[CHNOSZ-commits] r536 - in pkg/CHNOSZ/inst: . extdata/OBIGT

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

Author: jedick
Date: 2020-06-30 17:57:14 +0200 (Tue, 30 Jun 2020)
New Revision: 536

Modified:
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
Log:
Add DEW 2019 data


Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2020-06-30 14:45:56 UTC (rev 535)
+++ pkg/CHNOSZ/inst/CHECKLIST	2020-06-30 15:57:14 UTC (rev 536)
@@ -1,60 +1,84 @@
 ****************************
 release checklist for CHNOSZ
+    (updated 2020-06-30)
 ****************************
 
 - run examples() and demos() and inspect their output (especially plots)
 
-- check output of demo("sources") to make sure all data sources are cited
-
 - use test_package("CHNOSZ", reporter = "progress") to find warnings
   from tests that aren't shown in R CMD check
 
-- recreate extdata/adds/obigt_check.csv after all data updates:
-  co <- check.obigt()
-  write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
+- check that uniprot.aa() works with current UniProt web pages
 
-- recreate extdata/thermo/stoich.csv.xz after all data updates
+- check reverse dependencies on CRAN: canprot, ecipex, iemisc as of 2019-08-02
+
+**********************
+updating data in OBIGT
+**********************
+
+- Add data to relevant csv file in extdata/OBIGT.
+
+- Add bibtex references to vignettes/obigt.bib
+  (used in the obigt.Rmd vignette).
+
+- Add references *and notes* to extdata/OBIGT/refs.csv
+  (also used in the obigt.Rmd vignette and thermo.refs()).
+
+- Check output of demo/sources.R to make sure all references
+  are cited (printed results should be character(0)).
+
+- Rebuild extdata/thermo/stoich.csv.xz after all data updates
+  (used in retrieve() to search the databse by element):
   formula <- thermo()$obigt$formula
   stoich <- i2A(formula)
   write.csv(stoich, "stoich.csv")
   system("xz -f stoich.csv")
 
-- check that uniprot.aa() works with current UniProt web pages
+- Rebuild extdata/adds/obigt_check.csv after all data updates:
+  (not used elsewhere in CHNOSZ, but helpful to see which
+  species data have self inconsistencies):
+  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
+******************
+updating vignettes
+******************
 
-- run R CMD check using R compiled without long doubles (emulating Solaris checks on CRAN)
-  (CFLAGS=-ffloat-store ./configure --disable-long-double)
-
-- run R CMD check with Latin-1 locale (catches errors on CRAN's debian-clang)
-  LC_CTYPE=en_US R CMD check CHNOSZ_x.x.x.tar.gz
-
-- reduce the size of vignettes: after installing/upgrading rmarkdown, replace files in
+- Customize rmarkdown to reduce the size of vignettes:
+  after installing/upgrading rmarkdown, replace files in
   rmarkdown/rmd/h/bootstrap/fonts/ with empty files
 
-- build the package using both qpdf and ghostscript to compact vignettes:
+- Build the package using both qpdf and ghostscript to compact vignettes:
   R CMD build --compact-vignettes=both chnosz/
 
 - vignettes/obigt.bib: check correct year and version for CHNOSZ reference
 
-- documentation links: after installation, run doc/mklinks.sh
+- Documentation links: after installation, run doc/mklinks.sh
   and put the modified anintro.html and obigt.html in the package
 
+***************
+R compatibility
+***************
+
+- run R CMD check using R compiled without long doubles (emulating Solaris checks on CRAN)
+  (CFLAGS=-ffloat-store ./configure --disable-long-double)
+
+- run R CMD check with Latin-1 locale (catches errors on CRAN's debian-clang)
+  LC_CTYPE=en_US R CMD check CHNOSZ_x.x.x.tar.gz
+
 - backwards compatibility: build and check the package with the
   *minimum* R version (from the DESCRIPTION file)
 
-- check reverse dependencies on CRAN: canprot, ecipex, iemisc as of 2019-08-02
+*************
+documentation 
+*************
 
-OTHER THINGS TO DO (depending on changes made in development):
-
 - update list of documentation topics in examples() with any new ones
 
-- clean up all TODO, XXX, etc. in Rd files (and hopefully R files too)
-
-- update .Rinstignore with any new/deleted files
-
 - ensure all Rd files have \concept{...} as listed in CHNOSZ-package.Rd
 
 - although Rd files could use the \doi macro, it generates a largish (ca. 265K)
   build/partial.rdb file; just use \url for now.
+
+- run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/
+  and fix any lines truncated by page margins

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv	2020-06-30 14:45:56 UTC (rev 535)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv	2020-06-30 15:57:14 UTC (rev 536)
@@ -6,6 +6,7 @@
 AgCl2-,AgCl2(-),AgCl2-,aq,SSH97,DEW17.6,26.Sep.17,cal,-51560,-61130,47,7.7,53,12.2533,7.3832,-1.3527,-3.0842,19.1265,-1.4661,0.9169,-1
 Al+3,Al(+3),Al+3,aq,SSWS97,DEW17.05,26.Sep.17,cal,-115609,-126834,-77.7,-31.04,-44.4,-3.3802,-17.0071,14.5185,-2.0758,10.7,-8.06,2.753,3
 AlO2-,AlO2(-),AlO2-,aq,PH95,SHA14.1,26.Sep.17,cal,-198693,-222125,-7.22,-9.55,10,4.298,2.4976,-1.8258,-2.8823,19.1,-6.2,1.7418,-1
+AlO2(SiO2)-,AlO2(SiO2)-,AlO2(SiO2)-,aq,HS19,DEW19.1,30.Jun.20,cal,-403500,-440456,4,32,34.8,9.0313,4.3155,1.2196,-2.9574,39.3711,3.4838,1.5685,-1
 Ar,Ar(0),Ar,aq,SHS89,DEW17.04,26.Sep.17,cal,3900,-2870,14.3,53.35,31.71,6.0003,6.8698,3.0499,-3.063,35.6471,7.316,-0.3073,0
 Au+,Au(+),Au+,aq,SH88,DEW17.2,26.Sep.17,cal,39000,47580,24.5,0.6,11.1,3.3303,0.4233,5.6044,-2.7965,8.1767,-2.9123,0.18,1
 Au+3,Au(+3),Au+3,aq,SH88,DEW17.2,26.Sep.17,cal,103600,96930,-57.9,-36.2,-41.3,-8.0309,-2.3071,13.7983,-2.6836,7.5724,-10.4085,2.4554,3
@@ -13,13 +14,18 @@
 BaCl+,BaCl(+),BaCl+,aq,SSH97,DEW17.5,26.Sep.17,cal,-164730,-165770,22.5,6.18,16.8,4.8851,0.368,4.5296,-2.7942,11.7469,-1.7758,0.2126,1
 Be+2,Be(+2),Be+2,aq,SH88,DEW17.2,26.Sep.17,cal,-83500,-91500,-55.7,-1.3,-25.4,-1.4187,-9.4791,9.9786,-2.3871,22.9154,-3.2995,1.9007,2
 benzene,BENZENE,C6H6,aq,PS01,DEW17.3,26.Sep.17,cal,32000,12230,35.7,89.12,83,17.5199,12.3976,-5.5571,-3.2915,66.9,9.8,-0.25,0
+"bG,NaCl",extended_term_parameter,Z0,aq,OH90,DEW19,30.Jun.20,cal,175,NA,22,12.72,1.83,0.3006,-2.0255,-2.9092,2.0302,-1.5,5.33,-0.368,0
 BO(OH),BO(OH)(0),BO(OH),aq,SH88,SHA14.2,26.Sep.17,cal,-174854,-188505,24,3.76,20.49,5.54,1.38,3.1,-2.84,25,-10,0.1,0
 BO2-,BO2(-),BO2-,aq,SH88,SHA14.4,26.Sep.17,cal,-162240,-184600,-8.9,-9,-16.02,-0.855,-2.596,3.7,-2.6717,17.102,-4.8679,1.7595,-1
-Ca(HCO3)+,Ca(HCO3)(+),Ca(HCO3)+,aq,FDM+14,DEW17.03,26.Sep.17,cal,-273830,-294350,16,90.95,37.51,9.14,4.42,1.13,-2.96,65.9,15.5,0.7,1
+Ca(HCO3)+,Ca(HCO3)(+),Ca(HCO3)+,aq,HS19,DEW19.1,30.Jun.20,cal,-273830,-294350,26,51,30,7.4225,2.7838,2.5039,-2.8941,37.511,7.3541,0.158,1
+Ca(HCOO)+,Ca(HCOO)+,Ca(HCOO)+,aq,HS19,DEW19.1,30.Jun.20,cal,-217930,-232236,11,68,17.5,5.1038,0.5762,4.355,-2.8028,49.5668,10.817,0.3851,1
+Ca(HSiO3)+,Ca(HSiO3)+,Ca(HSiO3)+,aq,HS19,DEW19.1,30.Jun.20,cal,-376299,-397525,16.8,72,36,8.6546,3.9569,1.5203,-2.9426,51.1018,11.6318,0.2973,1
 CaOH+,Ca(OH)(+),Ca(OH)+,aq,SSWS97,DEW17.3,26.Sep.17,cal,-171300,-179600,6.7,1.4,1.9,2.1051,-2.2789,6.749,-2.6848,11.1292,-2.7494,0.4496,1
+Ca+2,Ca+2,Ca(+2),aq,FDM+14,DEW19.5,30.Jun.20,cal,-132120,-129800,-13.5,-7.51,-18.45,-0.245,-7.252,5,-2.48,9,-2.52,1.2366,2
 CaCl+,CaCl(+),CaCl+,aq,SSH97,DEW17.5,26.Sep.17,cal,-163100,-168607,4.5,17.5,11.3,3.9392,-0.5326,5.2847,-2.757,20.7297,0.5302,0.4675,1
 CaCl2,CaCl(0),CaCl,aq,SSH97,DEW17.5,26.Sep.17,cal,-194000,-211060,6,29.77,33.3,7.9694,3.3045,2.0673,-2.9156,23.2636,3.0296,-0.038,0
 CaCO3,CaCO3(0),CaCO3,aq,FDM+14,DEW17.03,26.Sep.17,cal,-262750,-287390,0,14.01,21.53,6.66,2.05,3.12,-2.86,32.8,-0.18,2,0
+CaOH+,CaO,CaO(0),NA,HS19,DEW19.3,30.Jun.20,cal,-152800,NA,16,12,5.5,2.5406,-1.8642,6.4013,-2.7019,12.2781,-0.5902,-0.1,0
 CaSO4,CaSO4(0),CaSO4,aq,SSWS97,DEW17.10,26.Sep.17,cal,-312930,-345900,5,-25,4.7,2.415,-1.9839,6.5015,-2.697,-8.835,-8.1271,-0.038,0
 Cd+2,Cd(+2),Cd+2,aq,SH88,DEW17.2,26.Sep.17,cal,-18560,-18140,-17.4,-3.5,-15.6,0.542,-8.9202,8.5551,-2.4102,15.6572,-3.7476,1.2528,2
 Ce+3,Ce(+3),Ce+3,aq,SH88,DEW17.2,26.Sep.17,cal,-161600,-167400,-49,-38.6,-39.8,-7.6866,-2.5596,13.5864,-2.6732,4.0444,-10.8973,2.2251,3
@@ -47,6 +53,8 @@
 Eu+3,Eu(+3),Eu+3,aq,SSWS97,DEW17.2,26.Sep.17,cal,-137300,-144700,-53,-36.6,-41.3,-8.1578,-2.214,13.8765,-2.6875,6.0547,-10.49,2.3161,3
 Fe(Ac)+,Fe(CH3COO)(+),Fe(CH3COO)+,aq,SSWS97,DEW17.6,26.Sep.17,cal,-111900,-139060,-1.5,81.2,25.2,6.6906,2.087,3.0882,-2.8653,59.0576,13.5058,0.5756,1
 Fe(Ac)2,Fe(CH3COO)2(0),Fe(CH3COO)2,aq,SSWS97,DEW17.6,26.Sep.17,cal,-201800,-259100,11.53,184.2,66.9,14.4948,9.5174,-3.1421,-3.1724,113.7691,34.4869,-0.038,0
+Fe(HCOO)+,Fe(HCOO)+,Fe(HCOO)+,aq,HS19,DEW19.1,30.Jun.20,cal,-111800,-112263,59,30,27,6.6001,2.0008,3.1604,-2.8617,20.5995,3.0764,-0.3418,1
+Fe(HSiO3)+,Fe(HSiO3)+,Fe(HSiO3)+,aq,HS19,DEW19.1,30.Jun.20,cal,-277500,-298539,14,77,38.2,9.1022,4.383,1.163,-2.9602,54.4228,12.6503,0.3397,1
 FeOH+,FeOH(+),FeOH+,aq,SSWS97,DEW17.13,26.Sep.17,cal,-65850,0,-10,15,2,2.2461,-2.1446,6.6364,-2.6903,21.4354,0.0209,0.7031,1
 Fe+2,Fe(+2),Fe+2,aq,SSWS97,DEW17.2,26.Sep.17,cal,-21870,,-25.3,-7.9,-22.2,-0.9153,-9.3356,9.6131,-2.3931,14.9634,-4.6439,1.4574,2
 Fe+3,Fe(+3),Fe+3,aq,SSWS97,DEW17.2,26.Sep.17,cal,-4120,-11850,-66.3,-18.6,-37,-6.3271,-3.5568,12.7493,-2.632,19.0461,-6.8234,2.5812,3
@@ -66,6 +74,7 @@
 glutamine,GLUTAMINE,C5H10N2O3,aq,SH90,DEW17.3,26.Sep.17,cal,-126280,-191860,62.41,43.78,93.72,19.8075,14.5756,-7.3834,-3.3816,33.4802,5.8825,0.18,0
 H-glutarate,GLUTARATE-,C5H7O4-,aq,SH90,DEW17.3,26.Sep.17,cal,-170860,-223570,52.9,20.11,85.91,18.6019,13.4277,-6.4209,-3.3341,25.5789,1.0616,0.8279,-1
 "glutaric acid",GLUTARIC-ACID,C5H8O4,aq,SH90,DEW17.3,26.Sep.17,cal,-176780,-223440,73.2,64.11,99.09,20.7169,15.4414,-8.1094,-3.4173,42.815,10.0236,-0.1,0
+glycinate,GLYCINATE,C2H4NO2-,aq,AH97b,DEW19.4,30.Jun.20,cal,-77610,-114190,30.07,-6.6,43.77,10.584,5.7938,-0.02,-3.0185,13.1119,-4.379,1.1737,-1
 glycine,GLYCINE,C2H5NO2,aq,PS01,DEW17.01,26.Sep.17,cal,-90950,-124780,39.3,9.49,43.29,10.8,1.3,7.6,-3.5,28,-8.2,0.2,0
 glycolate,GLYCOLATE,C2H3O3-,aq,SH90,DEW17.3,26.Sep.17,cal,-121170,-154700,26.2,6.5,39.85,6.7382,13.1933,1.8519,-3.3244,21.339,-1.7106,1.2334,-1
 "glycolic acid",GLYCOLIC-ACID,C2H4O3,aq,SH90,DEW17.3,26.Sep.17,cal,-126400,-154890,43.1,45.5,51.75,11.4261,6.5956,-0.6923,-3.0517,30.0532,6.2338,-0.3017,0
@@ -72,6 +81,7 @@
 H-succinate,H-SUCCINATE,C4H5O4-,aq,SH90,DEW17.3,26.Sep.17,cal,-172060,-217350,45.2,9.3,69.99,15.5663,10.5375,-3.9975,-3.2146,20.3194,-1.1402,0.9446,-1
 H2AsO3-,H2AsO3(-),H2AsO3-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-140330,-170840,26.4,-2.9,26.4,7.2377,2.6079,2.6514,-2.8868,15.8033,-3.6254,1.2305,-1
 H2AsO4-,H2AsO4(-),H2AsO4-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-180010,-217390,28,-0.7,35.1,8.9154,4.2052,1.3121,-2.9528,16.8623,-3.1772,1.2055,-1
+H2CO3,H2CO3,H2CO3,aq,HS19,DEW19.1,30.Jun.20,cal,-145400,-164229,43,86.5,46,10.3102,5.5332,0.1986,-3.0077,54.0971,14.5854,-0.3,0
 H2P2O7-2,H2P2O7(-2),H2P2O7-2,aq,SSWS97,DEW17.3,26.Sep.17,cal,-480400,-544600,39,-20.3,52.4,12.9546,8.0509,-1.9125,-3.1118,18.424,-7.1696,2.6218,-2
 H2PO4-,H2PO4(-),H2PO4-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-270140,-309820,21.6,-7,31.3,8.2228,3.5458,1.865,-2.9256,14.0436,-4.4605,1.3003,-1
 H2S,H2S(0),H2S,aq,SHS89,DEW17.3,26.Sep.17,cal,-6673,-9001,30,42.83,34.92,8.2543,3.5757,1.8399,-2.9268,30.3482,5.6905,-0.1,0
@@ -95,7 +105,7 @@
 HSe-,HSe(-),HSe-,aq,SSWS97,DEW17.3,26.Sep.17,cal,10500,3800,19,-12.6,19,5.8535,1.29,3.7565,-2.8323,11.1346,-5.6013,1.3408,-1
 HSeO3-,HSeO3(-),HSeO3-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-98340,-122980,32.3,4.9,32.3,8.3403,3.6577,1.7712,-2.9302,19.543,-2.0364,1.1402,-1
 HSeO4-,HSeO4(-),HSeO4-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-108100,-139000,35.7,-41.9,31,8.063,3.3936,1.9926,-2.9193,-8.3614,-11.5697,1.0885,-1
-HSiO3-,HSiO3(-),HSiO3-,aq,KUP+05,DEW17.20,26.Sep.17,cal,-242855,-273872,-2,10.5,18.2,5.851,1.2876,3.7585,-2.8322,27.608,-0.8958,1.6594,-1
+HSiO3-,HSiO3(-),HSiO3-,aq,HS19,DEW19.1,30.Jun.20,cal,-242855,-276479,-3.5,16,21.2,6.4445,1.8526,3.2847,-2.8556,31.0405,0.2246,1.6821,-1
 HSO3-,HSO3(-),HSO3-,aq,SSWS97,DEW17.21,26.Sep.17,cal,-126130,-149670,33.4,-1.4,33.3,6.7014,8.5816,2.3771,-3.1338,15.6949,-3.3198,1.1233,-1
 HSO4-,HSO4(-),HSO4-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-180630,-212500,30,5.3,35.2,8.9201,4.2097,1.3083,-2.953,20.096,-1.955,1.1748,-1
 HSO5-,HSO5(-),HSO5-,aq,SSWS97,DEW17.3,26.Sep.17,cal,-152370,-185380,50.7,29.2,50.7,11.7798,6.9324,-0.9747,-3.0656,31.2126,2.9134,0.8611,-1
@@ -116,7 +126,9 @@
 Mg(HSiO3)+,Mg(HSiO3)(+),Mg(HSiO3)+,aq,SSWS97,DEW17.4,26.Sep.17,cal,-353025,-385700,-23.78,37.82,2.5,2.4433,-1.9569,6.4789,-2.6981,36.7319,4.6693,0.9118,1
 MgCl+,MgCl(+),MgCl+,aq,SSWS97,DEW17.6,26.Sep.17,cal,-139700,-150933,-19,25,1.25,3.21,-4.92,6.27,-2.58,28.6,2.058,0.8449,1
 MgCO3,MgCO3(0),MgCO3,aq,SSWS97,DEW17.27,26.Sep.17,cal,-238760,-270570,-24,-24.8,17.9,5.1407,0.6113,4.3256,-2.8043,-5.6039,-8.0864,0.3,0
-MgOH+,MgOH(+),MgOH+,aq,SSWS97,DEW17.28,26.Sep.17,cal,-149225,-152955,-17,40,-7,0.5662,-3.7441,7.9775,-2.6242,37.393,5.1134,0.8449,1
+MgO,MgO,"MgO,aq",aq,HS19,DEW19.1,30.Jun.20,cal,-137500,-139804,24.6,-24.5,6.2,2.8684,-1.5521,6.1396,-2.7148,-5.4281,-8.0252,0.3,0
+MgOH+,MgOH(+),MgOH+,aq,SSWS97,DEW19.2,30.Jun.20,cal,-149225,-152955,-18,40,2,2.3141,-2.0799,6.5821,-2.693,37.393,5.1134,0.8449,1
+Mg(SiO2)(HCO3)+,Mg(SiO2)(HCO3)+,MgSiC+,aq,HS19,DEW19.1,30.Jun.20,cal,-454300,-479123,48,78.5,53.5,11.8266,6.977,-1.012,-3.0674,50.5582,12.9558,-0.1752,1
 MgSO4,MgSO4,MgSO4,aq,ARHB06,DEW17.29,26.Sep.17,cal,-289449,-327449,-1,20,35,8.3417,3.659,1.77,-2.9303,18.3485,1.0394,0.05,0
 Mn+2,Mn(+2),Mn+2,aq,SSWS97,DEW17.2,26.Sep.17,cal,-54500,-52724,-17.6,-4.1,-17.1,-1.1288,-5.3578,9.3306,-2.5575,16.6673,-3.8698,1.4006,2
 MnCl+,MnCl(+),MnCl+,aq,SSWS97,DEW17.4,26.Sep.17,cal,-86290,-88280,12,24.63,6.3,2.9207,-1.5023,6.0978,-2.7169,23.9969,1.9824,0.3686,1
@@ -129,7 +141,7 @@
 Na(Ac)2-,Na(CH3COO)2(-1),Na(CH3COO)2-1,aq,SK93,DEW17.3,26.Sep.17,cal,-238470,-292400,44,170,103.2,22.0247,16.6865,-9.1534,-3.4688,114.6669,31.5944,0.9628,-1
 NaCl,NaCl(0),NaCl,aq,SSWS97,DEW17.3,26.Sep.17,cal,-92910,-96120,28,8.51,24,6.1632,1.5849,3.5092,-2.8445,10.8029,-1.3014,-0.038,0
 NaCO3-,NaCO3(-),NaCO3-,aq,SBS13,DEW17.30,26.Sep.17,cal,-190562,,8,-1,27.8,7.6427,2.9935,2.3281,-2.9028,19.473,-3.2383,1.5079,-1
-NaHCO3,NaHCO3(0),NaHCO3,aq,SBS13,DEW17.31,26.Sep.17,cal,-203088,-150000,31,73.9,36.72,9.61,2.56,1.01,-2.88,55.5,12,0.65,0
+NaHCO3,NaHCO3(0),NaHCO3,aq,SBS13,DEW19.1,30.Jun.20,cal,-203100,-219552,32,62,39,9.4783,4.7412,0.8627,-2.975,49.8727,9.5948,0.8,0
 NaHSiO3,NaHSiO3(0),NaHSiO3,aq,SSWS97,DEW17.4,26.Sep.17,cal,-307140,-333044,19,2.34,18.7,5.1339,0.6048,4.3309,-2.804,7.188,-2.5579,-0.038,0
 NaOH,NaOH(0),NaOH,aq,HP97,DEW17.32,26.Sep.17,cal,-100900,,6.5,42,12,3.9469,-0.5253,5.2786,-2.7573,32.6238,5.5208,0.2,0
 Nd+3,Nd(+3),Nd+3,aq,SSWS97,DEW17.2,26.Sep.17,cal,-160600,-166500,-49.5,-43.2,-43.1,-8.8788,-1.6852,14.3204,-2.7093,1.6237,-11.8344,2.255,3
@@ -169,6 +181,7 @@
 SeO3-2,SeO3(-2),SeO3-2,aq,SH88,DEW17.1,26.Sep.17,cal,-88400,-121700,3,-68.1,16.4,9.3228,-6.4175,2.1797,-2.5137,-4.5783,-16.9066,3.1658,-2
 SeO4-2,SeO4(-2),SeO4-2,aq,SH88,DEW17.1,26.Sep.17,cal,-105500,-143200,12.9,-60.2,20.7,10.2644,-6.1491,1.496,-2.5248,-1.2987,-15.2973,3.0192,-2
 Si2O4,Si2O4(0),Si2O4,aq,SHA14,DEW17.37,26.Sep.17,cal,-400751,-427304,18,49,40,10.0724,2.6931,0.6715,-2.8903,35.8049,6.9467,0.1,0
+Si3O6,Si3O6,Si3O6(0),aq,HS19,DEW19.1,30.Jun.20,cal,-590200,-656130,13,119,67.7,15.1481,10.1393,-3.6636,-3.1982,85.1208,21.2057,1,0
 SiO2,SiO2(0),SiO2,aq,SHA14,DEW17.37,26.Sep.17,cal,-199557,-213937,5.3,27.7,18,4.8998,1.409,4.4066,-2.8372,25.7171,2.6079,0.36,0
 Sm+2,Sm(+2),Sm+2,aq,SH88,DEW17.1,26.Sep.17,cal,-123000,-120500,-6.2,3.7,-5.7,2.8947,-8.2497,6.8469,-2.438,19.6532,-2.2808,1.2285,2
 Sm+3,Sm(+3),Sm+3,aq,SH88,DEW17.1,26.Sep.17,cal,-159100,-165200,-50.7,-43.3,-42,-8.4354,-2.0104,14.0474,-2.6959,1.9384,-11.8547,2.2955,3

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-30 14:45:56 UTC (rev 535)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-06-30 15:57:14 UTC (rev 536)
@@ -37,6 +37,7 @@
 Ber90.1,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","almandine and ilmenite: modified H and/or S",http://ammin.geoscienceworld.org/content/75/3-4/328
 Eva90,"B. W. Evans",1990,"Lithos 25, 3-23","glaucophane and pumpellyite",https://doi.org/10.1016/0024-4937(90)90003-J
 Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.",
+OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-Hückel extended term parameter (<i>b</i><sub>$\gamma$</sub>)",https://doi.org/10.1016/0016-7037(90)90368-U
 SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
 HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,http://pubs.er.usgs.gov/publication/70016664
 SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
@@ -137,7 +138,6 @@
 Got04,"M. Gottschalk",2004,"Rev. Mineral. Geochem. 56, 83-124","zoisite, clinozoisite, and epidote",https://doi.org/10.2138/gsrmg.56.1.83
 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z
 SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001
-KUP+05,"R. Kessel et al.",2005,"Earth Planet. Sci. Lett. 237, 873-892",HSiO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/j.epsl.2005.06.018
 VPV05,"O. Vidal, T. Parra and P. Viellard",2005,"Am. Mineral. 90, 347-358",Fe-amesite,https://doi.org/10.2138/am.2005.1554
 ZZX+05,"Y. Zhu et al.",2005,"J. Hazard. Mater. A120, 37-44","barium arsenate and barium hydrogen arsenate: G",https://doi.org/10.1016/j.jhazmat.2004.12.025
 ARHB06,"C. Akilan et al.",2006,"ChemPhysChem 7, 2319-2330",MgSO<sub>4</sub>,https://doi.org/10.1002/cphc.200600342
@@ -181,11 +181,11 @@
 LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",https://doi.org/10.1016/j.gca.2011.11.041
 LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",https://doi.org/10.1016/j.gca.2011.11.041
 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
-SBS13,"A. Stefánsson, P. Benézéth and J. Schott",2013,"Geochim. Cosmochim. Acta 120, 600-611","NaCO<sub>3</sub><sup>-</sup> and NaHCO<sub>3</sub>",https://doi.org/10.1016/j.gca.2013.04.023
+SBS13,"A. Stefánsson, P. Benézéth and J. Schott",2013,"Geochim. Cosmochim. Acta 120, 600-611","NaCO<sub>3</sub><sup>-</sup>",https://doi.org/10.1016/j.gca.2013.04.023
 TBZ+13,"B. R. Tagirov et al.",2013,"Geochim. Cosmochim. Acta 117, 348-373","Pd<sup>+2</sup> and complexes",https://doi.org/10.1016/j.gca.2013.03.047
 AP14,"N. N. Akinfiev and A. V. Plyasunov",2014,"Geochim. Cosmochim. Acta 126, 338-351","B(OH)<sub>3</sub>, Si(OH)<sub>4</sub>, and As(OH)<sub>3</sub>",https://doi.org/10.1016/j.gca.2013.11.013
 AT14,"N. N. Akinfiev and B. R. Tagirov",2014,"Geochem. Int. 52, 197-214","Zn<sup>+2</sup> and complexes",https://doi.org/10.1134/S0016702914030021
-FDM+14,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","CO<sub>2</sub>, HCO<sub>3</sub><sup>-</sup>, CO<sub>3</sub><sup>-2</sup>, Ca(HCO<sub>3</sub>)<sup>+</sup>, CaCO<sub>3</sub>",https://doi.org/10.1016/j.gca.2014.01.030
+FDM+14,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","CO<sub>2</sub>, HCO<sub>3</sub><sup>-</sup>, CO<sub>3</sub><sup>-2</sup>, CaCO<sub>3</sub>, Ca<sup>+2</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","corrected H of AuHS",https://doi.org/10.1144/SP402.4
@@ -219,11 +219,11 @@
 CHNOSZ.7,"J. M. Dick",2019,"CHNOSZ package documentation","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",http://chnosz.net
 CHNOSZ.8,"J. M. Dick",2019,"CHNOSZ package documentation","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",http://chnosz.net
 LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine HKF parameters",https://doi.org/10.1016/j.jct.2017.04.005
-DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as @PS01)",http://www.dewcommunity.org
+DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as in @PS01)",http://www.dewcommunity.org
 DEW17.02,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(ethanol: parameters in DEW spreadsheet are different from @PS01; no comment provided)",http://www.dewcommunity.org
-DEW17.03,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(parameters in DEW spreadsheet are the same as @FDM+14)",http://www.dewcommunity.org
-DEW17.04,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(Ar, Xe: parameters in DEW spreadsheet are the same as @SHS89)",http://www.dewcommunity.org
-DEW17.05,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(Al<sup>+3</sup>: parameters in DEW spreadsheet are the same as @SSWS97)",http://www.dewcommunity.org
+DEW17.03,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(parameters in DEW spreadsheet are the same as in @FDM+14)",http://www.dewcommunity.org
+DEW17.04,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(Ar, Xe: parameters in DEW spreadsheet are the same as in @SHS89)",http://www.dewcommunity.org
+DEW17.05,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(Al<sup>+3</sup>: parameters in DEW spreadsheet are the same as in @SSWS97)",http://www.dewcommunity.org
 DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for ions",http://www.dewcommunity.org
 DEW17.2,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for cations",http://www.dewcommunity.org
 DEW17.3,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a<sub>1</sub> for complex species",http://www.dewcommunity.org
@@ -241,7 +241,6 @@
 DEW17.17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Revised 1/22/15 based on V at 25 C from @ZW07 and predicted a<sub>1</sub>, a<sub>2</sub>, and a<sub>4</sub>; c<sub>1</sub> and c<sub>2</sub> from fits to delCpr protonation of @ZW07; S from fitting temperature dependence of logK from @ZW07; omega predicted from S using ion correlation.",http://www.dewcommunity.org
 DEW17.18,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Revised 1/22/15 based on fitting Cp and V vs T data from @HDM+94 + revised correlation for a<sub>1</sub> from @SHA14; omega from delCPr above 100 °C [@ZW07]; G, H, and S from @AH97b",http://www.dewcommunity.org
 DEW17.19,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Regression of @RS87 & @TZA97 with new full correlations",http://www.dewcommunity.org
-DEW17.20,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Revised late Oct. (2014) to fit @BM77 along Psat. and high pressure logK's from fitting @KUP+05 eclogite solubility measurements.",http://www.dewcommunity.org
 DEW17.21,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","HSO<sub>3</sub><sup>-</sup>: revised using published estimated V and pred. a<sub>1</sub> from new correlation",http://www.dewcommunity.org
 DEW17.22,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","isobutane: G, H, S, Cp, V from @SH90; a<sub>1</sub> estimated with @SHA14; c2 estimated with a new hydrocarbon correlation.",http://www.dewcommunity.org
 DEW17.23,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","May, 2017 Fitted to logKs from @OH88 + retrieved logKs from Hemley experiments at 1.0 kb using the HCl referred to above",http://www.dewcommunity.org
@@ -248,10 +247,8 @@
 DEW17.25,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Revised G, S and Cp to fit @Noy07 & @SGX+06 with a<sub>1</sub> of the complex equal to the sum of the a<sub>1</sub> values of the ions",http://www.dewcommunity.org
 DEW17.26,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","Fit to @SBS14 & @SH77; plus revised V increased so that a<sub>1</sub> of the complex is the sum of the a<sub>1</sub> values of the ions",http://www.dewcommunity.org
 DEW17.27,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgCO<sub>3</sub>: @SSH97 revised volume increased in order that a<sub>1</sub> of the complex is the sum of the a<sub>1</sub> values of the ions; and Cp revised using isocoulombic reln with CaCO3,aq; also omega is set to +0.3 as for all neutral metal complexes.",http://www.dewcommunity.org
-DEW17.28,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgOH<sup>+</sup>: Revised by Dimitri, March, 2015",http://www.dewcommunity.org
 DEW17.29,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","S, Cp, V, omega from fit to @ARHB06 and @FDM94",http://www.dewcommunity.org
 DEW17.30,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaCO<sub>3</sub><sup>-</sup>: Fit to @SBS13 (80 to 200 C) & @GTS61 (at 25 C) to get G, S and Cp;  with a<sub>1</sub> pred. from the sum of the ions and used to predict the volume",http://www.dewcommunity.org
-DEW17.31,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaHCO<sub>3</sub>: Fit to @SBS13 (80 to 200 C) & @Nak71 (25 C) to get G, S and Cp;  with V, a<sub>1</sub>, and omega from fitting high PT Raman data (Facq et al., 2015)",http://www.dewcommunity.org
 DEW17.32,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaOH: Fitted to @HP97 data with a<sub>1</sub> pred. from the sum of the ions and used to predict the volume",http://www.dewcommunity.org
 DEW17.33,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","August 16th, 2013 fit to @BL06",http://www.dewcommunity.org
 DEW17.34,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propane: @SH90 with new a<sub>1</sub>-a<sub>4</sub> based on revised correlation to predict a<sub>1</sub> in Sverjensky et al. (2013)",http://www.dewcommunity.org
@@ -264,4 +261,11 @@
 DEW17.101,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","formate and lactate: revised with new predicted a<sub>1</sub> for ions",https://doi.org/10.1016/0016-7037(90)90429-O
 BDat17.1,"D. A. Sverjensky et al.",2017,"berman.dat file in SUPCRT92b.zip on the DEW website","antigorite: "Oct. 21, 2016: Revised volume coefficients consistent with @HDR06 and @YIY+14 "",http://www.dewcommunity.org/resources.html
 AKAE19,"M. R. Azadi et al.",2019,"Fluid Phase Equilib. 480, 25-40","metal-glycinate complexes",https://doi.org/10.1016/j.fluid.2018.10.002
+DEW19,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values listed in DEW spreadsheet)",http://www.dewcommunity.org
+DEW19.1,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(values from @HS19 listed in DEW spreadsheet)",http://www.dewcommunity.org
+DEW19.2,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","MgOH<sup>+</sup>: Revised by Dimitri, January, 2019; with minimum volume needed",http://www.dewcommunity.org
+DEW19.3,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","CaO: Fitted by Dimitri to high PT retrieval's from Fang",http://www.dewcommunity.org
+DEW19.4,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","glycinate: @AH97b for the G, H, S, Cp, V",http://www.dewcommunity.org
+DEW19.5,"D. A. Sverjensky et al.",2019,"Deep Earth Water (DEW) spreadsheet","(Ca<sup>+2</sup>: values listed in DEW spreadsheet)",http://www.dewcommunity.org
+HS19,"F. Huang and D. A. Sverjensky",2019,"Geochim. Cosmochim. Acta 254, 192-230","ions and metal complexes",https://doi.org/10.1016/j.gca.2019.03.027
 LA19,"D. E. LaRowe and J. P. Amend",2019,"Geomicrobiol. J. 36, 492-505","dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid",https://doi.org/10.1080/01490451.2019.1573278