.0573969280517,22.1172190784155,4.37267582861763,15.102937213689
+mean,PRJNA27831,NA,NA,1,22.8658880386629,4.38018525976641,18.3014498590415,21.9981876761981,15.3308497784938,22.8755537656061,6.68445428916633,23.3153443415223,22.8515908175594,30.2388240032219,9.54289166331053,17.5795408779702,12.4454289166331,11.619412001611,15.594039468385,20.2072090213452,18.7466774063633,21.2450664518727,4.56081353201771,15.2869512686267
+mean,PRJNA29071,NA,NA,1,20.7600661886376,4.35135135135135,18.0675675675676,20.1549917264203,11.8339768339768,18.8767236624379,4.96773303916161,22.3554881412024,21.11527854385,23.8996138996139,8.95863210148925,14.0857694429123,8.52702702702703,8.82432432432432,11.7073910645339,17.3968560397132,15.4567015995587,19.3334252619967,2.51847766133481,12.5107556536128
+mean,PRJNA29073,NA,NA,1,22.3793851717903,4.6745027124774,19.451356238698,21.5978300180832,12.4802893309223,21.0401446654611,4.8502712477396,25.5992766726944,22.9717902350814,24.9667269439421,9.99710669077757,16.4998191681736,8.74538878842676,8.42640144665461,12.0321880650995,18.8336347197107,16.8473779385172,22.2397830018083,2.39493670886076,13.7851717902351
+mean,PRJNA29263,NA,NA,1,24.212672337929,4.47902610736286,14.9325315341742,19.8437958345556,11.3575828688765,22.9741859782927,4.64799061308301,17.6485772953946,14.3099149310648,26.0786154297448,8.93825168671166,10.3354356116163,10.876943385157,9.21105896157231,15.6968319155178,15.5243473159284,14.349515987093,19.7263127016721,2.91038427691406,10.6694045174538
+mean,PRJNA30005,NA,NA,1,20.613129381772,4.21308689186317,16.1901423411939,21.9836413851711,11.600594858721,19.1397917994476,5.01317187168048,20.1916294879966,20.1142978542596,23.9572976418101,9.05821117484594,12.727002336945,8.60654344593163,9.55768005098788,12.0596983216486,16.0225196515828,15.6163161249202,18.9532611004885,2.68090078606332,12.2296579562354
+mean,PRJNA30025,NA,NA,1,22.0248726400959,4.21456397962241,17.7030266706623,20.0668264908601,13.9766257117171,20.3371291579263,6.29607431824993,20.8624513035661,22.8118070122865,26.8780341624213,9.36020377584657,15.6448906203177,10.643092598142,11.2553191489361,13.4560982918789,18.1087803416242,16.1744081510339,19.3685945459994,3.76385975427031,13.1000899011088
+mean,PRJNA30369,NA,NA,1,24.4454225352113,4.76458752515091,16.8835513078471,23.2100100603622,11.8677062374246,23.5301810865191,5.16146881287726,21.4034205231389,19.3375251509055,26.9278169014085,9.7381790744467,11.4864185110664,10.2424547283702,9.0067907444668,14.7560362173039,17.1099094567404,16.0978370221328,21.6408450704225,2.59607645875251,12.0928068410463
+mean,PRJNA30755,NA,NA,1,20.7923930269412,4.05731642894876,14.5608821975698,20.1255942947703,11.4363444268358,19.9665874273638,4.72068145800321,18.3419175911253,16.048996302166,24.4124405705227,8.62744321183313,10.6992868462758,9.67974115161115,8.4150818806127,13.2330956154253,15.8433703116746,14.5783148441628,18.1294241944003,2.98349181193871,11.2058901215001
+mean,PRJNA31503,NA,NA,1,19.9008097165992,1.63157894736842,17.6467611336032,19.9838056680162,13,19.0693319838057,5.29605263157895,23.6411943319838,24.3871457489879,28.6821862348178,7.81427125506073,17.0566801619433,9.48481781376519,10.8810728744939,11.3598178137652,18.3355263157895,16.7236842105263,21.0187246963563,2.83248987854252,11.9615384615385
+mean,PRJNA32495,NA,NA,1,17.9624697336561,3.9161622276029,17.5172518159806,19.464588377724,12.9228208232445,18.1413438256658,5.25605326876513,26.8150726392252,22.955205811138,27.4888014527845,8.11228813559323,17.5995762711864,8.330205811138,9.73153753026632,9.55901937046006,17.1180387409201,15.6694915254237,19.0575060532688,2.21428571428571,14.0493341404358
+mean,PRJNA32501,NA,NA,1,15.8007712082262,2.25749785775493,15.7022279348758,23.0278491859469,13.9828620394173,18.2506426735219,3.38474721508141,28.5955441302485,29.5205655526992,26.6473864610111,6.90274207369324,18.3170522707798,7.52527849185947,6.21893744644387,9.39460154241644,16.9185946872322,14.0008568980291,17.4284490145673,1.92416452442159,12.6439588688946
+mean,PRJNA32503,NA,NA,1,22.6450511945392,5.02445961319681,18.1527303754266,23.9453924914676,12.7457337883959,21.8873720136519,5.69368600682594,23.2372013651877,22.8947667804323,27.4081342434585,10,14.2195676905575,10.1871444823663,10.6023890784983,13.6217292377702,18.4374288964733,17.4667235494881,21.3765642775882,2.95449374288965,13.5056882821388
+mean,PRJNA33143,NA,NA,1,24.2819856704196,3.485670419652,15.618219037871,19.8464687819856,12.1750255885363,22.8372569089048,5.89508700102354,20.8137154554759,19.431934493347,25.6596724667349,9.18219037871034,11.3991811668373,10.4237461617195,7.85056294779938,14.5624360286592,16.6223132036848,15.1141248720573,19.74923234391,2.99539406345957,10.4437052200614
+mean,PRJNA34073,NA,NA,1,20.769375,3.361875,22.208125,23.385,13.61,22.703125,4.739375,29.139375,28.565625,30.22625,9.673125,17.28,9.51875,8.5975,14.01875,21.1075,15.54375,22.39375,2.03625,13.6675
+mean,PRJNA34091,NA,NA,1,24.4919678714859,1.48343373493976,19.0943775100401,21.0612449799197,14.0331325301205,21.0883534136546,5.71787148594378,21.382530120482,21.3865461847389,30.1275100401607,7.43222891566265,14.5005020080322,10.6872489959839,12.1184738955823,12.0200803212851,20.0557228915663,19.2615461847389,22.839859437751,2.84136546184739,12.2550200803213
+mean,PRJNA38743,NA,NA,1,45.4557402396598,2.73250869733282,20.1588712794743,19.8739853111712,8.79822187862389,31.2891379976807,7.33397758020873,13.9168921530731,7.59760340162351,35.1175106300735,6.98956320061848,6.74371859296483,19.8550444530344,11.0034789331272,25.676845767298,22.9559335137224,22.126401236954,29.652879783533,5.1217626594511,6.804793196753
+mean,PRJNA39151,NA,NA,1,29.1857246904589,5.1536780772032,16.027676620539,19.1496722505463,10.806627822287,21.1412964311726,5.45593590677349,15.8397669337218,15.8943918426803,28.424981791697,8.16788055353241,10.7840495265841,11.6059723233795,11.0742898761835,14.7549162418063,15.3943918426803,16.6871813546978,20.5138383102695,3.12053896576839,10.5924981791697
+mean,PRJNA39357,NA,NA,1,26.9234693877551,4.65816326530612,20.3077336197637,24.342642320086,16.7234156820623,25.6753490870032,7.15708915145006,24.2134801288936,23.6264769065521,33.7013963480129,10.4317937701396,18.1619226638024,13.953276047261,12.6466165413534,17.6643394199785,22.0679377013963,20.562298603652,23.9513963480129,4.84022556390975,16.5104726100966
+mean,PRJNA39383,NA,NA,1,25.8332058148432,5.56648814078042,19.0586074980872,26.9473603672533,15.4959449120123,25.3937260902831,5.89410864575364,24.0509563886764,21.1473603672532,33.0111706197398,10.8644223412395,14.5121652639633,12.5998469778118,11.4339709257842,16.7851568477429,20.5776587605203,17.8168324407039,22.1825554705432,4.13312930374904,15.1963274674828
+mean,PRJNA39397,NA,NA,1,26.703572033181,4.41171491450821,15.4691044523447,19.5268325715253,10.2310817673946,21.975960724564,5.13932622312511,14.6380565430844,12.8943626206196,27.5840528186897,7.32791603182665,9.28068393431522,12.0722871169799,9.82038259691891,16.7282884713053,15.3360419840867,15.6023362112747,19.2911799559845,3.27916031826646,10.1200270865075
+mean,PRJNA40027,NA,NA,1,22.9425170068027,4.27448979591837,17.7017006802721,25.7044217687075,12.4704081632653,22.0357142857143,5.12040816326531,22.4278911564626,23.7071428571429,26.3608843537415,9.228231292517,13.5625850340136,9.75204081632653,9.87959183673469,13.8636054421769,17.8078231292517,17.2925170068027,21.4663265306122,2.81360544217687,12.7972789115646
+mean,PRJNA40775,NA,NA,1,31.6019292604502,4.51897106109324,19.5154340836013,22.1845659163987,14.7186495176849,25.5308681672026,6.05530546623794,20.3929260450161,17.6170418006431,30.6659163987138,8.95401929260449,14.0594855305466,14.1565916398714,10.7581993569132,21.872347266881,20.0022508038585,20.0868167202572,23.6540192926045,4.36205787781351,14.2819935691318
+mean,PRJNA41955,NA,NA,1,24.8865823740328,4.44480090583128,20.0041517267409,24.0845442536328,16.5051896584261,24.6063408190224,6.60652953387431,25.0915267031516,24.6901302132478,32.4866956029439,9.86450273636535,19.2615587846764,13.4521607850538,12.7063596905076,16.5518022268353,22.6391772032459,20.9773542177769,22.8779014908473,4.84317795810529,16.7950556708813
+mean,PRJNA41965,NA,NA,1,29.0004206983593,4.11653344551956,16.4328986116954,21.0938157341186,14.0719394194363,23.7904922170804,5.71897349600337,19.7038283550694,20.7219183845183,31.4619267984855,8.12242322254943,12.8165755153555,14.2557846024401,10.7454774926378,16.2486327303323,19.9991586032815,16.6432477913336,22.8342448464451,3.80647875473285,9.10727808161548
+mean,PRJNA42541,NA,NA,1,28.0457581830327,4.88844355377422,17.1780227120908,21.0384101536406,11.6706746826987,23.8690714762859,5.60955243820975,17.4509018036072,15.4579158316633,31.5200400801604,8.74215096860387,10.4706078824315,12.8517034068136,12.6710086840347,16.4946559786239,17.3099532398129,17.2551770207081,22.2668670674683,3.4939879759519,10.8196392785571
+mean,PRJNA43469,NA,NA,1,24.7040320274521,4.48012582213326,19.4984272233343,24.7480697740921,16.9977123248499,24.8492993994853,6.45896482699457,25.5187303402917,23.8687446382614,34.1592793823277,9.38547326279668,17.613668859022,13.3122676579926,12.7752359164999,18.0780669144981,21.0346010866457,19.7843866171004,23.7331998856162,4.50185873605948,16.2490706319702
+mean,PRJNA46373,NA,NA,1,30.3820272572402,4.10988074957411,19.4463373083475,21.4041737649063,15.0494037478705,27.6379897785349,6.52683134582624,21.9557069846678,17.9246166950596,33.1946337308347,9.21933560477002,14.4667802385008,15.8211243611584,11.8790459965928,20.8317717206133,21.144804088586,20.2942930153322,24.7695911413969,4.29173764906303,14.0621805792163
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 119

From noreply at r-forge.r-project.org  Sat Jan  7 08:20:14 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  7 Jan 2017 08:20:14 +0100 (CET)
Subject: [CHNOSZ-commits] r120 - in pkg/CHNOSZ: . data inst
Message-ID: <20170107072015.0ECA2186ACE@r-forge.r-project.org>

Author: jedick
Date: 2017-01-07 08:20:14 +0100 (Sat, 07 Jan 2017)
New Revision: 120

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/OBIGT.csv
   pkg/CHNOSZ/inst/NEWS
Log:
correct charge (-2) of NAD(red)-2 in OBIGT.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-01-01 10:48:01 UTC (rev 119)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-07 07:20:14 UTC (rev 120)
@@ -1,6 +1,6 @@
-Date: 2017-01-01
+Date: 2017-01-07
 Package: CHNOSZ
-Version: 1.0.8-7
+Version: 1.0.8-9
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/data/OBIGT.csv
===================================================================
--- pkg/CHNOSZ/data/OBIGT.csv	2017-01-01 10:48:01 UTC (rev 119)
+++ pkg/CHNOSZ/data/OBIGT.csv	2017-01-07 07:20:14 UTC (rev 120)
@@ -1733,7 +1733,7 @@
 NicMP(ox)-,NicMP(ox)-,C11H14N2O8P-,aq,LH06b,NA,18.Aug.03,-321595,-451607,65,20.9799235181644,173,2.3608,117.0671,-18.926,-2.0606,90.2,-19.27,3.3,-1
 H2NAD(red),H2NAD(red),C21H29N7O14P2,aq,LH06b,NA,18.Aug.03,-529740,-780727,163,218.499043977055,346.4,-2.4077,248.0632,-40.2552,-1.9178,325.35,-29.71,5.1,0
 HNAD(red)-,HNAD(red)-,C21H28N7O14P2-,aq,LH06b,NA,18.Aug.03,-527640,-782627,149.6,197.108030592734,341,-2.576,247.6555,-40.1024,-1.9009,326.5,-34.07,6.6,-1
-NAD(red)-2,NAD(red)-2,C21H27N7O14P2-2,aq,LH06b,NA,18.Aug.03,-524440,-783127,137.2,177.198852772467,335.8,-2.6089,247.5732,-40.0662,-1.8975,331.15,-38.1,8.4,-1
+NAD(red)-2,NAD(red)-2,C21H27N7O14P2-2,aq,LH06b,NA,18.Aug.03,-524440,-783127,137.2,177.198852772467,335.8,-2.6089,247.5732,-40.0662,-1.8975,331.15,-38.1,8.4,-2
 H2NAD(ox)+,H2NAD(ox)+,C21H28N7O14P2+,aq,LH06b,NA,18.Aug.03,-535110,-773667,173.5,210.994263862333,346.5,-2.4073,248.1355,-40.2572,-1.9208,323.69,-32.58,5.1,1
 HNAD(ox),HNAD(ox),C21H27N7O14P2,aq,LH06b,NA,18.Aug.03,-533010,-775567,160,189.698852772467,341.1,-2.5756,247.7278,-40.1044,-1.9039,324.84,-36.94,6.6,0
 NAD(ox)-,NAD(ox)-,C21H26N7O14P2-,aq,LH06b,NA,18.Aug.03,-529810,-776067,147.6,169.694072657744,335.9,-2.6085,247.6455,-40.0682,-1.9005,329.5,-40.97,8.4,-1

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-01-01 10:48:01 UTC (rev 119)
+++ pkg/CHNOSZ/inst/NEWS	2017-01-07 07:20:14 UTC (rev 120)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-7 (2017-01-01)
+CHANGES IN CHNOSZ 1.0.8-8 (2017-01-07)
 --------------------------------------
 
 - Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -24,6 +24,9 @@
 
 - Add demo bugstab.R.
 
+- Correct charge (-2) of NAD(red)-2 in OBIGT.csv. Thanks to Peter
+  Canovas.
+
 CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
 ------------------------------------
 


From noreply at r-forge.r-project.org  Sat Jan 21 13:53:11 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 21 Jan 2017 13:53:11 +0100 (CET)
Subject: [CHNOSZ-commits] r121 - in pkg/CHNOSZ: . R inst man
Message-ID: <20170121125311.9C4C81883D6@r-forge.r-project.org>

Author: jedick
Date: 2017-01-21 13:53:11 +0100 (Sat, 21 Jan 2017)
New Revision: 121

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.fasta.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/util.fasta.Rd
Log:
read.fasta() extracts information from UniProt FASTA headers


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-01-07 07:20:14 UTC (rev 120)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-21 12:53:11 UTC (rev 121)
@@ -1,6 +1,6 @@
-Date: 2017-01-07
+Date: 2017-01-21
 Package: CHNOSZ
-Version: 1.0.8-9
+Version: 1.0.8-10
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R	2017-01-07 07:20:14 UTC (rev 120)
+++ pkg/CHNOSZ/R/util.fasta.R	2017-01-21 12:53:11 UTC (rev 121)
@@ -108,6 +108,7 @@
   organism <- bnf
   # protein/gene name is from header line for entry
   # (strip the ">" and go to the first space)
+  missid <- missing(id)
   if(is.null(id)) id <- as.character(palply("", 1:length(i), function(j) {
     # get the text of the line
     f1 <- linefun(i[j],i[j])
@@ -129,8 +130,19 @@
       # 20090507 made stringsAsFactors FALSE
       out <- cbind(data.frame(protein=id, organism=organism,
         ref=ref, abbrv=abbrv, chains=chains, stringsAsFactors=FALSE), counts)
+      # 20170117 extra processing for files from UniProt
+      isUniProt <- grepl("\\|......\\|.*_", out$protein[1])
+      if(isUniProt & missid) {
+        p1 <- sapply(strsplit(out$protein, "\\|"), "[", 1)
+        p2 <- sapply(strsplit(out$protein, "\\|"), "[", 2)
+        p3 <- sapply(strsplit(out$protein, "\\|"), "[", 3)
+        out$abbrv <- sapply(strsplit(p3, "_"), "[", 1)
+        out$organism <- sapply(strsplit(p3, "_"), "[", 2)
+        out$protein <- paste0(p1, "|", p2)
+      }
+      out
     } else if(type %in% c("DNA", "RNA")) {
-      out <- cbind(data.frame(gene=id, organism=organism,
+      cbind(data.frame(gene=id, organism=organism,
         ref=ref, abbrv=abbrv, chains=chains, stringsAsFactors=FALSE), counts)
     }
   } else return(sequences)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-01-07 07:20:14 UTC (rev 120)
+++ pkg/CHNOSZ/inst/NEWS	2017-01-21 12:53:11 UTC (rev 121)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.0.8-8 (2017-01-07)
---------------------------------------
+CHANGES IN CHNOSZ 1.0.8-10 (2017-01-21)
+---------------------------------------
 
 - Add "AA" as a keyword for preset species in basis() (cysteine,
   glutamic acid, glutamine, H2O, oxygen).
@@ -27,6 +27,10 @@
 - Correct charge (-2) of NAD(red)-2 in OBIGT.csv. Thanks to Peter
   Canovas.
 
+- read.fasta() extracts information from UniProt FASTA headers
+  (accession, name, organism) into columns of the output data frame
+  (protein, abbrv, organism).
+
 CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/util.fasta.Rd
===================================================================
--- pkg/CHNOSZ/man/util.fasta.Rd	2017-01-07 07:20:14 UTC (rev 120)
+++ pkg/CHNOSZ/man/util.fasta.Rd	2017-01-21 12:53:11 UTC (rev 121)
@@ -55,6 +55,7 @@
 If the line numbers of the header lines were previously determined, they can be supplied in \code{ihead}. 
 Optionally, the lines of a previously read file may be supplied in \code{lines} (in this case no file is needed so \code{file} should be set to "").
 When \code{ret} is \samp{count}, the names of the proteins in the resulting data frame are parsed from the header lines of the file, unless \code{id} is provided.
+If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
 
 \code{count.aa} counts the occurrences of each amino acid or nucleic-acid base in a sequence (\code{seq}).
 For amino acids, the columns in the returned data frame are in the same order as \code{thermo$protein}.


From noreply at r-forge.r-project.org  Sun Jan 22 11:27:32 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 22 Jan 2017 11:27:32 +0100 (CET)
Subject: [CHNOSZ-commits] r122 - in pkg/CHNOSZ: . R demo inst man
Message-ID: <20170122102732.2CFCA187D84@r-forge.r-project.org>

Author: jedick
Date: 2017-01-22 11:27:31 +0100 (Sun, 22 Jan 2017)
New Revision: 122

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/demo/copper.R
   pkg/CHNOSZ/demo/mosaic.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/mosaic.Rd
Log:
diagram() draws smoother-looking boundary lines


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-22 10:27:31 UTC (rev 122)
@@ -1,6 +1,6 @@
-Date: 2017-01-21
+Date: 2017-01-22
 Package: CHNOSZ
-Version: 1.0.8-10
+Version: 1.0.8-11
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/R/diagram.R	2017-01-22 10:27:31 UTC (rev 122)
@@ -18,7 +18,7 @@
   # sizes
   cex=par("cex"), cex.names=1, cex.axis=par("cex"),
   # line styles
-  lty=NULL, lwd=par("lwd"), dotted=0, 
+  lty=NULL, lwd=par("lwd"), dotted=NULL, 
   # colors
   bg=par("bg"), col=par("col"), col.names=par("col"), fill=NULL, 
   # labels
@@ -353,6 +353,35 @@
         if(!is.null(xrange)) xs <- clipfun(xs, xrange)
         lines(xs, ys, col=col, lwd=lwd)
       }
+      ## new line plotting function 20170122
+      contour.lines <- function(predominant, xlim, ylim, lty, col, lwd) {
+        # the x and y values
+        xs <- seq(xlim[1], xlim[2], length.out=dim(predominant)[1])
+        ys <- seq(ylim[1], ylim[2], length.out=dim(predominant)[2])
+        # reverse any axis that has decreasing values
+        if(diff(xlim) < 0) {
+          predominant <- predominant[nrow(predominant):1, ]
+          xs <- rev(xs)
+        }
+        if(diff(ylim) < 0) {
+          predominant <- predominant[, ncol(predominant):1]
+          ys <- rev(ys)
+        }
+	# the categories (species/groups/etc) on the plot
+	zvals <- unique(as.vector(predominant))
+	# take each possible pair
+	for(i in 1:(length(zvals)-1)) {
+	  for(j in (i+1):length(zvals)) {
+	    z <- predominant
+	    # draw contours only for this pair
+	    z[!z %in% c(zvals[i], zvals[j])] <- NA
+	    # give them neighboring values (so we get one contour line)
+	    z[z==zvals[i]] <- 0
+	    z[z==zvals[j]] <- 1
+	    contour(xs, ys, z, levels=0.5, drawlabels=FALSE, add=TRUE, lty=lty, col=col, lwd=lwd)
+	  }
+	}
+      }
       ## label plot function
       # calculate coordinates for field labels
       plot.names <- function(out, xs, ys, names) {
@@ -421,6 +450,7 @@
         if(!is.null(fill)) fill.color(xs, ys, zs, fill, ngroups)
         pn <- plot.names(zs, xs, ys, names)
         if(!is.null(dotted)) plot.line(zs, xlim, ylim, dotted, col, lwd, xrange=xrange)
+        else contour.lines(predominant, xlim, ylim, lty=lty, col=col, lwd=lwd)
       } # done with the 2D plot!
       out2D <- list(lx=pn$lx, ly=pn$ly, is=pn$is)
     } # end if(nd==2)

Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/demo/copper.R	2017-01-22 10:27:31 UTC (rev 122)
@@ -54,7 +54,7 @@
 }
 
 # add glycine ionization lines
-d <- diagram(m$A.bases, add=TRUE, col="darkblue", dotted=c(2, 3), names=NULL)
+d <- diagram(m$A.bases, add=TRUE, col="darkblue", lty=3, names=NULL)
 text(d$lx, -0.5, Gly, col="darkblue")
 
 # add water lines and title and re-draw a box around the plot

Modified: pkg/CHNOSZ/demo/mosaic.R
===================================================================
--- pkg/CHNOSZ/demo/mosaic.R	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/demo/mosaic.R	2017-01-22 10:27:31 UTC (rev 122)
@@ -24,15 +24,15 @@
 # compare with the plot in Garrels and Christ, 1965
 m1 <- mosaic(bases, bases2, TRUE, pH=pH, Eh=Eh, T=T)
 # make a diagram and add water stability lines
-diagram(m1$A.species)
+diagram(m1$A.species, lwd=2)
 water.lines("pH", "Eh", T=convert(T, "K"), col="seagreen", lwd=1.5)
 # show lines for Fe(aq) = 10^-4 M
 species(c("Fe+2", "Fe+3"), -4)
 m2 <- mosaic(bases, bases2, TRUE, pH=pH, Eh=Eh, T=T)
-diagram(m2$A.species, add=TRUE, names=NULL, dotted=3)
+diagram(m2$A.species, add=TRUE, names=NULL)
 title(main=paste("Iron oxides, sulfides and carbonate in water, log(total S) = -6,",
   "log(total C)=0, after Garrels and Christ, 1965", sep="\n"))
 # overlay the carbonate basis species predominance fields
-diagram(m1$A.bases2, add=TRUE, col="blue", col.names="blue", dotted=3)
+diagram(m1$A.bases2, add=TRUE, col="blue", col.names="blue", lty=3)
 # reset the database, as it was changed in this example
 data(thermo)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/inst/NEWS	2017-01-22 10:27:31 UTC (rev 122)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-10 (2017-01-21)
+CHANGES IN CHNOSZ 1.0.8-11 (2017-01-22)
 ---------------------------------------
 
 - Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -31,6 +31,10 @@
   (accession, name, organism) into columns of the output data frame
   (protein, abbrv, organism).
 
+- diagram() draws smoother boundary lines (with contour(); 'lty' is
+  usable), at the expense of not being precisely aligned with the grid
+  used for plotting colors. For the old behavior, use dotted=0.
+
 CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/man/diagram.Rd	2017-01-22 10:27:31 UTC (rev 122)
@@ -13,7 +13,7 @@
     xrange=NULL, mar=NULL, yline=par("mgp")[1]+0.7, side=1:4,
     ylog=TRUE, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
     cex=par("cex"), cex.names=1, cex.axis=par("cex"),
-    lty=NULL, lwd=par("lwd"), dotted=0,
+    lty=NULL, lwd=par("lwd"), dotted=NULL,
     bg=par("bg"), col=par("col"), col.names=par("col"), fill=NULL,
     names=NULL, main=NULL, legend.x="topright", add=FALSE, plot.it=TRUE,
     tplot=TRUE, ...)
@@ -85,8 +85,13 @@
 On 2-D diagrams, the fields represent the species with the highest equilibrium activity.
 \code{fill} determines the color of the predominance fields, \code{col} that of the boundary lines.
 By default, \code{\link{heat.colors}} are used to fill the predominance fields in diagrams on the screen plot device.
-The style of the boundary lines on 2-D diagrams can be altered by supplying one or more non-zero integers in \code{dotted}, which indicates the fraction of line segments to omit; a value of \samp{1} or NULL for \code{dotted} has the effect of not drawing the boundary lines.
 
+As of CHNOSZ 1.0.8-11, a new default line-drawing procedure has been implemented.
+This uses \code{\link{contour}} to draw smooth-looking diagonal and curved lines, at the expense of not coinciding exactly with the the rectangular grid (which is still used for drawing colors).
+\code{lty}, \code{col}, and \code{lwd} can be specified, but limiting the lines via \code{xrange} is not currently supported.
+To go back to the old behavior for drawing lines, set \code{dotted} to \samp{0}.
+The old behavior does not follow \code{lty}; instead, the style of the boundary lines on 2-D diagrams can be altered by supplying one or more non-zero integers in \code{dotted}, which indicates the fraction of line segments to omit; a value of \samp{1} or NULL for \code{dotted} has the effect of not drawing the boundary lines.
+
 \code{normalize} and \code{as.residue} apply only to the 2-D diagrams, and only when \code{eout} is the output from \code{affinity}.
 With \code{normalize}, the activity boundaries are calculated as between the residues of the species (the species divided by the balance coefficients), then the activities are rescaled to the whole species formulas.
 With \code{as.residue}, the activity boundaries are calculated as between the residues of the species, and no rescaling is performed.

Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd	2017-01-21 12:53:11 UTC (rev 121)
+++ pkg/CHNOSZ/man/mosaic.Rd	2017-01-22 10:27:31 UTC (rev 122)
@@ -63,16 +63,16 @@
 # calculate affinities using the predominant basis species
 m1 <- mosaic(bases, pH=pH, Eh=Eh, T=T)
 # make a diagram and add water stability lines
-diagram(m1$A.species)
+diagram(m1$A.species, lwd=2)
 water.lines("pH", "Eh", T=convert(T, "K"), col="seagreen", lwd=1.5)
 # show lines for Fe(aq) = 10^-4 M
 species(c("Fe+2", "Fe+3"), -4)
 m2 <- mosaic(bases, pH=pH, Eh=Eh, T=T)
-diagram(m2$A.species, add=TRUE, names=NULL, dotted=3)
+diagram(m2$A.species, add=TRUE, names=NULL)
 title(main=paste("Iron oxides and sulfides in water, log(total S) = -6",
   "After Garrels and Christ, 1965", sep="\n"))
 # we could overlay the basis species predominance fields
-#diagram(m1$A.bases, add=TRUE, col="blue", col.names="blue", dotted=3)
+#diagram(m1$A.bases, add=TRUE, col="blue", col.names="blue", lty=3)
 }
 
 \references{


From noreply at r-forge.r-project.org  Sat Jan 28 09:29:14 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 28 Jan 2017 09:29:14 +0100 (CET)
Subject: [CHNOSZ-commits] r123 - in pkg/CHNOSZ: . R inst man tests/testthat
Message-ID: <20170128082914.8923D185811@r-forge.r-project.org>

Author: jedick
Date: 2017-01-28 09:29:14 +0100 (Sat, 28 Jan 2017)
New Revision: 123

Removed:
   pkg/CHNOSZ/R/msgout.R
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/EOSregress.R
   pkg/CHNOSZ/R/affinity.R
   pkg/CHNOSZ/R/buffer.R
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/R/equilibrate.R
   pkg/CHNOSZ/R/examples.R
   pkg/CHNOSZ/R/findit.R
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/R/iprotein.R
   pkg/CHNOSZ/R/more.aa.R
   pkg/CHNOSZ/R/mosaic.R
   pkg/CHNOSZ/R/nonideal.R
   pkg/CHNOSZ/R/protein.info.R
   pkg/CHNOSZ/R/read.expr.R
   pkg/CHNOSZ/R/revisit.R
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/R/util.affinity.R
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/R/util.fasta.R
   pkg/CHNOSZ/R/util.program.R
   pkg/CHNOSZ/R/util.water.R
   pkg/CHNOSZ/R/water.R
   pkg/CHNOSZ/R/wjd.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/util.program.Rd
   pkg/CHNOSZ/tests/testthat/test-equilibrate.R
   pkg/CHNOSZ/tests/testthat/test-protein.info.R
Log:
remove msgout()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-28 08:29:14 UTC (rev 123)
@@ -1,6 +1,6 @@
-Date: 2017-01-22
+Date: 2017-01-28
 Package: CHNOSZ
-Version: 1.0.8-11
+Version: 1.0.8-13
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/EOSregress.R
===================================================================
--- pkg/CHNOSZ/R/EOSregress.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/EOSregress.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -167,7 +167,7 @@
   }
   # plot regression line at a single P
   P <- mean(exptdata$P)
-  msgout("EOSplot: plotting line for P=", P, " bar\n")
+  message("EOSplot: plotting line for P=", P, " bar")
   xs <- seq(xlim[1], xlim[2], length.out=200)
   calc.X <- EOScalc(coefficients, xs, P, ...)
   lines(xs, calc.X, lty=lty)

Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/affinity.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -65,7 +65,7 @@
     ibufbasis <- which(!can.be.numeric(mybasis$logact))
     if(!is.null(mybasis) & length(ibufbasis) > 0) {
       buffer <- TRUE
-      msgout('affinity: loading buffer species\n')
+      message('affinity: loading buffer species')
       if(!is.null(thermo$species)) is.species <- 1:nrow(thermo$species) else is.species <- numeric()
       is.buffer <- buffer(logK=NULL)
       thermo <- get("thermo", "CHNOSZ")

Modified: pkg/CHNOSZ/R/buffer.R
===================================================================
--- pkg/CHNOSZ/R/buffer.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/buffer.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -22,8 +22,8 @@
       if(state[1]=='') {
         thermo$buffers <- thermo$buffers[-imod,]
         assign("thermo", thermo, "CHNOSZ")
-        msgout(paste('mod.buffer: removed ',c2s(species),' in ',
-          c2s(unique(name)),' buffer.\n',sep=''))
+        message(paste('mod.buffer: removed ',c2s(species),' in ',
+          c2s(unique(name)),' buffer.',sep=''))
       } else {
         if(missing(state)) state <- thermo$buffers$state[imod]
         if(missing(logact)) logact <- thermo$buffers$logact[imod]
@@ -35,11 +35,11 @@
         thermo$buffers$logact[imod] <- logact
         assign("thermo", thermo, "CHNOSZ")
         if(identical(state.old,state) & identical(logact.old,logact)) {
-          msgout(paste('mod.buffer: nothing changed for ',
-            c2s(species),' in ',c2s(unique(name)),' buffer.\n',sep=''))
+          message(paste('mod.buffer: nothing changed for ',
+            c2s(species),' in ',c2s(unique(name)),' buffer.',sep=''))
         } else {
-          msgout(paste('mod.buffer: changed state and/or logact of ',
-            c2s(species),' in ',c2s(unique(name)),' buffer.\n',sep=''))
+          message(paste('mod.buffer: changed state and/or logact of ',
+            c2s(species),' in ',c2s(unique(name)),' buffer.',sep=''))
         }
       }
     } else {
@@ -51,7 +51,7 @@
     t <- data.frame(name=name,species=species,state=state,logact=logact)
     thermo$buffers <- rbind(thermo$buffers,t)
     assign("thermo", thermo, "CHNOSZ")
-    msgout(paste('mod.buffer: added ',c2s(unique(name)),'.\n',sep=''))
+    message(paste('mod.buffer: added ',c2s(unique(name)),'.',sep=''))
   }
   return(invisible(thermo$buffers[thermo$buffers$name %in% name,]))
 }
@@ -163,7 +163,7 @@
   if(is.null(newbasis)) context <- '' else context <- paste(', ',basisnames[newbasis],' (conserved)',sep='')
   reqtext <- paste(c2s(basisnames[ibasisrequested]),' (active)',sep='')
   if(length(ibasisadded)==0) addtext <- '' else addtext <- paste(', ',c2s(basisnames[ibasisadded]),sep='')
-  msgout(paste('buffer: ( ',bufname,' ) for activity of ',reqtext,addtext,context,'\n',sep=''))
+  message(paste('buffer: ( ',bufname,' ) for activity of ',reqtext,addtext,context,sep=''))
   #print(bufbasis)
   # there could still be stuff here (over-defined system?)
   xx <- bufbasis[,-ibasis,drop=FALSE]

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/diagram.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -72,7 +72,7 @@
     plotvar <- eout$property
     # we change 'A' to 'A/2.303RT' so the axis label is made correctly
     if(plotvar=="A") plotvar <- "A/2.303RT"
-    msgout(paste("diagram: plotting", plotvar, "from affinity(), divided by balancing coefficients\n"))
+    message(paste("diagram: plotting", plotvar, "from affinity(), divided by balancing coefficients"))
   }
 
   ## number of dimensions (T, P or chemical potentials that are varied)
@@ -85,8 +85,8 @@
     if(normalize & as.residue) stop("'normalize' and 'as.residue' can not both be TRUE")
     if(!eout.is.aout) stop("'normalize' or 'as.residue' can be TRUE only if 'eout' is the output from affinity()")
     if(nd!=2) stop("'normalize' or 'as.residue' can be TRUE only for a 2-D (predominance) diagram")
-    if(normalize) msgout("diagram: using 'normalize' in calculation of predominant species\n")
-    else msgout("diagram: using 'as.residue' in calculation of predominant species\n")
+    if(normalize) message("diagram: using 'normalize' in calculation of predominant species")
+    else message("diagram: using 'as.residue' in calculation of predominant species")
   }
 
   ## sum activities of species together in groups 20090524

Modified: pkg/CHNOSZ/R/equilibrate.R
===================================================================
--- pkg/CHNOSZ/R/equilibrate.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/equilibrate.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -19,7 +19,7 @@
   ispecies <- ispecies[!ina[ispecies]]
   if(length(ispecies)==0) stop("all species have NA affinities")
   if(!identical(ispecies, 1:nspecies)) {
-    msgout(paste("equilibrate: using", length(ispecies), "of", nspecies, "species\n"))
+    message(paste("equilibrate: using", length(ispecies), "of", nspecies, "species"))
     aout$species <- aout$species[ispecies, ]
     aout$values <- aout$values[ispecies]
     n.balance <- n.balance[ispecies]
@@ -27,7 +27,7 @@
   ## number of species that are left
   nspecies <- length(aout$values)
   ## say what the balancing coefficients are
-  if(length(n.balance) < 100) msgout(paste("equilibrate: n.balance is", c2s(n.balance), "\n"))
+  if(length(n.balance) < 100) message(paste("equilibrate: n.balance is", c2s(n.balance)))
   ## logarithm of total activity of the balance
   if(is.null(loga.balance)) {
     # sum up the activities, then take absolute value
@@ -35,15 +35,15 @@
     sumact <- abs(sum(10^aout$species$logact * n.balance))
     loga.balance <- log10(sumact)
   }
-  msgout(paste0("equilibrate: loga.balance is ", loga.balance, "\n"))
+  message(paste0("equilibrate: loga.balance is ", loga.balance))
   ## normalize -- normalize the molar formula by the balance coefficients
   m.balance <- n.balance
   isprotein <- grepl("_", as.character(aout$species$name))
   if(normalize | as.residue) {
     if(any(n.balance < 0)) stop("one or more negative balancing coefficients prohibit using normalized molar formulas")
     n.balance <- rep(1, nspecies)
-    if(as.residue) msgout(paste("equilibrate: using 'as.residue' for molar formulas\n"))
-    else msgout(paste("equilibrate: using 'normalize' for molar formulas\n"))
+    if(as.residue) message(paste("equilibrate: using 'as.residue' for molar formulas"))
+    else message(paste("equilibrate: using 'normalize' for molar formulas"))
   } else m.balance <- rep(1, nspecies)
   ## Astar: the affinities/2.303RT of formation reactions with
   ## formed species in their standard-state activities
@@ -57,7 +57,7 @@
     if(all(n.balance==1)) method <- method[1]
     else method <- method[2]
   }
-  msgout(paste("equilibrate: using", method[1], "method\n"))
+  message(paste("equilibrate: using", method[1], "method"))
   if(method[1]=="boltzmann") loga.equil <- equil.boltzmann(Astar, n.balance, loga.balance)
   else if(method[1]=="reaction") loga.equil <- equil.reaction(Astar, n.balance, loga.balance)
   ## if we normalized the formulas, get back to activities to species
@@ -253,16 +253,16 @@
   if(is.numeric(balance[1])) {
     # a numeric vector
     n.balance <- rep(balance, length.out=length(aout$values))
-    msgout("balance: from numeric argument value\n")
+    message("balance: from numeric argument value")
   } else {
     # "length" for balancing on protein length
     if(identical(balance, "length")) {
       if(!all(isprotein)) stop("length was the requested balance, but some species are not proteins")
       n.balance <- protein.length(aout$species$name)
-      msgout("balance: from protein length\n")
+      message("balance: from protein length")
     } else if(identical(balance, "volume")) {
       n.balance <- info(aout$species$ispecies, check.it=FALSE)$V
-      msgout("balance: from volume")
+      message("balance: from volume")
     } else {
       # is the balance the name of a basis species?
       if(length(ibalance)==0) {
@@ -271,7 +271,7 @@
       }
       # the name of the basis species (need this if we got ibalance which which.balance, above)
       balance <- colnames(aout$species)[ibalance[1]]
-      msgout(paste("balance: from moles of", balance, "in formation reactions\n"))
+      message(paste("balance: from moles of", balance, "in formation reactions"))
       # the balance vector
       n.balance <- aout$species[, ibalance[1]]
       # we check if that all formation reactions contain this basis species

Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/examples.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -36,11 +36,11 @@
   # run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
   for(i in 1:length(which)) {
     # say something so the user sees where we are
-    msgout("------------\n")
+    message("------------")
     if(which[i]=="dehydration" & !to.file) {
-      msgout("demos: skipping dehydration demo as to.file is FALSE\n")
+      message("demos: skipping dehydration demo as to.file is FALSE")
       next 
-    } else msgout(paste("demos: running '", which[i], "'\n", sep=""))
+    } else message(paste("demos: running '", which[i], "'", sep=""))
     if(to.file & !which[i]=="dehydration") {
       if(which[i]=="bugstab") png(paste(which[i], "%d.png", sep=""), width=700, height=500, pointsize=12)
       else png(paste(which[i], "%d.png", sep=""), width=500, height=500, pointsize=12)

Modified: pkg/CHNOSZ/R/findit.R
===================================================================
--- pkg/CHNOSZ/R/findit.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/findit.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -51,7 +51,7 @@
     else {
       # in the ith loop we consider intervals
       # of rat^(i-1) of the ranges specified at start
-      msgout(paste("optimal:",round(curr,4),"",""))
+      message(paste("optimal:",round(curr,4),"",""), appendLF=FALSE)
       range <- range(lim)
       int <- abs(diff(range)) * rat^(i-1)
       mylims <- c(curr-int/2, curr+int/2)
@@ -61,7 +61,7 @@
       # reverse the order if the axis is reversed
       if(diff(lim) < 0) mylims <- rev(mylims)
     }
-    msgout(paste("new limits:",round(mylims[1],4),round(mylims[2],4),"\n"))
+    message(paste("new limits:",round(mylims[1],4),round(mylims[2],4)))
     return(mylims)
   }
 
@@ -76,14 +76,14 @@
   # loop for the specified number of iterations
   # (todo: loop until an error threshhold is reached)
   for(i in 1:niter) {
-    msgout(paste("\n###### findit: iteration",i,"of",niter,"\n"))
+    message(paste("\n###### findit: iteration",i,"of",niter))
     # to generate the argument list for affinity
     # with the variables specified in lims
     aargs <- list()
     for(j in 1:length(lims)) {
       if(names(lims)[j] %in% rownames(basis)) {
         ibasis <- match(names(lims)[j],rownames(basis))
-        msgout(paste("###",rownames(basis)[ibasis],""))
+        message(paste("###",rownames(basis)[ibasis],""), appendLF=FALSE)
         # the starting search limits for this species
         lim <- lims[[j]]
         # center the search interval on the current values
@@ -93,7 +93,7 @@
         names(myarg) <- rownames(basis)[ibasis]
         aargs <- c(aargs,myarg)
       } else if(names(lims[j]) %in% c("T","P")) {
-        msgout(paste("###",names(lims[j]),""))
+        message(paste("###",names(lims[j]),""), appendLF=FALSE)
         if(names(lims[j])=="T") {
           lim <- lims$T
           curr <- T

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/info.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -67,8 +67,8 @@
       available.states <- thermo$obigt$state[matches.species]
       if(length(available.states)==1) a.s.verb <- "is" else a.s.verb <- "are"
       a.s.text <- paste("'", available.states, "'", sep="", collapse=" ")
-      msgout("info.character: requested state '", state, "' for ", species, 
-        " but only ", a.s.text, " ", a.s.verb, " available\n")
+      message("info.character: requested state '", state, "' for ", species, 
+        " but only ", a.s.text, " ", a.s.verb, " available")
       return(NA)
     }
     matches.species <- matches.state
@@ -83,8 +83,8 @@
   if(length(ispecies) > length(ispecies.out)) {
     ispecies.other <- ispecies[!ispecies %in% ispecies.out]
     othertext <- paste(thermo$obigt$state[ispecies.other], collapse=", ")
-    msgout("info.character: found ", species, "(", thermo$obigt$state[ispecies.out], 
-      "), also available in ", othertext, "\n")
+    message("info.character: found ", species, "(", thermo$obigt$state[ispecies.out], 
+      "), also available in ", othertext)
   }
   return(ispecies.out)
 }
@@ -113,8 +113,8 @@
   if(length(naGHS)==1) {
     # calculate a single missing one of G, H, or S from the others
     GHS <- as.numeric(GHS(as.character(this$formula), G=this[,8], H=this[,9], S=this[,10]))
-    msgout("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
-      this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2), "\n")
+    message("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
+      this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2))
     this[, naGHS+7] <- GHS[naGHS]
   } 
   # now perform consistency checks for GHS and EOS parameters if check.it=TRUE
@@ -125,7 +125,7 @@
     calcCp <- checkEOS(this, this$state, "Cp")
     # fill in NA heat capacity
     if(!is.na(calcCp) & is.na(this$Cp)) {
-      msgout("info.numeric: Cp of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcCp, 2), "\n")
+      message("info.numeric: Cp of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcCp, 2))
       this$Cp <- as.numeric(calcCp)
     }
     # check tabulated volumes - only for aq (HKF equation)
@@ -133,7 +133,7 @@
       calcV <- checkEOS(this, this$state, "V")
       # fill in NA volume
       if(!is.na(calcV) & is.na(this$V)) {
-        msgout("info.numeric: V of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcV, 2), "\n")
+        message("info.numeric: V of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcV, 2))
         this$V <- as.numeric(calcV)
       }
     }
@@ -158,20 +158,20 @@
   if(!is.na(approx.species[1])) {
     # show the names of the species
     if(length(approx.species)==1) {
-      msgout("info.approx: '", species, "' is similar to ", info.text(approx.species), "\n")
+      message("info.approx: '", species, "' is similar to ", info.text(approx.species))
     } else {
       napprox.max <- 25
       exttext <- ":"
       if(length(approx.species) > napprox.max) exttext <- paste(" (showing first ", napprox.max, ")", sep="")
-      msgout("info.approx: '", species, "' is ambiguous; has approximate matches to ", 
-        length(approx.species), " species", exttext, "\n")
+      message("info.approx: '", species, "' is ambiguous; has approximate matches to ", 
+        length(approx.species), " species", exttext)
       printout <- capture.output(print(thermo$obigt$name[head(approx.species, napprox.max)]))
-      msgout(paste(printout, collapse="\n"), "\n")
+      message(paste(printout, collapse="\n"))
     }
     return(approx.species)
   }
   # if we got here there were no approximate matches
-  msgout("info.approx: '", species, "' has no approximate matches\n")
+  message("info.approx: '", species, "' has no approximate matches")
   return(NA)
 }
 
@@ -180,13 +180,13 @@
   ## if no species are requested, summarize the available data  20101129
   thermo <- get("thermo")
   if(is.null(species)) {
-    msgout("info: 'species' is NULL; summarizing information about thermodynamic data...\n")
-    msgout(paste("thermo$obigt has", nrow(thermo$obigt[thermo$obigt$state=="aq", ]), "aqueous,",
-      nrow(thermo$obigt), "total species\n"))
-    msgout(paste("number of literature sources: ", nrow(thermo$refs), ", elements: ",
-      nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), "\n", sep=""))
-    msgout(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
-      length(unique(thermo$protein$organism)), "organisms\n"))
+    message("info: 'species' is NULL; summarizing information about thermodynamic data...")
+    message(paste("thermo$obigt has", nrow(thermo$obigt[thermo$obigt$state=="aq", ]), "aqueous,",
+      nrow(thermo$obigt), "total species"))
+    message(paste("number of literature sources: ", nrow(thermo$refs), ", elements: ",
+      nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), sep=""))
+    message(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
+      length(unique(thermo$protein$organism)), "organisms"))
     # print information about SGD.csv, ECO.csv, HUM.csv
     more.aa(organism="Sce")
     more.aa(organism="Eco")

Modified: pkg/CHNOSZ/R/iprotein.R
===================================================================
--- pkg/CHNOSZ/R/iprotein.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/iprotein.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -31,7 +31,7 @@
   if(any(is.na(iprotein))) {
     nNA <- sum(is.na(iprotein))
     if(nNA==1) ptext <- "" else ptext <- "s"
-    msgout("iprotein: ", sum(is.na(iprotein)), " protein", ptext, " not matched\n")
+    message("iprotein: ", sum(is.na(iprotein)), " protein", ptext, " not matched")
   }
   return(iprotein)
 }
@@ -88,9 +88,9 @@
     # now the species name
     name <- paste(aa$protein, aa$organism, sep="_")
     # make some noise for the user
-    msgout("aa2eos: found ")
-    msgout(name, " (", f, ", ")
-    msgout(round(length, 3), " residues)\n")
+    message("aa2eos: found ", appendLF=FALSE)
+    message(name, " (", f, ", ", appendLF=FALSE)
+    message(round(length, 3), " residues)")
     ref <- aa$ref
     header <- data.frame(name=name, abbrv=NA, formula=f, state=state, ref1=ref, ref2=NA, date=NA, stringsAsFactors=FALSE)
     eosout <- cbind(header, eos)
@@ -128,7 +128,7 @@
   if(any(ina)) {
     aa <- aa[!ina, ]
     abundance <- abundance[!ina]
-    msgout("aasum: dropped ", sum(ina), " proteins with NA composition and/or abundance\n")
+    message("aasum: dropped ", sum(ina), " proteins with NA composition and/or abundance")
   }
   # we don't know how to deal with different numbers of polypeptide chains
   if(!all(aa$chains==aa$chains[1])) stop("different numbers of polypeptide chains")
@@ -183,7 +183,7 @@
   # return the new rownumbers
   ip <- iprotein(po)
   # make some noise
-  if(!all(ipdup)) msgout("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo$protein\n")
-  if(any(ipdup)) msgout("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo$protein\n")
+  if(!all(ipdup)) message("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo$protein")
+  if(any(ipdup)) message("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo$protein")
   return(ip)
 }

Modified: pkg/CHNOSZ/R/more.aa.R
===================================================================
--- pkg/CHNOSZ/R/more.aa.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/more.aa.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -12,7 +12,7 @@
   mydata <- read.csv(datafile, as.is=TRUE)
   # if protein is not supplied, just give some information about the datafile
   if(is.null(protein)) {
-    msgout("more.aa: ", datapath, " has data for ", nrow(mydata), " proteins\n")
+    message("more.aa: ", datapath, " has data for ", nrow(mydata), " proteins")
     return(invisible())
   }
   # which columns to search for matches
@@ -41,7 +41,7 @@
     inotmatch <- which(is.na(imatch)) 
     if(length(inotmatch) > 0) {
       if(length(inotmatch)==1) verb <- " was" else verb <- " were"
-      msgout("more.aa: ", paste(protein[[i]][inotmatch], collapse=" "), verb, " not matched\n")
+      message("more.aa: ", paste(protein[[i]][inotmatch], collapse=" "), verb, " not matched")
     }
     aa <- data.frame(mydata[imatch, iaa])
     # add the identifying columns

Modified: pkg/CHNOSZ/R/mosaic.R
===================================================================
--- pkg/CHNOSZ/R/mosaic.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/mosaic.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -21,7 +21,7 @@
   # a list where we'll keep the affinity calculations
   affs <- list()
   for(i in seq_along(bases)) {
-    msgout(paste("mosaic: current basis species is", bases[i], "\n", sep=" "))
+    message(paste("mosaic: current basis species is", bases[i], sep=" "))
     # set up argument list: name of swapped-in basis species
     if(!is.na(iswap)) names(myargs)[iswap] <- bases[i]
     # calculate affinities
@@ -46,7 +46,7 @@
     }
   }
   # calculate affinities of formation of basis species
-  msgout(paste("mosaic: combining diagrams for", paste(bases, collapse=" "), "\n", sep=" "))
+  message(paste("mosaic: combining diagrams for", paste(bases, collapse=" "), sep=" "))
   ispecies <- species()$ispecies
   species.logact <- species()$logact
   species(delete=TRUE)

Deleted: pkg/CHNOSZ/R/msgout.R
===================================================================
--- pkg/CHNOSZ/R/msgout.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/msgout.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -1,57 +0,0 @@
-# CHNOSZ/msgout.R
-# msgout() is a variation on message() from base R
-# 20120117 jmd, adapted from...
-
-#  File src/library/base/R/message.R
-#  Part of the R package, http://www.R-project.org
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation; either version 2 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  A copy of the GNU General Public License is available at
-#  http://www.r-project.org/Licenses/
-
-
-# a variant of message(), using stdout instead of stderr
-# and with a default setting of appendLF = FALSE
-# this is now used for informative messages in CHNOSZ 
-# (in info() and other functions)
-# so that they show up on the console and in Sweave output, but are suppressed
-# when running the 'test_that' testing scripts
-# (messages produced by cat() would mess up the rows of green dots)
-# the appendLF = FALSE is so that the cat("...\n") statements used previously
-# can all be replaced with msgout without further modification
-msgout <-
-function(..., domain = NULL, appendLF = FALSE)
-{
-    args <- list(...)
-    cond <- if (length(args) == 1L && inherits(args[[1L]], "condition")) {
-        if(nargs() > 1L)
-            warning("additional arguments ignored in message()")
-        args[[1L]]
-    } else {
-        msg <- .makeMessage(..., domain=domain, appendLF = appendLF)
-        call <- sys.call()
-        simpleMessage(msg, call)
-    }
-    defaultHandler <- function(c) {
-        ## Maybe use special connection here?
-        #cat(conditionMessage(c), file=stderr(), sep="")
-        cat(conditionMessage(c), file="", sep="")
-    }
-    withRestarts({
-        signalCondition(cond)
-        ## We don't get to the default handler if the signal
-        ## is handled with a non-local exit, e.g. by
-        ## invoking the muffleMessage restart.
-        defaultHandler(cond)
-    }, muffleMessage = function() NULL)
-    invisible()
-}

Modified: pkg/CHNOSZ/R/nonideal.R
===================================================================
--- pkg/CHNOSZ/R/nonideal.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/nonideal.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -62,7 +62,7 @@
     proptable[[i]] <- myprops
     if(didit) ndid <- ndid + 1
   }
-  if(ndid > 0) msgout(paste('nonideal:',ndid,'species were nonideal\n'))
+  if(ndid > 0) message(paste('nonideal:',ndid,'species were nonideal'))
   return(proptable)
 }
 

Modified: pkg/CHNOSZ/R/protein.info.R
===================================================================
--- pkg/CHNOSZ/R/protein.info.R	2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/protein.info.R	2017-01-28 08:29:14 UTC (rev 123)
@@ -163,7 +163,7 @@
 
 protein.equil <- function(protein, T=25, loga.protein=0, digits=4) {
   # show the individual steps in calculating metastable equilibrium among proteins
-  msgout("protein.equil: temperature from argument is ", T, " degrees C\n")
+  message("protein.equil: temperature from argument is ", T, " degrees C")
   TK <- convert(T, "K")
   # get the amino acid compositions of the proteins
   aa <- ip2aa(protein)
@@ -179,13 +179,13 @@
     ionize.it <- TRUE
     iword <- "ionized"
     pH <- -thermo$basis$logact[match("H+", rownames(bmat))]
-    msgout("protein.equil: pH from thermo$basis is ", pH, "\n")
+    message("protein.equil: pH from thermo$basis is ", pH)
   }
   # tell the user whose [Met] is in thermo$obigt
   info.Met <- info(info('[Met]', "aq"))
-  msgout("protein.equil: [Met] is from reference ", info.Met$ref1, "\n")
+  message("protein.equil: [Met] is from reference ", info.Met$ref1)
   ## first set of output: show results of calculations for a single protein
-  msgout("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1], "\n")
+  message("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1])
   # standard Gibbs energies of basis species
   G0basis <- unlist(suppressMessages(subcrt(thermo$basis$ispecies, T=T, property="G")$out))
   # coefficients of basis species in formation reactions of proteins
@@ -196,67 +196,67 @@
   G0prot <- unlist(suppressMessages(subcrt(pname, T=T, property="G")$out))
   # standard Gibbs energy of formation reaction of nonionized protein, cal/mol
   G0protform <- G0prot - G0basissum
-  msgout("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits), "\n")
+  message("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits))
   if(ionize.it) {
     # standard Gibbs energy of ionization of protein, cal/mol
     G0ionization <- suppressMessages(ionize.aa(aa, property="G", T=T, pH=pH))[1, ]
-    msgout("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits), "\n")
+    message("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits))
     # standard Gibbs energy of formation reaction of ionized protein, cal/mol
     G0protform <- G0protform + G0ionization
   }
   # standard Gibbs energy of formation reaction of non/ionized residue equivalents, dimensionless
   G0res.RT <- G0protform/thermo$opt$R/TK/plength
-  msgout("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits), "\n")
+  message("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits))
   # coefficients of basis species in formation reactions of residues
   resbasis <- suppressMessages(protein.basis(aa, T=T, normalize=TRUE))
   # logQstar and Astar/RT
   logQstar <- colSums(t(resbasis) * - thermo$basis$logact)
-  msgout("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits), "\n")
+  message("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits))
   Astar.RT <- -G0res.RT - log(10)*logQstar
-  msgout("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits), "\n")
-  if(!is.numeric(protein)) msgout("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric\n")
+  message("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits))
+  if(!is.numeric(protein)) message("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric")
   else {
     # for **Astar** we have to set the activities of the proteins to zero, not loga.protein!
     a <- suppressMessages(affinity(iprotein=protein, T=T, loga.protein=0))
     aAstar.RT <- log(10) * as.numeric(a$values) / plength
-    msgout("check it!       per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits), "\n")
+    message("check it!       per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits))
     if(!isTRUE(all.equal(Astar.RT, aAstar.RT, check.attributes=FALSE)))
       stop("Bug alert! The same value for Astar/RT cannot be calculated manually as by using affinity()")
   }
-  if(length(pname)==1) msgout("protein.equil [all]: all done... give me more than one protein for equilibrium calculations\n")
+  if(length(pname)==1) message("protein.equil [all]: all done... give me more than one protein for equilibrium calculations")
   else {
     ## next set of output: equilibrium calculations
-    msgout("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "), "\n")
-    msgout("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "), "\n")
+    message("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "))
+    message("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "))
     expAstar.RT <- exp(Astar.RT)
     sumexpAstar.RT <- sum(expAstar.RT)
-    msgout("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits), "\n")
+    message("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits))
     # boltzmann distribution
     alpha <- expAstar.RT / sumexpAstar.RT    
-    msgout("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "), "\n")
+    message("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "))
     # check with equilibrate()
     if(is.numeric(protein)) {
       loga.equil.protein <- unlist(suppressMessages(equilibrate(a, normalize=TRUE))$loga.equil)
       # here we do have to convert from logarithms of activities of proteins to degrees of formation of residue equivalents
       a.equil.residue <- plength*10^loga.equil.protein
       ealpha <- a.equil.residue/sum(a.equil.residue)
-      msgout("check it!     alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "), "\n")
+      message("check it!     alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "))
       if(!isTRUE(all.equal(alpha, ealpha, check.attributes=FALSE)))
         stop("Bug alert! The same value for alpha cannot be calculated manually as by using equilibrate()")
     }
     # total activity of residues
     loga.residue <- log10(sum(plength * 10^loga.protein))
-    msgout("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits), "\n")
+    message("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits))
     # equilibrium activities of residues
     loga.residue.equil <- log10(alpha*10^loga.residue)
-    msgout("protein.equil [all]: log10 equilibrium activities of residue equivalents are ", paste(signif(loga.residue.equil, digits), collapse=" "), "\n")
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 123

From noreply at r-forge.r-project.org  Tue Jan 31 16:07:37 2017
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 31 Jan 2017 16:07:37 +0100 (CET)
Subject: [CHNOSZ-commits] r124 - in pkg/CHNOSZ: . inst vignettes
Message-ID: <20170131150737.4AD06188365@r-forge.r-project.org>

Author: jedick
Date: 2017-01-31 16:07:36 +0100 (Tue, 31 Jan 2017)
New Revision: 124

Added:
   pkg/CHNOSZ/vignettes/vig.css
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/EOSregress.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
reduce size of EOSregress.html


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/DESCRIPTION	2017-01-31 15:07:36 UTC (rev 124)
@@ -1,6 +1,6 @@
-Date: 2017-01-28
+Date: 2017-01-29
 Package: CHNOSZ
-Version: 1.0.8-13
+Version: 1.0.8-14
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/inst/NEWS	2017-01-31 15:07:36 UTC (rev 124)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-13 (2017-01-28)
+CHANGES IN CHNOSZ 1.0.8-14 (2017-01-29)
 ---------------------------------------
 
 - Add "AA" as a keyword for preset species in basis() (cysteine,

Modified: pkg/CHNOSZ/vignettes/EOSregress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/EOSregress.Rmd	2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/vignettes/EOSregress.Rmd	2017-01-31 15:07:36 UTC (rev 124)
@@ -4,7 +4,9 @@
 author: "Jeffrey M. Dick"
 date: "`r Sys.Date()`"
 output:
-  tufte::tufte_html: default
+  tufte::tufte_html:
+    tufte_features: ["background", "italics"]
+    css: "vig.css"
   tufte::tufte_handout:
     citation_package: natbib
     latex_engine: xelatex

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/vignettes/vig.bib	2017-01-31 15:07:36 UTC (rev 124)
@@ -1,624 +1,575 @@
-% This file was created with JabRef 2.11b4.
-% Encoding: ISO8859_1
+% Encoding: UTF-8
 
-
 @Article{AD01,
-  Title                    = {{E}lectrochemistry of copper in aqueous glycine solutions},
-  Author                   = {Aksu, Serdar and Doyle, Fiona M.},
-  Journal                  = {Journal of the Electrochemical Society},
-  Year                     = {2001},
-  Number                   = {1},
-  Pages                    = {B51--B57},
-  Volume                   = {148},
-  Abstract                 = {Potential-pH equilibria and potentiodynamic polarization studies were used to examine the electrochemical behavior of copper in aqueous glycine solutions. Potential-pH diagrams for the copper-water-glycine system were derived at different total copper \{Cu-T\} and glycine \{L-T\} activities. The diagrams show that glycine significantly extended the solubility range of copper. Polarization experiments were conducted in deaerated and aerated aqueous solutions of 10(-2) M glycine with 10(-5) M cupric nitrate and 10(-1) M glycine with 10(-4) M cupric nitrate at pH values between 9 and 12. The results of these experiments are discussed in terms of the relevant potential-pH diagrams. Good correlations were observed. (C) 2000 The Electrochemical Society. All rights reserved.},
-  Doi                      = {10.1149/1.1344532},
+  author =        {Aksu, Serdar and Doyle, Fiona M.},
+  journal =       {Journal of the Electrochemical Society},
+  title =         {{E}lectrochemistry of copper in aqueous glycine solutions},
+  year =          {2001},
+  volume =        {148},
+  number =        {1},
+  pages =         {B51--B57},
+  doi =           {10.1149/1.1344532},
 }
 
 @Article{AH97a,
-  Title                    = {{G}roup additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures},
-  Author                   = {Amend, Jan P. and Helgeson, Harold C.},
-  Journal                  = {Geochimica et Cosmochimica Acta},
-  Year                     = {1997},
-  Pages                    = {11 -- 46},
-  Volume                   = {61},
-  Abstract                 = {Group additivity equations of state for aqueous organic molecules have been generated by combining the revised Helgeson-Kirkham-Flowers (HKF) equations of state (Shock and Helgeson, 1988, 1990; Tanger and Helgeson, 1988; Shock et al., 1989, 1992) with experimental values of the standard molal properties of aqueous alkanes, alkanols, alkylbenzenes, carboxylic acids, amides, and amines. Equations of state parameters for the groups represented by -cn2 , -CH3, -CHCH3-, -C6H5, -CH2OH, -COOH, -CONH2, and -CH2NH2 were determined by regression of the experimental data. This procedure permits calculation of the standard molal thermodynamic properties of these groups at elevated tempera-tures and pressures. Although curves representing the apparent standard molal Gibbs free energies ( A G ?) and enthalpies ( A H ?) of formation, and the standard molal entropies (S ?) of the groups as a function of temperature and pressure are respectively similar for each of them, the temperature dependence of the standard molal heat capacities (C~) and volumes (V?) of a number of the groups are quite different from one another. For example, the standard molal heat capacities of the hydrocarbon groups minimize with increasing temperature, but those of -CHEOH and -CH2NH2 maximize. Computed values of AG ?, A H ?, S ?, C~, V ?, and the equations of state parameters for the various groups were used together with group additivity relations to generate corresponding values of these properties for aqueous n-alkanes, 2-methylalkanes, n-alkylbenzenes, n-alkanols, n-carboxylic acids, n-amides, and n-amines at temperatures -< 250?C and pressures - 1 kbar. The validity and generality of the equations of state are supported by the fact that predicted equilibrium constants for liquid n-alkane solubility reactions in water compare favorably with experimental values reported in the literature for temperatures as high as 200?C. Furthermore, equilibrium constants for aqueous ethane coexisting with ethene at 325 and 350?C at 350 bars predicted from the equations of state are in close agreement with independently determined experimental values reported by Seewald (1994). The standard molal thermodynamic properties and equations of state parameters reported below provide the means to characterize the thermodynamic behavior of a wide variety of aqueous organic species involved in hydrothermal reactions at elevated temperatures and pressures.},
-  Doi                      = {10.1016/S0016-7037(96)00306-7},
+  author =        {Amend, Jan P. and Helgeson, Harold C.},
+  journal =       {Geochimica et Cosmochimica Acta},
+  title =         {{G}roup additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures},
+  year =          {1997},
+  volume =        {61},
+  pages =         {11 -- 46},
+  doi =           {10.1016/S0016-7037(96)00306-7},
 }
 
 @Book{And05,
-  Title                    = {{T}hermodynamics of {N}atural {S}ystems},
-  Author                   = {Anderson, G. M.},
-  Publisher                = {Cambridge University Press},
-  Year                     = {2005},
-  Address                  = {Cambridge},
-  Edition                  = {2nd},
-  Abstract                 = {The fugacity was introduced by G.N. Lewis in 1901, and became widely used after the appearance of Thermodynamics, a very influential textbook by Lewis and Randall in 1923. Lewis describes the need for such a function in terms of an analogy with temperature in the attainment of equilibrium between phases. Just as equilibrium requires that heat must flow such that temperature is the same in all parts of the system, so matter must flow such that chemical potentials are also equalized. He referred to the flow of matter from one phase to another as an ?escaping tendency,? such as a liquid escaping to the gas form to achieve an equilibrium vapor pressure. He pointed out that in fact vapor pressure is equilibrated between phases under many conditions (and in fact is the basis for the isopiestic method of activity determinations, ?5.8.4), and could serve as a good measure of escaping tendency if it behaved always as an ideal gas.},
-  Pages                    = {648},
-  Url                      = {http://www.worldcat.org/oclc/474880901}
+  author    = {Anderson, G. M.},
+  publisher = {Cambridge University Press},
+  title     = {{T}hermodynamics of {N}atural {S}ystems},
+  year      = {2005},
+  address   = {Cambridge},
+  edition   = {2nd},
+  pages     = {648},
+  url       = {http://www.worldcat.org/oclc/474880901},
 }
 
 @Article{AA02,
-  Title                    = {{T}he human plasma proteome - {H}istory, character, and diagnostic prospects},
-  Author                   = {Anderson, N. Leigh and Anderson, Norman G.},
-  Journal                  = {Molecular \& Cellular Proteomics},
-  Year                     = {2002},
-  Number                   = {11},
-  Pages                    = {845--867},
-  Volume                   = {1},
-  Abstract                 = {The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed. Plasma is not only the primary clinical specimen but also represents the largest and deepest version of the human proteome present in any sample: in addition to the classical "plasma proteins," it contains all tissue proteins (as leakage markers) plus very numerous distinct immunoglobulin sequences, and it has an extraordinary dynamic range in that more than 10 orders of magnitude in concentration separate albumin and the rarest proteins now measured clinically. Although the restricted dynamic range of conventional proteomic technology (two-dimensional gels and mass spectrometry) has limited its contribution to the list of 289 proteins (tabulated here) that have been reported in plasma to date, very recent advances in multidimensional survey techniques promise at least double this number in the near future. Abundant scientific evidence, from proteomics and other disciplines, suggests that among these are proteins whose abundances and structures change in ways indicative of many, if not most, human diseases. Nevertheless, only a handful of proteins are currently used in routine clinical diagnosis, and the rate of introduction of new protein tests approved by the United States Food and Drug Administration (FDA) has paradoxically declined over the last decade to less than one new protein diagnostic marker per year. We speculate on the reasons behind this large discrepancy between the expectations arising from proteomics and the realities of clinical diagnostics and suggest approaches by which protein-disease associations may be more effectively translated into diagnostic tools in the future.},
-  Doi                      = {10.1074/mcp.R200007-MCP200},
-  Sn                       = {1535-9476},
+  author    = {Anderson, N. Leigh and Anderson, Norman G.},
+  journal   = {Molecular \& Cellular Proteomics},
+  title     = {{T}he human plasma proteome - {H}istory, character, and diagnostic prospects},
+  year      = {2002},
+  volume    = {1},
+  number    = {11},
+  pages     = {845--867},
+  doi       = {10.1074/mcp.R200007-MCP200},
+  sn        = {1535-9476},
 }
 
 @Article{AA03,
-  Title                    = {{T}he human plasma proteome: {H}istory, character, and diagnostic prospects (vol 1, pg 845, 2002)},
-  Author                   = {Anderson, N. L. and Anderson, N. G.},
-  Journal                  = {Molecular \& Cellular Proteomics},
-  Year                     = {2003},
-  Number                   = {1},
-  Pages                    = {50--50},
-  Volume                   = {2},
-  Doi                      = {10.1074/mcp.A300001-MCP200},
-  Sn                       = {1535-9476},
+  author    = {Anderson, N. L. and Anderson, N. G.},
+  journal   = {Molecular \& Cellular Proteomics},
+  title     = {{T}he human plasma proteome: {H}istory, character, and diagnostic prospects (vol 1, pg 845, 2002)},
+  year      = {2003},
+  volume    = {2},
+  number    = {1},
+  pages     = {50--50},
+  doi       = {10.1074/mcp.A300001-MCP200},
+  sn        = {1535-9476},
 }
 
 @Article{AWP+09,
-  Title                    = {{T}he {GAAS} {M}etagenomic {T}ool and {I}ts {E}stimations of {V}iral and {M}icrobial {A}verage {G}enome {S}ize in {F}our {M}ajor {B}iomes},
-  Author                   = {Angly, Florent E. and Willner, Dana and Prieto-Dav\'o, Alejandra and Edwards, Robert A. and Schmieder, Robert and Vega-Thurber, Rebecca and Antonopoulos, Dionysios A. and Barott, Katie and Cottrell, Matthew T. and Desnues, Christelle and Dinsdale, Elizabeth A. and Furlan, Mike and Haynes, Matthew and Henn, Matthew R. and Hu, Yongfei and Kirchman, David L. and McDole, Tracey and McPherson, John D. and Meyer, Folker and Miller, R. Michael and Mundt, Egbert and Naviaux, Robert K. and Rodriguez-Mueller, Beltran and Stevens, Rick and Wegley, Linda and Zhang, Lixin and Zhu, Baoli and Rohwer, Forest},
-  Journal                  = {PLoS Computational Biology},
-  Year                     = {2009},
-  Number                   = {12},
-  Pages                    = {e1000593},
-  Volume                   = {5},
-  Abstract                 = {Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.},
-  Doi                      = {10.1371/journal.pcbi.1000593},
-  ISSN                     = {1553-734X},
+  author =        {Angly, Florent E. and Willner, Dana and Prieto-Dav\'o, Alejandra and Edwards, Robert A. and Schmieder, Robert and Vega-Thurber, Rebecca and Antonopoulos, Dionysios A. and Barott, Katie and Cottrell, Matthew T. and Desnues, Christelle and Dinsdale, Elizabeth A. and Furlan, Mike and Haynes, Matthew and Henn, Matthew R. and Hu, Yongfei and Kirchman, David L. and McDole, Tracey and McPherson, John D. and Meyer, Folker and Miller, R. Michael and Mundt, Egbert and Naviaux, Robert K. and Rodriguez-Mueller, Beltran and Stevens, Rick and Wegley, Linda and Zhang, Lixin and Zhu, Baoli and Rohwer, Forest},
+  journal =       {PLoS Computational Biology},
+  title =         {{T}he {GAAS} {M}etagenomic {T}ool and {I}ts {E}stimations of {V}iral and {M}icrobial {A}verage {G}enome {S}ize in {F}our {M}ajor {B}iomes},
+  year =          {2009},
+  volume =        {5},
+  number =        {12},
+  pages =         {e1000593},
+  doi =           {10.1371/journal.pcbi.1000593},
+  issn =          {1553-734X},
 }
 
 @Article{BKM60,
-  Title                    = {{L}imits of the natural environment in terms of p{H} and oxidation-reduction potentials},
-  Author                   = {Baas Becking, L. G. M. and Kaplan, I. R. and Moore, D.},
-  Journal                  = {Journal of Geology},
-  Year                     = {1960},
-  Number                   = {3},
-  Pages                    = {243--284},
-  Volume                   = {68},
-  Abstract                 = {The electron and the proton content (measured as electrode potential [Eh] and pH) of an environment characterize this environment in many ways. In this paper the electrode potential and the pH are used as empirical parameters rather than as electrochemical data capable of thermodynamic interpretation. From published and unpublished work by the authors and from the literature, more than 6,200 pairs of characteristics were gathered, covering most types of the aqueous environment as well as the potential milieu of the chief actors in these environments: algae and bacteria. It appears that the Eh-pH limits of biological systems and of the naturally occurring aqueous environment almost coincide. This would indicate that there are few, if any, sterile terrestrial environments caused by limiting Eh-pH characteristics. As it seems unlikely that environments will be found outside the limits outlined in this paper, physico-chemical speculations on the sedimentary environment should be limited by this outline. Substances which do not occur (sulfuric acid, sulfide ion) should not be used in the electrochemical characterization of the environment. The biogenic master reaction in the environment, changing one or both characteristics (Eh-pH), is reductive photosynthesis by algae and by colored bacteria. A photosynthetic mass may raise the pH of a water to 9.4; and in the absence of bivalent cations, to 12.6. The intensity of sulfate reduction depends upon the sulfate content of the water and on the available hydrogen, in both organic and inorganic form. The iron concentration is also important, as iron is the principal acceptor of the H2S formed. The highly reactive, black iron sulfides may be partly oxidized with the formation of the more stable pyrite and marcasite. The reduction of iron from ferric to ferrous state takes place even in surface soil. Denitrification, another biologically important reduction, may be of lesser geochemical influence. Oxidative reactions comprise, apart from nitrification, chiefly the oxidation of H2S and SH- to sulfur, thiosulfate, sulfite, hydrosulfite, sulfate, and hydrosulfate and the oxidation of ferrous and manganous compounds. In contrast with the reductions, these oxidations are only in part biological. The oxidation of pyrite may give rise to extremely low pH values. Heterotrophic oxidation (respiration) results in the conversion of organic matter into CO2 and H2O. Acid formation in peat bogs is caused largely by cation exchange on plant cell walls, chiefly, but not exclusively, on Sphagnum. In sediments the reaction between iron phosphate complexes and H2S may liberate the acid H2P04- ion. 10. Certain environments are restricted, others cover almost the maximal area outlined in this paper. A progressive increase in the environmental range, arranged in a series, follows: rain water, mine water, peat bogs, sea water, rivers and lakes, marine sediments, and evaporites, while the geothermal environment shows the maximal area. The potential milieu of the green bacteria is highly restricted. Less restricted is the environment of the iron bacteria, followed by sulfate-reducing bacteria, purple bacteria, and denitrifying bacteria. Thio-bacteria have a very wide potential milieu, and algae are found literally everywhere. The Eh-pH characteristics are determined chiefly by photosynthesis, by respiration and by oxido-reductive changes in the iron and sulfur systems.},
-  Url                      = {http://www.jstor.org/stable/30059218}
+  author =        {Baas Becking, L. G. M. and Kaplan, I. R. and Moore, D.},
+  journal =       {Journal of Geology},
+  title =         {{L}imits of the natural environment in terms of p{H} and oxidation-reduction potentials},
+  year =          {1960},
+  volume =        {68},
+  number =        {3},
+  pages =         {243--284},
+  url =           {http://www.jstor.org/stable/30059218}
 }
 
 @Book{BPJ85,
-  Title                    = {{S}tandard {P}otentials in {A}queous {S}olution},
-  Author                   = {Bard, A. J. and Parsons, R. and Jordan, J.},
-  Publisher                = {M. Dekker},
-  Year                     = {1985},
-  Address                  = {New York},
-  Url                      = {http://www.worldcat.org/oclc/12106344}
+  author =        {Bard, A. J. and Parsons, R. and Jordan, J.},
+  publisher =     {M. Dekker},
+  title =         {{S}tandard {P}otentials in {A}queous {S}olution},
+  year =          {1985},
+  address =       {New York},
+  url =           {http://www.worldcat.org/oclc/12106344}
 }
 
 @Article{BB58,
-  Title                    = {{A}dditivity rules for the estimation of molecular properties. {T}hermodynamic properties},
-  Author                   = {Benson, Sidney W. and Buss, Jerry H.},
-  Journal                  = {Journal of Chemical Physics},
-  Year                     = {1958},
-  Pages                    = {546 -- 572},
-  Volume                   = {29},
-  Abstract                 = {A general limiting law is proposed which can be used to systematize the various laws of additivity of molecularproperties. This can be stated asfollows: Ii I! is a molecularproperty, then for the disproportionation reaction: RNR+SNSz:;>2RNS, A<I1*> as ! the separation between R and S becomes large compared to their dimensions. It is shown that the zero-orderapproximation is equivalent to the law of additivity of atomic properties, the first-order approximation to the law oi additivity of bond properties, the second-orderapproximation to the law of additivity of group properties, and so forth. It is shown that for Cpand5? idealgases!, the additivity oi atomic properties works to about 3:2 cal/mole-?K, while the additivity of bond properties is usually good to about ;l;1 cal/mole-?K. The latter alsoestimates AH;? to about :l:3 kcal/ mole. T he group additivity relation is generally obeyed to within :l:O.5cal/mole-K for C Pand S? and about $0.6 kcalf mole for AH;?. Tablesare presentedfor each of the partial properties at 25?C. The agreements found for the various additivity rules is examined from a molecular point of view and certain extensions and limitations indicated. The application and utility of the rules in estimation of thermodynamic properties is discussed. The estimation of bond dissociation energies is possible with the additivity rules as are the thermodynamic properties of free radicals. An application of the rules to species NR2 and NS2 show that R and S may be ordered according to their general bond-weakening or bond-strengthening properties. For systems where N is C2H4 it is shown that the first and second bond dissociation energies for RC2H4R is very likely a constant=59.5 kcal, the excitation energy of C2H4.},
-  Doi                      = {10.1063/1.1744539},
-  Size                     = {27 p.},
+  author =        {Benson, Sidney W. and Buss, Jerry H.},
+  journal =       {Journal of Chemical Physics},
+  title =         {{A}dditivity rules for the estimation of molecular properties. {T}hermodynamic properties},
+  year =          {1958},
+  volume =        {29},
+  pages =         {546 -- 572},
+  doi =           {10.1063/1.1744539},
+  size =          {27 p.},
 }
 
 @Article{BBA+03,
-  Title                    = {{T}he {SWISS}-{PROT} protein knowledgebase and its supplement {T}r{EMBL} in 2003},
-  Author                   = {Boeckmann, Brigitte and Bairoch, Amos and Apweiler, Rolf and Blatter, Marie-Claude and Estreicher, Anne and Gasteiger, Elisabeth and Martin, Maria J. and Michoud, Karine and O'Donovan, Claire and Phan, Isabelle and Pilbout, Sandrine and Schneider, Michel},
-  Journal                  = {Nucleic Acids Research},
-  Year                     = {2003},
-  Number                   = {1},
-  Pages                    = {365 -- 370},
-  Volume                   = {31},
-  Abstract                 = {The SWISS-PROT protein knowledgebase (http: / / www. expasy. org/ sprot/ and http: / / www. ebi. ac. uk/ swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human ( the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot at expasy.org.},
-  Doi                      = {10.1093/nar/gkg095},
-  Size                     = {6 p.},
+  author =        {Boeckmann, Brigitte and Bairoch, Amos and Apweiler, Rolf and Blatter, Marie-Claude and Estreicher, Anne and Gasteiger, Elisabeth and Martin, Maria J. and Michoud, Karine and O'Donovan, Claire and Phan, Isabelle and Pilbout, Sandrine and Schneider, Michel},
+  journal =       {Nucleic Acids Research},
+  title =         {{T}he {SWISS}-{PROT} protein knowledgebase and its supplement {T}r{EMBL} in 2003},
+  year =          {2003},
+  volume =        {31},
+  number =        {1},
+  pages =         {365 -- 370},
+  doi =           {10.1093/nar/gkg095},
+  size =          {6 p.},
 }
 
 @Book{BJH84,
-  Title                    = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600$^\circ${C}},
-  Author                   = {Bowers, Teresa S. and Jackson, Kenneth J. and Helgeson, Harold C.},
-  Publisher                = {Springer-Verlag},
-  Year                     = {1984},
-  Address                  = {Heidelberg},
-  Abstract                 = {This book represents a revision and expansion of an earlier set of diagrams for temperatures from 25 to 300 C along the equilibrium vapor-liquid curve for H20 (Helgeson, Brown, and Leeper, 1969). The activity diagrams summarized in the following pages were generated over a six year period from 1977 to 1983 in the Laboratory of Theoretical Geochemistry (otherwise known as Prediction Central) at the University of California, Berkeley. They represent the culmination of research efforts to generate a comprehensive and internally consistent set of thermodynamic data and equations for minerals, gases, and aqueous solutions at high pressures and temperatures.},
-  Pages                    = {397},
-  Url                      = {http://www.worldcat.org/oclc/11133620}
+  author        = {Bowers, Teresa S. and Jackson, Kenneth J. and Helgeson, Harold C.},
+  publisher     = {Springer-Verlag},
+  title         = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600$^\circ${C}},
+  year          = {1984},
+  address       = {Heidelberg},
+  pages         = {397},
+  url           = {http://www.worldcat.org/oclc/11133620},
 }
 
 @Article{CGM+81,
-  Title                    = {{G}roup contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution},
-  Author                   = {Cabani, Sergio and Gianni, Paolo and Mollica, Vincenzo and Lepori, Luciano},
-  Journal                  = {Journal of Solution Chemistry},
-  Year                     = {1981},
-  Pages                    = {563 -- 595},
-  Volume                   = {10},
-  Abstract                 = {The thermodynamic properties DeltaGh0,DeltaHh0, and DeltaCp,h0 associated with the transfer of non-ionic organic compounds from gas to dilute aqueous solution and the limiting partial molar properties Cp0,2 and V20 of these compounds in water are described through a simple scheme of group contributions. A distinction is made between groups made only of carbon and hydrogen, and functional groups i.e. groups containing at least one atom different from carbon and hydrogen. Each group is assigned a contribution, for each property, through a least squares procedure which utilizes only molecules containing at most one functional group. Finally, for compounds containing more than one functional group, correction parameters are evaluated as the differences between the experimental values and those calculated by means of the group contributions. The different behavior of hydrophilic compared with hydrophobic groups is discussed for the various properties. A rationale for the correction parameters, i.e. for the effects of the interactions among hydrophilic groups on the thermodynamic properties, is attempted.},
-  Doi                      = {10.1007/BF00646936},
+  author =        {Cabani, Sergio and Gianni, Paolo and Mollica, Vincenzo and Lepori, Luciano},
+  journal =       {Journal of Solution Chemistry},
+  title =         {{G}roup contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution},
+  year =          {1981},
+  volume =        {10},
+  pages =         {563 -- 595},
+  doi =           {10.1007/BF00646936},
 }
 
 @Article{DLE64,
-  Title                    = {{T}hermodynamic {E}quilibria {I}n {P}rebiological {A}tmospheres},
-  Author                   = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V.},
-  Journal                  = {Science},
-  Year                     = {1964},
-  Number                   = {3650},
-  Pages                    = {1461--1464},
-  Volume                   = {146},
-  Abstract                 = {The concentrations of a large number of compounds of biological interest which would be present in the atmosphere at thermodynamic equilibrium were computed under many combinations of temperature, pressure, and elemental composition. These computations revealed a possible mechanism for the abiological formation of asphaltic tar and an oxidative threshold at which all but the simplest compounds disappear.},
-  Doi                      = {10.1126/science.146.3650.1461},
-  Sn                       = {0036-8075},
-  Z8                       = {0},
-  Z9                       = {60},
-  Zb                       = {13}
+  author =        {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V.},
+  journal =       {Science},
+  title =         {{T}hermodynamic {E}quilibria {I}n {P}rebiological {A}tmospheres},
+  year =          {1964},
+  volume =        {146},
+  number =        {3650},
+  pages =         {1461--1464},
+  doi =           {10.1126/science.146.3650.1461},
+  sn =            {0036-8075},
+  z8 =            {0},
+  z9 =            {60},
+  zb =            {13}
 }
 
 @TechReport{DLEN67,
-  Title                    = {{T}hermodynamic {E}quilibrium in {P}rebiological {A}tmospheres of {C}, {H}, {O}, {N}, {P}, {S}, and {C}l},
-  Author                   = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. and Nagarajan, G.},
-  Institution              = {National Aeronautics and Space Administration},
-  Year                     = {1967},
-  Address                  = {Washington, D. C.},
-  Number                   = {SP-3040},
-  Type                     = {Report},
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 124