[CHNOSZ-commits] r195 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/thermo man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue May 2 06:44:02 CEST 2017 

Author: jedick
Date: 2017-05-02 06:44:02 +0200 (Tue, 02 May 2017)
New Revision: 195

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/makeup.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
   pkg/CHNOSZ/man/CHNOSZ-package.Rd
   pkg/CHNOSZ/man/add.protein.Rd
   pkg/CHNOSZ/man/basis.Rd
   pkg/CHNOSZ/man/buffer.Rd
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/equilibrate.Rd
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/man/extdata.Rd
   pkg/CHNOSZ/man/findit.Rd
   pkg/CHNOSZ/man/info.Rd
   pkg/CHNOSZ/man/makeup.Rd
   pkg/CHNOSZ/man/more.aa.Rd
   pkg/CHNOSZ/man/nonideal.Rd
   pkg/CHNOSZ/man/objective.Rd
   pkg/CHNOSZ/man/protein.Rd
   pkg/CHNOSZ/man/read.expr.Rd
   pkg/CHNOSZ/man/revisit.Rd
   pkg/CHNOSZ/man/species.Rd
   pkg/CHNOSZ/man/taxonomy.Rd
   pkg/CHNOSZ/man/transfer.Rd
   pkg/CHNOSZ/man/util.array.Rd
   pkg/CHNOSZ/man/util.blast.Rd
   pkg/CHNOSZ/man/util.expression.Rd
   pkg/CHNOSZ/man/util.fasta.Rd
   pkg/CHNOSZ/man/util.list.Rd
   pkg/CHNOSZ/man/util.matrix.Rd
   pkg/CHNOSZ/man/util.misc.Rd
   pkg/CHNOSZ/man/util.plot.Rd
   pkg/CHNOSZ/man/util.program.Rd
   pkg/CHNOSZ/man/util.seq.Rd
Log:
minor documentation changes #2


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/DESCRIPTION	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,6 +1,6 @@
-Date: 2017-05-01
+Date: 2017-05-02
 Package: CHNOSZ
-Version: 1.0.8-83
+Version: 1.0.8-84
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/makeup.R
===================================================================
--- pkg/CHNOSZ/R/makeup.R	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/R/makeup.R	2017-05-02 04:44:02 UTC (rev 195)
@@ -199,7 +199,7 @@
     if(length(iopen) != length(iclose)) stop("formula has unpaired parentheses")
     # are the parentheses unnested?
     iparen <- as.numeric(matrix(c(iopen, iclose), nrow=2, byrow=TRUE))
-    if(any(diff(iparen) < 0)) stop("formula has nested parentheses")
+    if(any(diff(iparen) < 0)) stop(paste("formula has nested parentheses: ", formula))
     # iend will be the last position including coefficients
     # (e.g. the position of 2 in (OH)2)
     iend <- iclose

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/inst/CHECKLIST	2017-05-02 04:44:02 UTC (rev 195)
@@ -11,8 +11,13 @@
 
 - check output of demo("sources") to make sure all data sources are cited
 
-- check output of R CMD Rd2pdf: fix lines truncated by page margins
+- recreate extdata/thermo/obigt_check.csv after all data updates:
+  co <- check.obigt()
+  write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
 
+- run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/
+  and fix any lines truncated by page margins
+
 - run R CMD check using R compiled without long doubles (as in Solaris checks on CRAN)
   (CFLAGS=-ffloat-store ./configure --disable-long-double)
 
@@ -26,10 +31,6 @@
 
 - update list of documentation topics in examples() with any new ones
 
-- recreate extdata/thermo/obigt_check.csv after all data updates:
-  co <- check.obigt()
-  write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
-
 - especially on Windows:  
   - data files are uncompressed on installation? (from BuildResaveData: no)
     (so that users can copy and modify the thermodynamic database)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/inst/NEWS	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-83 (2017-05-01)
+CHANGES IN CHNOSZ 1.0.8-84 (2017-05-02)
 ---------------------------------------
 
 DOCUMENTATION:

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,4 +1,4 @@
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\ No newline at end of file

Modified: pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv	2017-05-02 04:44:02 UTC (rev 195)
@@ -3,241 +3,240 @@
 "OBIGT",20,"HPO4-2","aq",,-1.02,
 "OBIGT",49,"BO2-","aq",,-19.31,
 "OBIGT",62,"Cu+2","aq",3.62,,
-"OBIGT",81,"ethane","aq",-9.4,,
-"OBIGT",82,"propane","aq",-15.14,-1.45,
-"OBIGT",104,"ethylbenzene","aq",-2.52,2.16,
-"OBIGT",105,"n-propylbenzene","aq",,5.63,
-"OBIGT",106,"n-butylbenzene","aq",-10.62,6.55,
-"OBIGT",107,"n-pentylbenzene","aq",-14.71,4.34,
-"OBIGT",108,"n-hexylbenzene","aq",-18.81,4.93,
-"OBIGT",109,"n-heptylbenzene","aq",-22.9,5.51,
-"OBIGT",110,"n-octylbenzene","aq",-27,6.1,
-"OBIGT",254,"urea","aq",-23.26,23.32,
-"OBIGT",281,"LaSO4+","aq",-6.02,,
-"OBIGT",324,"NdF2+","aq",16.64,6.19,
-"OBIGT",370,"EuF+","aq",4.11,-19.19,
-"OBIGT",371,"EuF2","aq",9.75,-40.4,
-"OBIGT",372,"EuF3-","aq",17.18,-64.45,
-"OBIGT",373,"EuF4-2","aq",26.07,-91.02,
-"OBIGT",374,"EuCl+","aq",-4.11,19.2,
-"OBIGT",375,"EuCl2","aq",-9.84,40.4,
-"OBIGT",376,"EuCl3-","aq",-17.19,64.47,
-"OBIGT",377,"EuCl4-2","aq",-26.15,91.04,
-"OBIGT",516,"propanoic acid","aq",1.42,,
-"OBIGT",539,"formate","aq",1.96,,
-"OBIGT",541,"propanoate","aq",1.68,,
-"OBIGT",548,"n-decanoate","aq",-1.93,,
-"OBIGT",564,"oxalate","aq",-3.19,,
-"OBIGT",591,"alanate","aq",-24.28,,
-"OBIGT",898,"UO4-2","aq",,-1.11,
-"OBIGT",935,"Ag(CO3)2-3","aq",,-1.56,
-"OBIGT",953,"AgCl4-3","aq",,-1.31,
-"OBIGT",1006,"CuCl4-2","aq",,-1.07,
-"OBIGT",1008,"ReO4-","aq",-1.26,,
-"OBIGT",1017,"PO4-3","aq",,-1.72,
-"OBIGT",1019,"Al+3","aq",1.74,,
-"OBIGT",1027,"UO2+2","aq",-1.1,,
-"OBIGT",1028,"Th+4","aq",,-1.14,
-"OBIGT",1047,"P2O7-4","aq",,-2.11,
-"OBIGT",1048,"HP2O7-3","aq",,-1.42,
-"OBIGT",1057,"AsO4-3","aq",,-1.65,
-"OBIGT",1068,"SO3-2","aq",,-1.02,
-"OBIGT",1102,"VO4-3","aq",,-1.63,
-"OBIGT",1114,"Zr+4","aq",,-1.18,
-"OBIGT",1121,"Hf+4","aq",,-1.18,
-"OBIGT",1126,"U+4","aq",,-1.13,
-"OBIGT",1142,"Ce+4","aq",,-1.13,
-"OBIGT",1143,"Pr+4","aq",,-1.12,
-"OBIGT",1144,"Nd+4","aq",,-1.12,
-"OBIGT",1145,"Pm+4","aq",,-1.13,
-"OBIGT",1146,"Sm+4","aq",,-1.14,
-"OBIGT",1147,"Eu+4","aq",,-1.14,
-"OBIGT",1148,"Gd+4","aq",,-1.16,
-"OBIGT",1149,"Tb+4","aq",,-1.15,
-"OBIGT",1150,"Dy+4","aq",,-1.15,
-"OBIGT",1151,"Ho+4","aq",,-1.15,
-"OBIGT",1152,"Er+4","aq",,-1.15,
-"OBIGT",1153,"Tm+4","aq",,-1.16,
-"OBIGT",1154,"Yb+4","aq",,-1.16,
-"OBIGT",1155,"Lu+4","aq",,-1.17,
-"OBIGT",1164,"BeO2-2","aq",,-1.17,
-"OBIGT",1210,"MnO2-2","aq",,-1.05,
-"OBIGT",1221,"CoO2-2","aq",,-1.14,
-"OBIGT",1226,"NiO2-2","aq",,-1.16,
-"OBIGT",1230,"CuO2-2","aq",,-1.09,
-"OBIGT",1234,"ZnO2-2","aq",,-1.17,
-"OBIGT",1249,"CdO2-2","aq",,-1.08,
-"OBIGT",1267,"RuCl4-2","aq",,-1.09,
-"OBIGT",1270,"Ru(SO4)3-4","aq",,-1.8,
-"OBIGT",1277,"RuCl5-2","aq",,-1.49,
-"OBIGT",1278,"RuCl6-3","aq",,-2.39,
-"OBIGT",1281,"Ru(SO4)3-3","aq",,-1.3,
-"OBIGT",1287,"RhCl4-2","aq",,-1.14,
-"OBIGT",1290,"Rh(SO4)3-4","aq",,-1.82,
-"OBIGT",1294,"RhCl2+","aq",,4.67,
-"OBIGT",1299,"Rh(SO4)3-3","aq",,-1.33,
-"OBIGT",1305,"PdCl4-2","aq",,-1.05,
-"OBIGT",1308,"Pd(SO4)3-4","aq",,-1.8,
-"OBIGT",1311,"PtCl+","aq",-3.52,1.25,
-"OBIGT",1312,"PtCl2","aq",-7.11,2.29,
-"OBIGT",1313,"PtCl3-","aq",-10.48,1.78,
-"OBIGT",1314,"PtCl4-2","aq",-13.86,,
-"OBIGT",1317,"Pt(SO4)3-4","aq",,-1.79,
-"OBIGT",1324,"Li(Mal)-","aq",,-3.22,
-"OBIGT",1328,"Al(Mal)+","aq",,-2.19,
-"OBIGT",1329,"Pb(Mal)","aq",,1.16,
-"OBIGT",1333,"Pb(Succ)","aq",,1.49,
-"OBIGT",1334,"Na(Oxal)-","aq",,-3.14,
-"OBIGT",1335,"K(Oxal)-","aq",,-2.75,
-"OBIGT",1336,"Fe(Oxal)+","aq",,-2.19,
-"OBIGT",1338,"Na(Mal)-","aq",,-3.11,
-"OBIGT",1339,"K(Mal)-","aq",,-2.63,
-"OBIGT",1341,"La(Mal)+","aq",,-1.92,
-"OBIGT",1342,"Gd(Mal)+","aq",,-1.73,
-"OBIGT",1343,"Lu(Mal)+","aq",,-2.25,
-"OBIGT",1344,"Yb(Mal)+","aq",,-2.05,
-"OBIGT",1345,"Th(Mal)+2","aq",-1.29,-4.79,
-"OBIGT",1347,"Ce(Mal)+","aq",,-1.75,
-"OBIGT",1348,"Nd(Mal)+","aq",4.52,,
-"OBIGT",1349,"Sm(Mal)+","aq",,-1.77,
-"OBIGT",1350,"Pr(Mal)+","aq",,-1.75,
-"OBIGT",1351,"Eu(Mal)+","aq",,-1.87,
-"OBIGT",1352,"Tb(Mal)+","aq",,-1.92,
-"OBIGT",1353,"Dy(Mal)+","aq",,-1.89,
-"OBIGT",1354,"Tm(Mal)+","aq",,-2.08,
-"OBIGT",1355,"Ho(Mal)+","aq",,-2.08,
-"OBIGT",1356,"Er(Mal)+","aq",,-2.11,
-"OBIGT",1357,"Sc(Mal)+","aq",,-1.97,
-"OBIGT",1358,"Fe(Mal)+","aq",,-1.97,
-"OBIGT",1359,"Na(Succ)-","aq",,-2.82,
-"OBIGT",1360,"K(Succ)-","aq",,-2.39,
-"OBIGT",1366,"Th(Succ)+2","aq",-1.21,-4.47,
-"OBIGT",1371,"NH4(Oxal)-","aq",,-2.62,
-"OBIGT",1376,"Al(Oxal)+","aq",,-2.62,
-"OBIGT",1377,"Yb(Oxal)+","aq",,-2.02,
-"OBIGT",1378,"Ce(Oxal)+","aq",,-1.8,
-"OBIGT",1379,"Nd(Oxal)+","aq",,-1.8,
-"OBIGT",1380,"Eu(Oxal)+","aq",,-1.89,
-"OBIGT",1381,"Gd(Oxal)+","aq",,-1.8,
-"OBIGT",1382,"Ru(Oxal)+","aq",,-2.41,
-"OBIGT",1383,"Pa(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1384,"Th(Oxal)+2","aq",-1.27,-4.69,
-"OBIGT",1385,"U(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1386,"Np(Oxal)+2","aq",-1.27,-4.69,
-"OBIGT",1389,"Am(Oxal)+","aq",,-1.8,
-"OBIGT",1390,"Cm(Oxal)+","aq",,-1.8,
-"OBIGT",1391,"Y(Oxal)+","aq",,-2.11,
-"OBIGT",1396,"La(Oxal)+","aq",,-1.87,
-"OBIGT",1397,"Tb(Oxal)+","aq",,-1.92,
-"OBIGT",1398,"Er(Oxal)+","aq",,-2.05,
-"OBIGT",1399,"Lu(Oxal)+","aq",,-2.19,
-"OBIGT",1400,"Cr(Oxal)+","aq",,-2.58,
-"OBIGT",1401,"Ga(Oxal)+","aq",,-2.66,
-"OBIGT",1402,"Sc(Oxal)+","aq",,-2.13,
-"OBIGT",1403,"In(Oxal)+","aq",,-2.19,
-"OBIGT",1404,"Pu(Oxal)+","aq",-1.2,-4.44,
-"OBIGT",1405,"NpO2(Oxal)","aq",,-1.94,
-"OBIGT",1406,"Sm(Oxal)+","aq",,-1.84,
-"OBIGT",1407,"Cs(Mal)-","aq",,-2.39,
-"OBIGT",1408,"NH4(Mal)-","aq",,-2.54,
-"OBIGT",1413,"In(Mal)+","aq",,-2.11,
-"OBIGT",1414,"Y(Mal)+","aq",,-2.02,
-"OBIGT",1422,"La(Succ)+","aq",,-1.52,
-"OBIGT",1423,"NH4(Succ)-","aq",,-2.26,
-"OBIGT",1425,"Fe(Succ)+","aq",,-1.92,
-"OBIGT",1426,"Sc(Succ)+","aq",,-1.77,
-"OBIGT",1429,"NpO2(Succ)","aq",,-3.16,
-"OBIGT",1430,"Sm(Succ)+","aq",,-1.48,
-"OBIGT",1431,"Er(Succ)+","aq",,-1.68,
-"OBIGT",1432,"U(Succ)+2","aq",-1.15,-4.27,
-"OBIGT",1436,"La(Glut)+","aq",,-1.23,
-"OBIGT",1437,"Y(Glut)+","aq",,-1.46,
-"OBIGT",1438,"Sc(Glut)+","aq",,-1.5,
-"OBIGT",1439,"Th(Glut)+2","aq",-1.09,-4.05,
-"OBIGT",1442,"Fe(Glut)+","aq",,-1.05,
-"OBIGT",1443,"Sm(Glut)+","aq",,-1.2,
-"OBIGT",1446,"Er(Glut)+","aq",,-1.4,
-"OBIGT",1448,"Ba(Adip)","aq",,1.19,
-"OBIGT",1455,"Pb(Adip)","aq",,1.25,
-"OBIGT",1456,"Sc(Adip)+","aq",,-1.22,
-"OBIGT",1458,"Th(Adip)+2","aq",-1.02,-3.76,
-"OBIGT",1459,"U(Adip)+2","aq",-1,-3.71,
-"OBIGT",1461,"Li(Oxal)-","aq",,-3.3,
-"OBIGT",1465,"Li(Succ)-","aq",,-2.94,
-"OBIGT",1467,"Na(Glut)-","aq",,-2.34,
-"OBIGT",1468,"K(Glut)-","aq",,-2.05,
-"OBIGT",1469,"Li(Glut)-","aq",,-2.66,
-"OBIGT",1474,"Na(Adip)-","aq",,-2.05,
-"OBIGT",1475,"K(Adip)-","aq",,-1.76,
-"OBIGT",1476,"Li(Adip)-","aq",,-2.38,
-"OBIGT",1482,"CF4","aq",5.9,,
-"OBIGT",1489,"AsH3","aq",-2.67,,
-"OBIGT",1492,"cyclohexane","aq",9.35,6.64,
-"OBIGT",1499,"xylose","aq",1.18,,
-"OBIGT",1500,"arabinose","aq",1.18,,
-"OBIGT",1501,"lyxose","aq",1.11,,
-"OBIGT",1502,"xylulose","aq",1.11,,
-"OBIGT",1503,"ribulose","aq",1.11,,
-"OBIGT",1504,"glucose","aq",1.31,,
-"OBIGT",1505,"mannose","aq",1.46,,
-"OBIGT",1507,"fructose","aq",1.3,,
-"OBIGT",1508,"sorbose","aq",1.3,,
-"OBIGT",1512,"n-butanethiol","aq",2.19,,
-"OBIGT",1571,"dH2TMP","aq",,-1,
-"OBIGT",1573,"dHUMP-","aq",1.84,,
-"OBIGT",1681,"HNicMP(ox)","aq",,9.54,
-"OBIGT",1689,"ribose-5-phosphate","aq",,7.48,
-"OBIGT",1692,"H4NADP(red)","aq",1.73,,
-"OBIGT",1694,"H2NADP(red)-2","aq",1.72,,
-"OBIGT",1695,"HNADP(red)-3","aq",1.9,,
-"OBIGT",1776,"Gly-Ala-Gly","aq",,-126.09,
-"OBIGT",1777,"Gly-Arg+-Gly","aq",,-182.01,
-"OBIGT",1778,"Gly-Asn-Gly","aq",,-145.77,
-"OBIGT",1779,"Gly-Asp-Gly","aq",,-139.16,
-"OBIGT",1780,"Gly-Cys-Gly","aq",,-139.2,
-"OBIGT",1781,"Gly-Gln-Gly","aq",,-158.09,
-"OBIGT",1782,"Gly-Glu-Gly","aq",,-155.4,
-"OBIGT",1783,"Gly-Gly-Gly","aq",,-107.83,
-"OBIGT",1784,"Gly-His-Gly","aq",,-167.84,
-"OBIGT",1785,"Gly-Ile-Gly","aq",,-172.24,
-"OBIGT",1786,"Gly-Leu-Gly","aq",,-171.74,
-"OBIGT",1787,"Gly-Lys+-Gly","aq",,-175.45,
-"OBIGT",1788,"Gly-Met-Gly","aq",,-172.45,
-"OBIGT",1789,"Gly-Phe-Gly","aq",,-188.52,
-"OBIGT",1790,"Gly-Pro-Gly","aq",,-140.68,
-"OBIGT",1791,"Gly-Ser-Gly","aq",,-125.79,
-"OBIGT",1792,"Gly-Thr-Gly","aq",,-141.19,
-"OBIGT",1793,"Gly-Tyr-Gly","aq",,-190.24,
-"OBIGT",1794,"Gly-Val-Gly","aq",,-155.72,
-"OBIGT",1795,"[GXGBB]","aq",,-98.93,
-"OBIGT",1839,"methyldiethanolamine","aq",1.61,,
-"OBIGT",1871,"MgAsO4-","aq",1.3,,
-"OBIGT",1874,"MnAsO4-","aq",-1.45,,
-"OBIGT",1970,"antigorite","cr1",,,812
-"OBIGT",2004,"clinochlore,7a","cr1",,,666
-"OBIGT",2023,"daphnite,14a","cr",,,-836
-"OBIGT",2048,"ferrosilite","cr1",,,694
-"OBIGT",2049,"ferrosilite","cr2",,,694
-"OBIGT",2064,"greenalite","cr",,,142507
-"OBIGT",2079,"hydromagnesite","cr",,,-2569
-"OBIGT",2210,"n-octadecane","cr",-2.63,,
-"OBIGT",2211,"n-nonadecane","cr",-13.32,,
-"OBIGT",2212,"n-eicosane","cr",-2.79,,
-"OBIGT",2213,"n-heneicosane","cr",-8.61,,
-"OBIGT",2214,"n-docosane","cr",-2.63,,
-"OBIGT",2215,"n-tricosane","cr",-5.22,,
-"OBIGT",2216,"n-tetracosane","cr",-2.02,,
-"OBIGT",2217,"n-pentacosane","cr",-2.93,,
-"OBIGT",2218,"n-hexacosane","cr",-1.29,,
-"OBIGT",2219,"n-heptacosane","cr",-1.23,,
-"OBIGT",2271,"carbazole","cr",-43.39,,
-"OBIGT",2312,"triphenylene","cr",,,541
-"OBIGT",2625,"deoxyadenosine","cr",,,-2977
-"OBIGT",2632,"acetamide","cr",-67.91,,
-"OBIGT",2677,"jarosite","cr",,,20697
-"OBIGT",2678,"natrojarosite","cr",,,17554
-"OBIGT",2750,"n-nonacontane","liq",,,635
-"OBIGT",2757,"2-methyloctane","liq",10,,
-"OBIGT",3170,"5,6-dithiadecane","liq",2,,
-"OBIGT",3245,"ethylene","gas",-4.59,,
-"OBIGT",3255,"3,5-dimethylphenol","gas",,,628
+"OBIGT",66,"NH3","aq",2.75,,
+"OBIGT",75,"SO2","aq",11.1,,
+"OBIGT",93,"LaSO4+","aq",-6.02,,
+"OBIGT",136,"NdF2+","aq",16.64,6.19,
+"OBIGT",182,"EuF+","aq",4.11,-19.19,
+"OBIGT",183,"EuF2","aq",9.75,-40.4,
+"OBIGT",184,"EuF3-","aq",17.18,-64.45,
+"OBIGT",185,"EuF4-2","aq",26.07,-91.02,
+"OBIGT",186,"EuCl+","aq",-4.11,19.2,
+"OBIGT",187,"EuCl2","aq",-9.84,40.4,
+"OBIGT",188,"EuCl3-","aq",-17.19,64.47,
+"OBIGT",189,"EuCl4-2","aq",-26.15,91.04,
+"OBIGT",343,"UO4-2","aq",,-1.11,
+"OBIGT",380,"Ag(CO3)2-3","aq",,-1.56,
+"OBIGT",398,"AgCl4-3","aq",,-1.31,
+"OBIGT",451,"CuCl4-2","aq",,-1.07,
+"OBIGT",453,"ReO4-","aq",-1.26,,
+"OBIGT",462,"PO4-3","aq",,-1.72,
+"OBIGT",464,"Al+3","aq",1.74,,
+"OBIGT",472,"UO2+2","aq",-1.1,,
+"OBIGT",473,"Th+4","aq",,-1.14,
+"OBIGT",492,"P2O7-4","aq",,-2.11,
+"OBIGT",493,"HP2O7-3","aq",,-1.42,
+"OBIGT",502,"AsO4-3","aq",,-1.65,
+"OBIGT",513,"SO3-2","aq",,-1.02,
+"OBIGT",547,"VO4-3","aq",,-1.63,
+"OBIGT",559,"Zr+4","aq",,-1.18,
+"OBIGT",566,"Hf+4","aq",,-1.18,
+"OBIGT",571,"U+4","aq",,-1.13,
+"OBIGT",587,"Ce+4","aq",,-1.13,
+"OBIGT",588,"Pr+4","aq",,-1.12,
+"OBIGT",589,"Nd+4","aq",,-1.12,
+"OBIGT",590,"Pm+4","aq",,-1.13,
+"OBIGT",591,"Sm+4","aq",,-1.14,
+"OBIGT",592,"Eu+4","aq",,-1.14,
+"OBIGT",593,"Gd+4","aq",,-1.16,
+"OBIGT",594,"Tb+4","aq",,-1.15,
+"OBIGT",595,"Dy+4","aq",,-1.15,
+"OBIGT",596,"Ho+4","aq",,-1.15,
+"OBIGT",597,"Er+4","aq",,-1.15,
+"OBIGT",598,"Tm+4","aq",,-1.16,
+"OBIGT",599,"Yb+4","aq",,-1.16,
+"OBIGT",600,"Lu+4","aq",,-1.17,
+"OBIGT",609,"BeO2-2","aq",,-1.17,
+"OBIGT",655,"MnO2-2","aq",,-1.05,
+"OBIGT",666,"CoO2-2","aq",,-1.14,
+"OBIGT",671,"NiO2-2","aq",,-1.16,
+"OBIGT",675,"CuO2-2","aq",,-1.09,
+"OBIGT",679,"ZnO2-2","aq",,-1.17,
+"OBIGT",694,"CdO2-2","aq",,-1.08,
+"OBIGT",712,"RuCl4-2","aq",,-1.09,
+"OBIGT",715,"Ru(SO4)3-4","aq",,-1.8,
+"OBIGT",722,"RuCl5-2","aq",,-1.49,
+"OBIGT",723,"RuCl6-3","aq",,-2.39,
+"OBIGT",726,"Ru(SO4)3-3","aq",,-1.3,
+"OBIGT",732,"RhCl4-2","aq",,-1.14,
+"OBIGT",735,"Rh(SO4)3-4","aq",,-1.82,
+"OBIGT",739,"RhCl2+","aq",,4.67,
+"OBIGT",744,"Rh(SO4)3-3","aq",,-1.33,
+"OBIGT",750,"PdCl4-2","aq",,-1.05,
+"OBIGT",753,"Pd(SO4)3-4","aq",,-1.8,
+"OBIGT",756,"PtCl+","aq",-3.52,1.25,
+"OBIGT",757,"PtCl2","aq",-7.11,2.29,
+"OBIGT",758,"PtCl3-","aq",-10.48,1.78,
+"OBIGT",759,"PtCl4-2","aq",-13.86,,
+"OBIGT",762,"Pt(SO4)3-4","aq",,-1.79,
+"OBIGT",765,"CF4","aq",5.9,,
+"OBIGT",772,"AsH3","aq",-2.67,,
+"OBIGT",843,"MgAsO4-","aq",1.3,,
+"OBIGT",846,"MnAsO4-","aq",-1.45,,
+"OBIGT",910,"methane","aq",-2.61,,
+"OBIGT",915,"hexane","aq",1.43,3.21,
+"OBIGT",918,"ethylene","aq",6.12,-3.82,
+"OBIGT",942,"propanol","aq",-1.89,,
+"OBIGT",1084,"urea","aq",-23.26,23.32,
+"OBIGT",1097,"propanoic acid","aq",1.42,,
+"OBIGT",1120,"formate","aq",1.96,,
+"OBIGT",1122,"propanoate","aq",1.68,,
+"OBIGT",1129,"n-decanoate","aq",-1.93,,
+"OBIGT",1145,"oxalate","aq",-3.19,,
+"OBIGT",1172,"alanate","aq",-24.28,,
+"OBIGT",1466,"Li(Mal)-","aq",,-3.22,
+"OBIGT",1470,"Al(Mal)+","aq",,-2.19,
+"OBIGT",1471,"Pb(Mal)","aq",,1.16,
+"OBIGT",1475,"Pb(Succ)","aq",,1.49,
+"OBIGT",1476,"Na(Oxal)-","aq",,-3.14,
+"OBIGT",1477,"K(Oxal)-","aq",,-2.75,
+"OBIGT",1478,"Fe(Oxal)+","aq",,-2.19,
+"OBIGT",1480,"Na(Mal)-","aq",,-3.11,
+"OBIGT",1481,"K(Mal)-","aq",,-2.63,
+"OBIGT",1483,"La(Mal)+","aq",,-1.92,
+"OBIGT",1484,"Gd(Mal)+","aq",,-1.73,
+"OBIGT",1485,"Lu(Mal)+","aq",,-2.25,
+"OBIGT",1486,"Yb(Mal)+","aq",,-2.05,
+"OBIGT",1487,"Th(Mal)+2","aq",-1.29,-4.79,
+"OBIGT",1489,"Ce(Mal)+","aq",,-1.75,
+"OBIGT",1490,"Nd(Mal)+","aq",4.52,,
+"OBIGT",1491,"Sm(Mal)+","aq",,-1.77,
+"OBIGT",1492,"Pr(Mal)+","aq",,-1.75,
+"OBIGT",1493,"Eu(Mal)+","aq",,-1.87,
+"OBIGT",1494,"Tb(Mal)+","aq",,-1.92,
+"OBIGT",1495,"Dy(Mal)+","aq",,-1.89,
+"OBIGT",1496,"Tm(Mal)+","aq",,-2.08,
+"OBIGT",1497,"Ho(Mal)+","aq",,-2.08,
+"OBIGT",1498,"Er(Mal)+","aq",,-2.11,
+"OBIGT",1499,"Sc(Mal)+","aq",,-1.97,
+"OBIGT",1500,"Fe(Mal)+","aq",,-1.97,
+"OBIGT",1501,"Na(Succ)-","aq",,-2.82,
+"OBIGT",1502,"K(Succ)-","aq",,-2.39,
+"OBIGT",1508,"Th(Succ)+2","aq",-1.21,-4.47,
+"OBIGT",1513,"NH4(Oxal)-","aq",,-2.62,
+"OBIGT",1518,"Al(Oxal)+","aq",,-2.62,
+"OBIGT",1519,"Yb(Oxal)+","aq",,-2.02,
+"OBIGT",1520,"Ce(Oxal)+","aq",,-1.8,
+"OBIGT",1521,"Nd(Oxal)+","aq",,-1.8,
+"OBIGT",1522,"Eu(Oxal)+","aq",,-1.89,
+"OBIGT",1523,"Gd(Oxal)+","aq",,-1.8,
+"OBIGT",1524,"Ru(Oxal)+","aq",,-2.41,
+"OBIGT",1525,"Pa(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1526,"Th(Oxal)+2","aq",-1.27,-4.69,
+"OBIGT",1527,"U(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1528,"Np(Oxal)+2","aq",-1.27,-4.69,
+"OBIGT",1531,"Am(Oxal)+","aq",,-1.8,
+"OBIGT",1532,"Cm(Oxal)+","aq",,-1.8,
+"OBIGT",1533,"Y(Oxal)+","aq",,-2.11,
+"OBIGT",1538,"La(Oxal)+","aq",,-1.87,
+"OBIGT",1539,"Tb(Oxal)+","aq",,-1.92,
+"OBIGT",1540,"Er(Oxal)+","aq",,-2.05,
+"OBIGT",1541,"Lu(Oxal)+","aq",,-2.19,
+"OBIGT",1542,"Cr(Oxal)+","aq",,-2.58,
+"OBIGT",1543,"Ga(Oxal)+","aq",,-2.66,
+"OBIGT",1544,"Sc(Oxal)+","aq",,-2.13,
+"OBIGT",1545,"In(Oxal)+","aq",,-2.19,
+"OBIGT",1546,"Pu(Oxal)+2","aq",-1.2,-4.44,
+"OBIGT",1547,"NpO2(Oxal)","aq",,-1.94,
+"OBIGT",1548,"Sm(Oxal)+","aq",,-1.84,
+"OBIGT",1549,"Cs(Mal)-","aq",,-2.39,
+"OBIGT",1550,"NH4(Mal)-","aq",,-2.54,
+"OBIGT",1555,"In(Mal)+","aq",,-2.11,
+"OBIGT",1556,"Y(Mal)+","aq",,-2.02,
+"OBIGT",1564,"La(Succ)+","aq",,-1.52,
+"OBIGT",1565,"NH4(Succ)-","aq",,-2.26,
+"OBIGT",1567,"Fe(Succ)+","aq",,-1.92,
+"OBIGT",1568,"Sc(Succ)+","aq",,-1.77,
+"OBIGT",1571,"NpO2(Succ)","aq",,-3.16,
+"OBIGT",1572,"Sm(Succ)+","aq",,-1.48,
+"OBIGT",1573,"Er(Succ)+","aq",,-1.68,
+"OBIGT",1574,"U(Succ)+2","aq",-1.15,-4.27,
+"OBIGT",1578,"La(Glut)+","aq",,-1.23,
+"OBIGT",1579,"Y(Glut)+","aq",,-1.46,
+"OBIGT",1580,"Sc(Glut)+","aq",,-1.5,
+"OBIGT",1581,"Th(Glut)+2","aq",-1.09,-4.05,
+"OBIGT",1584,"Fe(Glut)+","aq",,-1.05,
+"OBIGT",1585,"Sm(Glut)+","aq",,-1.2,
+"OBIGT",1588,"Er(Glut)+","aq",,-1.4,
+"OBIGT",1590,"Ba(Adip)","aq",,1.19,
+"OBIGT",1597,"Pb(Adip)","aq",,1.25,
+"OBIGT",1598,"Sc(Adip)+","aq",,-1.22,
+"OBIGT",1600,"Th(Adip)+2","aq",-1.02,-3.76,
+"OBIGT",1601,"U(Adip)+2","aq",-1,-3.71,
+"OBIGT",1603,"Li(Oxal)-","aq",,-3.3,
+"OBIGT",1607,"Li(Succ)-","aq",,-2.94,
+"OBIGT",1609,"Na(Glut)-","aq",,-2.34,
+"OBIGT",1610,"K(Glut)-","aq",,-2.05,
+"OBIGT",1611,"Li(Glut)-","aq",,-2.66,
+"OBIGT",1616,"Na(Adip)-","aq",,-2.05,
+"OBIGT",1617,"K(Adip)-","aq",,-1.76,
+"OBIGT",1618,"Li(Adip)-","aq",,-2.38,
+"OBIGT",1624,"cyclohexane","aq",9.35,6.64,
+"OBIGT",1625,"argon","aq",-1.24,-8.59,
+"OBIGT",1626,"benzene","aq",,-1.14,
+"OBIGT",1627,"CO2","aq",-4.94,,
+"OBIGT",1628,"xenon","aq",2.8,,
+"OBIGT",1638,"n-butanethiol","aq",2.19,,
+"OBIGT",1660,"methyldiethanolamine","aq",1.61,,
+"OBIGT",1670,"cysteinate","aq",-1,,
+"OBIGT",1697,"glucose","aq",1.11,,
+"OBIGT",1726,"adenine","aq",-1.2,,
+"OBIGT",1727,"guanine","aq",-4.26,,
+"OBIGT",1771,"dHUMP-","aq",-3.13,,
+"OBIGT",1868,"MgADP-","aq",-1.01,,
+"OBIGT",1879,"HNicMP(ox)","aq",,9.4,
+"OBIGT",1887,"ribose-5-phosphate","aq",,7.48,
+"OBIGT",1889,"ribose-5-phosphate-2","aq",1.53,,
+"OBIGT",1890,"H4NADP(red)","aq",1.73,,
+"OBIGT",1891,"H3NADP(red)-","aq",2.41,,
+"OBIGT",1892,"H2NADP(red)-2","aq",1.28,,
+"OBIGT",1893,"HNADP(red)-3","aq",2.09,,
+"OBIGT",1894,"NADP(red)-4","aq",1.09,,
+"OBIGT",1896,"H3NADP(ox)","aq",1.05,,
+"OBIGT",1944,"Gly-Ala-Gly","aq",,-126.09,
+"OBIGT",1945,"Gly-Arg+-Gly","aq",,-182.01,
+"OBIGT",1946,"Gly-Asn-Gly","aq",,-145.77,
+"OBIGT",1947,"Gly-Asp-Gly","aq",,-139.16,
+"OBIGT",1948,"Gly-Cys-Gly","aq",,-139.2,
+"OBIGT",1949,"Gly-Gln-Gly","aq",,-158.09,
+"OBIGT",1950,"Gly-Glu-Gly","aq",,-155.4,
+"OBIGT",1951,"Gly-Gly-Gly","aq",,-107.83,
+"OBIGT",1952,"Gly-His-Gly","aq",,-167.84,
+"OBIGT",1953,"Gly-Ile-Gly","aq",,-172.24,
+"OBIGT",1954,"Gly-Leu-Gly","aq",,-171.74,
+"OBIGT",1955,"Gly-Lys+-Gly","aq",,-175.45,
+"OBIGT",1956,"Gly-Met-Gly","aq",,-172.45,
+"OBIGT",1957,"Gly-Phe-Gly","aq",,-188.52,
+"OBIGT",1958,"Gly-Pro-Gly","aq",,-140.68,
+"OBIGT",1959,"Gly-Ser-Gly","aq",,-125.79,
+"OBIGT",1960,"Gly-Thr-Gly","aq",,-141.19,
+"OBIGT",1961,"Gly-Tyr-Gly","aq",,-190.24,
+"OBIGT",1962,"Gly-Val-Gly","aq",,-155.72,
+"OBIGT",1963,"[GXGBB]","aq",,-98.93,
+"OBIGT",1996,"antigorite","cr1",,,812
+"OBIGT",2030,"clinochlore,7a","cr1",,,666
+"OBIGT",2049,"daphnite,14a","cr",,,-836
+"OBIGT",2074,"ferrosilite","cr1",,,694
+"OBIGT",2075,"ferrosilite","cr2",,,694
+"OBIGT",2090,"greenalite","cr",,,142507
+"OBIGT",2105,"hydromagnesite","cr",,,-2569
+"OBIGT",2256,"jarosite","cr",,,20697
+"OBIGT",2257,"natrojarosite","cr",,,17554
+"OBIGT",2279,"n-octadecane","cr",-2.63,,
+"OBIGT",2280,"n-nonadecane","cr",-13.32,,
+"OBIGT",2281,"n-eicosane","cr",-2.79,,
+"OBIGT",2282,"n-heneicosane","cr",-8.61,,
+"OBIGT",2283,"n-docosane","cr",-2.63,,
+"OBIGT",2284,"n-tricosane","cr",-5.22,,
+"OBIGT",2285,"n-tetracosane","cr",-2.02,,
+"OBIGT",2286,"n-pentacosane","cr",-2.93,,
+"OBIGT",2287,"n-hexacosane","cr",-1.29,,
+"OBIGT",2288,"n-heptacosane","cr",-1.23,,
+"OBIGT",2340,"carbazole","cr",-43.39,,
+"OBIGT",2381,"triphenylene","cr",,,541
+"OBIGT",2694,"deoxyadenosine","cr",,,-2977
+"OBIGT",2795,"n-nonacontane","liq",,,635
+"OBIGT",2802,"2-methyloctane","liq",10,,
+"OBIGT",3215,"5,6-dithiadecane","liq",2,,
+"OBIGT",3291,"ethylene","gas",-4.59,,
+"OBIGT",3301,"3,5-dimethylphenol","gas",,,628

Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
 \name{CHNOSZ-package}
 \alias{CHNOSZ-package}
 \docType{package}
@@ -9,7 +10,7 @@
 
 \section{Getting Help}{
 The major features of the package are outlined in the Overview given below, with links to specific help topics.
-See the vignette \emph{An Introduction to CHNOSZ} for more in-depth example of the usage the functions.
+See the vignette \emph{An Introduction to CHNOSZ} (\code{anintro.Rmd}) for more in-depth example of the usage the functions.
 The help pages have been given either keywords or \dQuote{concept index entries} which are visible to \code{\link{help.search}} (aka \code{??}).
 Use \code{??primary} to browse the most commonly used functions and \code{??secondary} to see other high-level, but less often-used functions.
 \code{??protein} shows functions for working with proteins, and \code{??extra} lists functions with extra functionality (beyond the main workflow).
@@ -51,6 +52,8 @@
 
   \item Buffer calculations - compute activities of basis species that are determined by a buffer of one or more species (e.g., pyrite-pyrrhotite-magnetite; acetic acid-CO2) (\code{\link{buffer}}).
 
+  \item Activity coefficients (\bold{experimental}) - calculate activity coefficients of aqueous species using the extended Debye-Hückel equation (\code{\link{nonideal}}).
+
   \item Activity statistics (\bold{experimental}) - calculate summary statistics for equilibrium activities of species (\code{\link{revisit}}).
 
   \item Multidimensional optimization (\bold{experimental}) - using an iterative gridded optimization, find a combination of chemical activities of basis species, temperature and/or pressure that maximize or minimize the value of a target statistic (\code{\link{findit}}).

Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/man/add.protein.Rd	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
 \name{add.protein}
 \alias{add.protein}
 \alias{seq2aa}

Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd	2017-05-01 03:46:53 UTC (rev 194)
+++ pkg/CHNOSZ/man/basis.Rd	2017-05-02 04:44:02 UTC (rev 195)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
 \name{basis}
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 195

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