[CHNOSZ-commits] r382 - in pkg/CHNOSZ: . data demo inst inst/extdata/OBIGT man tests/testthat vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Feb 6 18:29:10 CET 2019 

Author: jedick
Date: 2019-02-06 18:29:09 +0100 (Wed, 06 Feb 2019)
New Revision: 382

Added:
   pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/demo/Shh.R
   pkg/CHNOSZ/demo/bugstab.R
   pkg/CHNOSZ/demo/copper.R
   pkg/CHNOSZ/demo/protein.equil.R
   pkg/CHNOSZ/demo/sources.R
   pkg/CHNOSZ/demo/yeastgfp.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv.xz
   pkg/CHNOSZ/man/add.obigt.Rd
   pkg/CHNOSZ/tests/testthat/test-add.protein.R
   pkg/CHNOSZ/tests/testthat/test-affinity.R
   pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
   pkg/CHNOSZ/tests/testthat/test-recalculate.R
   pkg/CHNOSZ/tests/testthat/test-wjd.R
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/equilibrium.Rnw
   pkg/CHNOSZ/vignettes/equilibrium.lyx
   pkg/CHNOSZ/vignettes/hotspring.Rnw
   pkg/CHNOSZ/vignettes/hotspring.lyx
   pkg/CHNOSZ/vignettes/obigt.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
add/update data for glycine and related species from Kitadai (2014)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-06 17:29:09 UTC (rev 382)
@@ -1,6 +1,6 @@
 Date: 2019-02-06
 Package: CHNOSZ
-Version: 1.1.3-89
+Version: 1.1.3-90
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/data/refs.csv	2019-02-06 17:29:09 UTC (rev 382)
@@ -61,6 +61,7 @@
 DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,http://dx.doi.org/10.1016/0016-7037(95)00403-3
 AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
 AH97b.1,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","alanate and glycinate GHS",https://doi.org/10.1039/A608126F
+AH97b.2,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","glycine and glycinium GHS",https://doi.org/10.1039/A608126F
 DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
 DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
 DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
@@ -105,6 +106,7 @@
 Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250","aqueous H<sub>4</sub>SiO<sub>4</sub>",http://dx.doi.org/10.1016/S0009-2541(00)00263-1
 SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
 TS01,"B. Tagirov and J. Schott",2001,"Geochim. Cosmochim. Acta 65, 3965-3992","aqueous Al species",http://dx.doi.org/10.1016/S0016-7037(01)00705-0
+GKL02,"R. N. Goldberg et al.",2002,"J. Phys. Chem. Ref. Data 31, 231-370","glycine, diglycine, and triglycine (+1 and -1 ions) GHS",http://dx.doi.org/10.1063/1.1416902
 MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614
 NA03,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","As oxide and sulfide minerals",
 NA03.1,"D. K. Nordstrom and D. G. Archer",2003,"Arsenic thermodynamic data and environmental geochemistry. In Arsenic in Groundwater, eds. Welch and Stollenwerk, Kluwer","aqueous As oxides and sulfides",
@@ -120,7 +122,10 @@
 LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","pyridine and piperidine",https://doi.org/10.1016/j.tca.2006.06.008
 DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acid, protein, and organic groups",https://doi.org/10.5194/bg-3-311-2006
 DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","amino acids HKF parameters",https://doi.org/10.5194/bg-3-311-2006
-DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides",https://doi.org/10.5194/bg-3-311-2006
+DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","Gly-X-Gly tripeptides Cp, V, and HKF c1, c2, omega parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.3,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","glycine, [Gly], and [UPBB] HKF parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.4,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","methionine HKF parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.5,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","triglycine Cp, V, and HKF c1, c2, omega parameters",https://doi.org/10.5194/bg-3-311-2006
 LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006
 MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
 Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
@@ -143,6 +148,7 @@
 DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",https://doi.org/10.1016/j.gca.2013.08.020
 FDM+14,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","CO<sub>2</sub>, CO<sub>3</sub><sup>-2</sup>, and HCO<sub>3</sub><sup>-</sup>",https://doi.org/10.1016/j.gca.2014.01.030
 FDM+14.1,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","aragonite; source of data: `berman.dat`",https://doi.org/10.1016/j.gca.2014.01.030
+Kit14,"N. Kitadai",2014,"J. Mol. Evol. 78, 171-187","glycine, diglycine, and triglycine (zwitterions and ions); diketopiperazine, [Gly] and [UPBB] groups",https://doi.org/10.1007/s00239-014-9616-1
 PAB+14,"G. S. Pokrovski, N. N. Akinfiev et al., 2014",2014,"Geol. Soc. Spec. Publ. 402, 9-70","Au<sup>+</sup>, Au(OH)<sub>2</sub><sup>-</sup>, AuCl, and AuOH",https://doi.org/10.1144/SP402.4
 PAB+14.1,"G. S. Pokrovski, N. N. Akinfiev et al., 2014",2014,"Geol. Soc. Spec. Publ. 402, 9-70","corrected H of AuHS",https://doi.org/10.1144/SP402.4
 SHA14,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","SiO<sub>2</sub> and Si<sub>2</sub>O<sub>4</sub>",https://doi.org/10.1016/j.gca.2013.12.019

Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/Shh.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -1,6 +1,9 @@
 # Compare affinities of Sonic hedgehog and transcription factors involved in dorsal-ventral patterning
 # (Dick, 2015. Chemical integration of proteins in signaling and development. https://doi.org/10.1101/015826)
 
+# to reproduce the calculations in the paper, use superseded data for [Gly] 20190206
+add.obigt("OldAA")
+
 # UniProt names of the proteins
 pname <- c("SHH", "OLIG2", "NKX22", "FOXA2", "IRX3", "PAX6", "NKX62", "DBX1",
   "DBX2", "NKX61", "PAX7", "GLI1", "GLI2", "GLI3", "PTC1", "SMO", "GLI3R")[1:11]
@@ -197,3 +200,4 @@
 # all done!
 par(opar)
 if(pdf) dev.off()
+data(thermo)

Modified: pkg/CHNOSZ/demo/bugstab.R
===================================================================
--- pkg/CHNOSZ/demo/bugstab.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/bugstab.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -2,6 +2,8 @@
 # based on "bugstab" function in Supporting Information of Dick, 2016
 # (https://doi.org/10.7717/peerj.2238)
 
+# to reproduce the calculations in the paper, use superseded data for [Gly] 20190206
+add.obigt("OldAA")
 # set up graphics device
 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)))
@@ -70,3 +72,5 @@
 # reset graphics device to default
 par(opar)
 layout(1)
+# reset thermodynamic database
+data(thermo)

Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/copper.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -3,6 +3,8 @@
 ## (Aksu, S. and Doyle, F. M., 2001. Electrochemistry of copper in aqueous glycine 
 ## solutions. J. Electrochem. Soc., 148, B51-B57. doi:10.1149/1.1344532)
 
+# we need some superseded Cu-Gly complexes 20190206
+add.obigt("OldAA")
 # add some new species to thermo$obigt
 m1 <- makeup(info(c("Cu+", "glycinate", "glycinate")), sum=TRUE)
 mod.obigt(name="Cu(Gly)2-", formula=as.chemical.formula(m1))
@@ -35,8 +37,8 @@
 species(Cu_s)
 species(c(Cu_aq, CuGly), -4)
 names <- c(Cu_s, Cu_aq, CuGly)
-# mosaic diagram with to speciate glycine as a function of pH
-m <- mosaic(bases=Gly, pH=c(0, 16, 300), Eh=c(-0.6, 1.0, 300))
+# mosaic diagram with speciate glycine as a function of pH
+m <- mosaic(bases=Gly, pH=c(0, 16, 500), Eh=c(-0.6, 1.0, 500))
 fill <- c(rep("lightgrey", 3), rep("white", 4), rep("lightblue", 4))
 d <- diagram(m$A.species, fill=fill, names=NULL, xaxs="i", yaxs="i", fill.NA="pink2")
 # to make the labels look nicer

Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/protein.equil.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -6,6 +6,8 @@
 data(thermo)
 # use properties of the "old" [Met] sidechain group (Dick et al., 2006)
 mod.obigt("[Met]", G=-35245, H=-59310)
+# also use parameters for [Gly] from DLH06 20190206
+add.obigt("OldAA")
 # set up the basis species to those used in DS11
 basis("CHNOS+")
 # note this yields logaH2 = -4.657486

Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/sources.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -16,8 +16,11 @@
 tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
 os5 <- gsub("\ .*", "", tdata$ref1)
 os6 <- gsub("\ .*", "", tdata$ref2)
+tdata <- read.csv(system.file("extdata/OBIGT/OldAA.csv", package="CHNOSZ"), as.is=TRUE)
+os7 <- gsub("\ .*", "", tdata$ref1)
+os8 <- gsub("\ .*", "", tdata$ref2)
 # all of the thermodynamic data sources - some of them might be NA
-obigt.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6))
+obigt.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6, os7, os8))
 obigt.source <- obigt.source[!is.na(obigt.source)]
 # these all produce character(0) if the sources are all accounted for
 print("missing these sources for thermodynamic properties:")

Modified: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/demo/yeastgfp.R	2019-02-06 17:29:09 UTC (rev 382)
@@ -3,6 +3,8 @@
 # use old properties of [Met] (Dick et al., 2006) to reproduce this example
 data(thermo)
 mod.obigt("[Met]", G=-35245, H=-59310)
+# also use parameters for [Gly] from DLH06 20190206
+add.obigt("OldAA")
 # arranged by decreasing metastability:
 # order of this list of locations is based on the 
 # (dis)appearance of species on the current set of diagrams

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/inst/NEWS	2019-02-06 17:29:09 UTC (rev 382)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-89 (2019-02-06)
+CHANGES IN CHNOSZ 1.1.3-90 (2019-02-06)
 ---------------------------------------
 
 BUG FIXES
@@ -166,6 +166,10 @@
 - Add test-recalculate.R to check that some recalculated values are
   correctly entered in OBIGT.
 
+- Add or update glycine, diglycine, and triglycine (zwitterions and
+  ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai,
+  2014. Superseded data have been moved to OBIGT/OldAA.csv.
+
 DIAGRAMS
 
 - Lines in 1-D diagram()s can optionally be drawn as splines using the

Added: pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv	2019-02-06 17:29:09 UTC (rev 382)
@@ -0,0 +1,63 @@
+name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+alanylglycine,NA,C5H10N2O3,aq,Sho92,CHNOSZ.6,28.Feb.92,-116730,-186110,50.7,60.3,95.22,14.6503,21.164,12.0751,-3.6538,54.7374,0.7979,-0.4278,0
+leucylglycine,NA,C8H16N2O3,aq,Sho92,CHNOSZ.6,27.Aug.06,-110620,-202660,72.6,118.8,145.34,21.3967,34.6501,13.1805,-4.2113,98.6389,6.4783,-0.7594,0
+diglycine,NA,C4H8N2O3,aq,Sho92,CHNOSZ.6,28.Feb.92,-117020,-175640,54.2,38,76.27,12.0393,15.9447,11.6466,-3.4381,36.349,-1.3673,-0.4808,0
+diketopiperazine,NA,C4H6N2O2,aq,Sho92,CHNOSZ.6,28.Feb.92,-57440,-99300,53.5,17,76.73,12.1058,16.0764,11.6608,-3.4435,19.5904,-3.4064,-0.4702,0
+glycine,Gly,C2H5NO2,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
+glycinium,Gly+,C2H6NO2+,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
+[Gly],NA,H,aq,"DLH06 [S15]",NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0
+[UPBB],NA,C2H2NO,aq,"DLH06 [S15]",NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0
+alanate,NA,C3H6NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-75360,-121470,30.71,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
+glycinate,NA,C2H4NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-77610,-114190,30.07,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
+Ca(Gly)+,NA,Ca(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-211570,-240519,34.375,59.3,32.6,6.2431,7.4595,2.8241,-3.0873,41.4246,9.0464,0.0543,1
+Ca(Gly)2,NA,Ca(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-290215,-351722,77.929,131,89,13.9371,26.2517,-4.5733,-3.8641,82.6597,23.6485,-0.03,0
+Mg(Gly)+,NA,Mg(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-190820,-227064,7.788,64.2,28.7,5.8466,6.4953,3.1944,-3.0474,48.0086,10.0502,0.4555,1
+Mg(Gly)2,NA,Mg(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-272534,-343783,43.136,140.6,84.7,13.3443,24.8034,-4.0028,-3.8043,88.2942,25.6069,-0.03,0
+Sr(Gly)+,NA,Sr(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-213664,-241197,42.515,53.6,33.3,6.3007,7.6019,2.7652,-3.0932,36.9719,7.8914,-0.0684,1
+Sr(Gly)2,NA,Sr(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-291859,-351200,88.581,119.9,89.8,14.0476,26.5176,-4.6704,-3.8751,76.1763,21.395,-0.03,0
+Ba(Gly)+,NA,Ba(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-213671,-237698,55.917,48.6,38.7,6.9656,9.2295,2.1164,-3.1604,32.1389,6.8602,-0.2709,1
+Ba(Gly)2,NA,Ba(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-292479,-347082,106.12,110.1,95.8,14.8647,28.514,-5.4575,-3.9577,70.3874,19.383,-0.03,0
+Mn(Gly)+,NA,Mn(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-137101,-167693,26.59,67,33.7,6.4299,7.9186,2.6372,-3.1063,47.0493,10.6185,0.1739,1
+Mn(Gly)2,NA,Mn(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-218761,-282627,67.741,146.1,90.2,14.1002,26.6481,-4.7253,-3.8805,91.4846,26.7157,-0.03,0
+Fe(Gly)+,NA,Fe(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-105368,-137141,21.59,58,28,5.6774,6.0837,3.3533,-3.0304,42.4593,8.7852,0.2482,1
+Fe(Gly)2,NA,Fe(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-187369,-252307,61.198,128.5,83.9,13.2339,24.5311,-3.8903,-3.793,81.1932,23.1388,-0.03,0
+Ni(Gly)+,NA,Ni(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-96871,-131179,13.59,49.9,20.4,4.6813,3.6515,4.3097,-2.9299,38.8214,7.1352,0.3686,1
+Ni(Gly)2,NA,Ni(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-181191,-249835,51.18,112.7,75.4,12.0787,21.7107,-2.7819,-3.6764,71.9311,19.9195,-0.03,0
+Cu(Gly)+,NA,Cu(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-73625,-104298,26.59,63.4,25.3,5.2864,5.1238,3.7413,-2.9907,44.9395,9.8852,0.1739,1
+Cu(Gly)2,NA,Cu(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-161137,-225550,66.18,139,80.9,12.8262,23.5338,-3.4944,-3.7518,87.3679,25.285,-0.03,0
+Zn(Gly)+,NA,Zn(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-120148,-153499,19.59,62.1,25.6,5.3677,5.3226,3.6628,-2.9989,45.1185,9.6102,0.2792,1
+Zn(Gly)2,NA,Zn(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-203799,-271188,58.18,136.4,81.3,12.8771,23.6625,-3.5537,-3.7571,85.8243,24.7484,-0.03,0
+Pb(Gly)+,NA,Pb(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-90780,-114202,58.508,47.7,35.3,6.4949,8.079,2.5712,-3.1129,31.2483,6.6769,-0.3103,1
+Pb(Gly)2,NA,Pb(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-173013,-226772,109.51,108.3,92.1,14.355,27.2722,-4.9746,-3.9063,69.3582,19.0253,-0.03,0
+Co(Gly)+,NA,Co(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-97525,-130972,16.59,58.7,25.5,5.3683,5.3273,3.6539,-2.9991,43.5722,8.9227,0.326,1
+Co(Gly)2,NA,Co(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-180617,-247207,58.18,129.8,81.2,12.8601,23.6197,-3.5341,-3.7553,81.9652,23.407,-0.03,0
+Cd(Gly)+,NA,Cd(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-102566,-133978,28.59,68.4,35.3,6.6477,8.4525,2.4231,-3.1283,47.5446,10.8935,0.1417,1
+Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-185236,-250387,68.18,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
+Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-208959,-236026,49.509,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
+Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-288477,-346709,97.734,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
+Ca(Alan)+,NA,Ca(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-209172,-247643,35.015,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
+Ca(Alan)2,NA,Ca(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-285446,-365834,79.755,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
+Mg(Alan)+,NA,Mg(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-186539,-232305,8.428,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
+Mg(Alan)2,NA,Mg(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-263631,-353761,44.962,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
+Sr(Alan)+,NA,Sr(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-211130,-248184,43.155,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
+Sr(Alan)2,NA,Sr(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-286831,-365053,90.407,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
+Ba(Alan)+,NA,Ba(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-210713,-244263,56.557,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
+Ba(Alan)2,NA,Ba(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-286687,-360171,107.946,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
+Mn(Alan)+,NA,Mn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-134280,-173740,29.425,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
+Mn(Alan)2,NA,Mn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-213474,-295365,72.44,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
+Fe(Alan)+,NA,Fe(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-103952,-146326,18.518,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
+Fe(Alan)2,NA,Fe(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-184387,-269655,58.166,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
+Ni(Alan)+,NA,Ni(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-94227,-137691,15.46,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
+Ni(Alan)2,NA,Ni(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-175945,-264092,50.92,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
+Cu(Alan)+,NA,Cu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,06.Feb.19,-71295,-110530,25.46,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
+Cu(Alan)2,NA,Cu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,06.Feb.19,-156054,-238480,65.92,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
+Zn(Alan)+,NA,Zn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-117313,-161024,17.46,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
+Zn(Alan)2,NA,Zn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-198512,-284509,60.92,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
+Pb(Alan)+,NA,Pb(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-87891,-120835,59.148,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
+Pb(Alan)2,NA,Pb(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-167671,-240311,111.336,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
+Co(Alan)+,NA,Co(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-94799,-136805,20.46,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
+Co(Alan)2,NA,Co(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-175193,-260392,60.92,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
+Cd(Alan)+,NA,Cd(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-100782,-141576,29.698,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
+Cd(Alan)2,NA,Cd(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-181340,-264540,72.797,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
+Eu(Alan)+,NA,Eu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-206029,-242617,50.149,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
+Eu(Alan)2,NA,Eu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-282521,-359634,99.56,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-02-06 06:35:06 UTC (rev 381)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-02-06 17:29:09 UTC (rev 382)
@@ -1,104 +1,91 @@
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[TRUNCATED]

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    svnlook diff /svnroot/chnosz -r 382

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