[CHNOSZ-commits] r170 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT inst/extdata/thermo man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 22 17:46:33 CET 2017
Author: jedick
Date: 2017-02-22 17:46:33 +0100 (Wed, 22 Feb 2017)
New Revision: 170
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/Marini_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Tardy_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Tremaine_aq.csv
pkg/CHNOSZ/inst/extdata/thermo/BZA10.csv
pkg/CHNOSZ/inst/extdata/thermo/Ste01.csv
Removed:
pkg/CHNOSZ/demo/add.obigt.R
pkg/CHNOSZ/inst/extdata/OBIGT/Other_aq.csv
pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/anim.R
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/data/thermo.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/demo/dehydration.R
pkg/CHNOSZ/demo/protein.equil.R
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv
pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/transfer.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/tests/testthat/test-subcrt.R
pkg/CHNOSZ/tests/testthat/test-util.data.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/eos-regress.Rmd
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
Log:
remove OBIGT-2.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-22 16:46:33 UTC (rev 170)
@@ -1,6 +1,6 @@
Date: 2017-02-22
Package: CHNOSZ
-Version: 1.0.8-59
+Version: 1.0.8-60
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/anim.R
===================================================================
--- pkg/CHNOSZ/R/anim.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/R/anim.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -7,9 +7,6 @@
# we depend on an empty png directory
if(!"png" %in% dir()) stop("directory 'png' not present")
else if(length(dir("png")) > 0) stop("directory 'png' not empty")
- # add supplementary data (from default location of data/OBIGT-2.csv)
- # which includes properties for the metabolites
- add.obigt()
# expand default logfO2 range if we're at high temperature
if(high.T & missing(redox)) redox <- list(O2=c(-100,-40))
# the name of 'redox' should be either O2 or H2
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/R/examples.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -27,7 +27,7 @@
cat("Time elapsed: ", proc.time() - .ptime, "\n")
}
-demos <- function(which=c("sources", "protein.equil", "add.obigt", "affinity", "NaCl", "density",
+demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
"ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic",
"copper", "solubility", "wjd", "dehydration", "bugstab", "Shh", "activity_ratios"), to.file=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/R/util.data.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -97,14 +97,9 @@
return(ispecies)
}
-add.obigt <- function(file=system.file("extdata/thermo/OBIGT-2.csv",package="CHNOSZ"),
- force=FALSE,E.units="cal") {
+add.obigt <- function(file, force=FALSE, E.units="cal") {
# add/replace entries in thermo$obigt from values saved in a file
# only replace if force==TRUE
- if(missing(file)) {
- # we use force=TRUE for the default data file
- if(missing(force)) force <- TRUE
- }
thermo <- get("thermo")
to1 <- thermo$obigt
id1 <- paste(to1$name,to1$state)
@@ -192,12 +187,6 @@
ns1.2 <- sapply(x$key, function(x) length(which(thermo$obigt$ref2==x)) )
ns1 <- ns1 + ns1.2
ns1[ns1==0] <- ""
- # count the times each source is listed in OBIGT-2.csv
- o2 <- read.csv(system.file("extdata/thermo/OBIGT-2.csv", package = "CHNOSZ"))
- ns2 <- sapply(x$key, function(x) length(which(o2$ref1==x)) )
- ns2.2 <- sapply(x$key, function(x) length(which(o2$ref2==x)) )
- ns2 <- ns2 + ns2.2
- ns2[ns2==0] <- ""
# count the times each source is listed in protein.csv
npr <- sapply(x$key, function(x) length(which(thermo$protein$ref==x)) )
npr[npr==0] <- ""
@@ -207,7 +196,7 @@
nst <- sapply(x$key, function(x) length(which(stressdat[2,]==x)) )
nst[nst==0] <- ""
# append the counts to the table to be shown
- x <- c(x,list(ns1=ns1,ns2=ns2,npr=npr,nst=nst))
+ x <- c(x,list(ns1=ns1,npr=npr,nst=nst))
# title to display for web page
title <- "Sources of Thermodynamic Data in CHNOSZ"
### the following is adapted from print.findFn in package 'sos'
@@ -233,7 +222,6 @@
.cat("<h3>Click on column headers to sort</h3>")
.cat("<h3>Columns 'n..' give number of times each reference appears in data tables:</h3>")
.cat("ns1: 'ref1' and 'ref2' in data/OBIGT.csv<br>")
- .cat("ns2: 'ref1' and 'ref2' in extdata/thermo/OBIGT-2.csv<br>")
.cat("npr: 'ref' in data/protein.csv<br>")
.cat("nst: second row in data/stress.csv<br><p>")
### start table and headers
@@ -408,12 +396,8 @@
# and among G, H, S values
# 20110808 jmd replaces 'check=TRUE' argument of info()
checkfun <- function(what) {
- # looking at thermo$obigt or OBIGT-2.csv
+ # looking at thermo$obigt
if(what=="OBIGT") to <- get("thermo")$obigt
- else if(what=="OBIGT-2") {
- file <- system.file("extdata/thermo/OBIGT-2.csv",package="CHNOSZ")
- to <- read.csv(file,as.is=1:7)
- }
ntot <- nrow(to)
# where to keep the results
DCp <- DV <- DG <- rep(NA,ntot)
@@ -441,10 +425,8 @@
out <- data.frame(table=what,ispecies=1:ntot,name=to$name,state=to$state,DCp=DCp,DV=DV,DG=DG)
return(out)
}
- # check both databases in CHNOSZ
- out1 <- checkfun("OBIGT")
- out2 <- checkfun("OBIGT-2")
- out <- rbind(out1,out2)
+ # check OBIGT database in CHNOSZ
+ out <- checkfun("OBIGT")
# set differences within a tolerance to NA
out$DCp[abs(out$DCp) < 1] <- NA
out$DV[abs(out$DV) < 1] <- NA
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/data/refs.csv 2017-02-22 16:46:33 UTC (rev 170)
@@ -5,29 +5,16 @@
AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4
APW+05,"J. Aguilera, T. Petit et al.",2001,"FEMS Yeast Res. 5, 579-593",http://dx.doi.org/10.1016/j.femsyr.2004.09.009
AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
-AVZP06,"N. N. Akinfiev, M. V. Voronin et al.",2006,"Geochem. Int. 44, 867-878",http://dx.doi.org/10.1134/S0016702906090035
-AZ01,"N. N. Akinfiev and A. V. Zotov",2001,"Geochem. Int. 39, 990-1006",http://www.maik.ru/cgi-perl/search.pl?type=abstract&name=geochem&number=10&year=1&page=990
-AZ99,"N. Akinfiev and A. Zotov",1999,"Geochim. Cosmochim. Acta 63, 2025-2041",http://dx.doi.org/10.1016/S0016-7037(98)00304-4
BBA+03,"B. Boeckmann, A. Bairoch et al.",2003,"Nucleic Acids Res. 31, 365-370",http://dx.doi.org/10.1093/nar/gkg095
-BDP+97,"P. Benezeth, I. I. Diakonov et al.",1997,"Geochim. Cosmochim. Acta 61, 1345-1357",http://dx.doi.org/10.1016/S0016-7037(97)00012-4
BH83a,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2
BWP+03,"V. M. Boer, J. H. de Winde et al.",2003,"J. Biol. Chem. 278, 3265-3274",http://dx.doi.org/10.1074/jbc.M209759200
-BZA10,"E. F. Bazarkina, A. V. Zotov and N. N. Akinfiev",2010,"Geol. Ore Deposits 52, 167-178",http://dx.doi.org/10.1134/S1075701510020054
-CGM+81,"S. Cabani, P. Gianni, V. Mollica and L. Lepori",1981,"J. Solution Chem. 10, 563-595",http://dx.doi.org/10.1007/BF00646936
CHNOSZ,"J. M. Dick",2007,"CHNOSZ package documentation",http://chnosz.net
CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
-CSM+07,"M. Censky, J. Sedlbauer et al.",2007,"Geochim. Cosmochim. Acta 71, 580-603",http://dx.doi.org/10.1016/j.gca.2006.10.022
CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968
Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, U.C. Berkeley",
DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
-DPB+97,"I. I. Diakonov, G. S. Pokrovski et al.",1997,"Geochim. Cosmochim. Acta 61, 1333-1343",http://dx.doi.org/10.1016/S0016-7037(97)00011-2
-DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",http://dx.doi.org/10.1016/0016-7037(95)00403-3
-DRT98,"I. I. Diakonov, K. V. Ragnarsdottir and B. R. Tagirov",1998,"Chem. Geol. 151, 327-347",http://dx.doi.org/10.1016/S0009-2541(98)00088-6
-DS09,"P. Dalla-Betta and M. Schulte",2009,"Int. J. Mol. Sci. 10, 2809-2837",http://dx.doi.org/10.3390/ijms10062809
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-DSM+99,"I. I. Diakonov, J. Schott et al.",1999,"Geochim. Cosmochim. Acta 63, 2247-2261",http://dx.doi.org/10.1016/S0016-7037(99)00070-8
FDK+04,"P. M. B. Fernandes, T. Domitrovic et al.",2004,"FEBS Lett. 556, 153-160",http://dx.doi.org/10.1016/S0014-5793(03)01396-6
-FPC+04,"D. Fenclova, S. Perez-Casas, M. Costas, and V. Dohnal",2004,"J. Chem. Eng. Data 49, 1833-1838",http://dx.doi.org/10.1021/je049738c
GLL+98,"C. Godon, G. Lagniel et al.",1998,"J. Biol. Chem. 273, 22480-22489",http://dx.doi.org/10.1074/jbc.273.35.22480
GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005
Gur96,"S. Gurrieri",1996,"personal communication",
@@ -57,21 +44,15 @@
MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z
MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
-MWW09,"Art. A. Migdisov, A. E. Williams-Jones and T. Wagner",2009,"Geochim. Cosmochim. Acta 73, 7087-7109",http://dx.doi.org/10.1016/j.gca.2009.08.023
MYB+05,"L. M. Maurer, E. Yohannes et al.",2005,"J. Bacteriol. 187, 304-319",http://dx.doi.org/10.1128/JB.187.1.304-319.2005
Nei86,"F. C. Neidhardt",1986,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827
Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245
PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4
-PGS+96,"G. Pokrovski, R. Gout et al.",1996,"Geochim. Cosmochim. Acta 60, 737-749",http://dx.doi.org/10.1016/0016-7037(95)00427-0
PI04,"S. Phadtare and M. Inouye",2004,"J. Bacteriol. 186, 7007-7014",http://dx.doi.org/10.1128/JB.186.20.7007-7014.2004
PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292
PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964
-PPB+08,"E. Perfetti and G. S. Pokrovski et al.",2008,"Geochim. Cosmochim. Acta 72, 713-731",http://dx.doi.org/10.1016/j.gca.2007.11.017
-PRH+05,"G. S. Pokrovski, J. Roux et al.",2005,"Chem. Geol. 217, 127-145",http://dx.doi.org/10.1016/j.chemgeo.2005.01.006
PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
-PS98,"G. S. Pokrovski and J. Schott",1998,"Geochim. Cosmochim. Acta 62, 1631-1642",http://dx.doi.org/10.1016/S0016-7037(98)00081-7
PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
-PSS95,"G. S. Pokrovski, J. Schott and A. S. Sergeyev",1995,"Chem. Geol. 124, 253-265",http://dx.doi.org/10.1016/0009-2541(95)00057-S
RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030
RGM+99,"C. S. Richmond, J. D. Glasner et al.",1999,"Nucleic Acids Res. 27, 3821-3835",http://dx.doi.org/10.1093/nar/27.19.3821
RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131
@@ -86,7 +67,6 @@
Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V
Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
Sho95,"E. L. Shock",1990,"Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496
-Sho09,"E. L. Shock",2009,"Econ. Geol. 104, 1235-1248",http://dx.doi.org/10.2113/gsecongeo.104.8.1235
SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4
SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8
@@ -100,20 +80,12 @@
SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V
SS98,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSB+07,"M.Slavik, J. Sedlbauer, K. Ballerat-Busserolles, and V. Majer",2007,"J. Solution Chem. 36, 107-134",http://dx.doi.org/10.1007/s10953-006-9097-y
SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4
SSW+97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7
-Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250",http://dx.doi.org/10.1016/S0009-2541(00)00263-1
TBD+05,"S. L. Tai, V. M. Boer et al.",2005,"J. Biol. Chem. 280, 437-447",http://dx.doi.org/10.1074/jbc.M410573200
-TBZ+06,"B. R. Tagirov, N. N. Baranova et al.",2006,"Geochim. Cosmochim. Acta 70, 3689-3701",http://dx.doi.org/10.1016/j.gca.2006.05.006
TDW+07,"S. L. Tai, P. Daran-Lapujade et al.",2007,"Mol. Biol. Cell. 18, 5100-5112",http://dx.doi.org/10.1091/mbc.E07-02-0131
-TS01,"B. Tagirov and J. Schott",2001,"Geochim. Cosmochim. Acta 65, 3965-3992",http://dx.doi.org/10.1016/S0016-7037(01)00705-0
TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X
TWS+06,"E. T. Hayes, J. C. Wilks et al.",2006,"BMC Microbiol. 6, 89",http://dx.doi.org/10.1186/1471-2180-6-89
-TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",1997,"Geochim. Cosmochim. Acta 61, 4267-4280",http://dx.doi.org/10.1016/S0016-7037(97)00274-3
-TZS+07,"B. Tagirov, A. Zotov et al.",2007,"Geochim. Cosmochim. Acta 71, 1689-1708",http://dx.doi.org/10.1016/j.gca.2007.01.003
+UniProt,"The UniProt Consortium",2017,"The UniProt knowledgebase",http://www.uniprot.org/
WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
-WP02,"W. Wagner and A. Pruss",2002,"J. Phys. Chem. Ref. Data 31, 387-355",http://dx.doi.org/10.1063/1.1461829
-ZKO06,"A. V. Zotov, L. A. Koroleva and E. G. Osadchii",2006,"Geochem. Int. 44, 384-394",http://dx.doi.org/10.1134/S0016702906040057
-ZSA03,"A. V. Zotov, N. D. Shikina and N. N. Akinfiev",2003,"Geochim. Cosmochim. Acta 67, 1821-1836",http://dx.doi.org/10.1016/S0016-7037(02)01281-4
Modified: pkg/CHNOSZ/data/thermo.R
===================================================================
--- pkg/CHNOSZ/data/thermo.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/data/thermo.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -9,7 +9,8 @@
local({
# create obigt data frame
- sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", "Canovas", "Other", "CHNOSZ"), "_aq")
+ sources_aq <- paste0(c("H2O", "Shock", "Amend", "Schulte", "LaRowe", "Dick", "Canovas",
+ "Tardy", "Tremaine", "Marini", "CHNOSZ"), "_aq")
sources_cr <- paste0(c("Helgeson", "Shock", "Richard", "LaRowe", "Other", "CHNOSZ"), "_cr")
sources_liq <- paste0(c("Richard", "LaRowe"), "_liq")
sources_gas <- paste0(c("Wagman", "Shock", "Richard", "Other"), "_gas")
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/demo/00Index 2017-02-22 16:46:33 UTC (rev 170)
@@ -1,6 +1,5 @@
sources cross-check the reference list with the thermodynamic database
protein.equil chemical activities of two proteins in metastable equilibrium
-add.obigt a couple of diagrams using the secondary thermodynamic database
affinity affinities of metabolic reactions and amino acid synthesis
NaCl equilibrium constant for aqueous NaCl dissociation
density density of H2O, inverted from IAPWS-95 equations
Deleted: pkg/CHNOSZ/demo/add.obigt.R
===================================================================
--- pkg/CHNOSZ/demo/add.obigt.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/demo/add.obigt.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -1,37 +0,0 @@
-## pe-pH diagram for hydrated iron sulfides,
-## goethite and pyrite, after Majzlan et al., 2006
-## Majzlan, J., Navrotsky, A., McClesky, R. B. and Alpers, C. N. (2006) Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe2(SO4)3(H2O)5. \emph{Eur. J. Mineral.} \bold{18}, 175--186. \url{http://dx.doi.org/10.1127/0935-1221/2006/0018-0175}
-# add some of these species to the database
-add.obigt()
-basis(c("Fe+2", "SO4-2", "H2O", "H+", "e-"),
- c(0, log10(3), log10(0.75), 999, 999))
-species(c("rhomboclase", "ferricopiapite", "hydronium jarosite",
- "goethite", "melanterite", "pyrite"))
-a <- affinity(pH=c(-1, 4, 256), pe=c(-5, 23, 256))
-d <- diagram(a, main="Fe-S-O-H, after Majzlan et al., 2006")
-# the first four species show up along the top of the diagram
-stopifnot(all.equal(unique(t(d$predominant)[256,]), 1:4))
-water.lines(yaxis="pe")
-text(3, 22, describe.basis(thermo$basis[2:3,], digits=2, oneline=TRUE))
-text(3, 21, describe.property(c("T", "P"), c(25, 1), oneline=TRUE))
-# reset the database
-data(thermo)
-
-## Aqueous Aluminum Species F-/OH-, after Tagirov and Schott, 2001
-## Tagirov, B. and Schott, J. (2001) Aluminum speciation in crustal fluids revisited. \emph{Geochim. Cosmochim. Acta} \bold{65}, 3965--3992. \url{http://dx.doi.org/10.1016/S0016-7037(01)00705-0}
-# some of the species are not in the default databse
-add.obigt()
-# the 999s have no effect on the diagram:
-# pH and log_a(F-) are plotting variables
-# O2 is not in the formation reactions
-# Al+3 is the balanced quantity
-basis(c("Al+3", "F-", "H+", "O2", "H2O"), c(rep(999, 4), 0))
-species(c("Al+3", "Al(OH)4-", "AlOH+2", "Al(OH)2+", "Al(OH)3",
- "AlF+2", "AlF2+", "AlF3", "AlF4-", "Al(OH)2F2-", "Al(OH)2F",
- "AlOHF2"), "aq")
-a <- affinity(pH=c(0, 10), "F-"=c(-1, -9), T=200)
-diagram(a, fill="heat")
-title(main=paste("Aqueous aluminium species, T=200 C, P=Psat\n",
- "after Tagirov and Schott, 2001"))
-# restore thermodynamic database to default
-data(thermo)
Modified: pkg/CHNOSZ/demo/dehydration.R
===================================================================
--- pkg/CHNOSZ/demo/dehydration.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/demo/dehydration.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -14,9 +14,6 @@
plot(range(T), c(-2, 1), type="n", xlab="T, °C", ylab="log K")
title(main="Dehydration reactions")
-# add.obigt is used to add malate and fumarate,
-# and epsomite and hexahydrite to thermo$obigt
-add.obigt()
reactants <- c("[AABB]", "[AABB]", "malate-2", "goethite", "gypsum", "epsomite", "ethanol")
products <- c("[UPBB]", "[PBB]", "fumarate-2", "hematite", "anhydrite", "hexahydrite", "ethylene")
rstate <- c("aq", "cr", "aq", "cr", "cr", "cr", "aq")
Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/demo/protein.equil.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -25,3 +25,5 @@
Aref.residue <- Astar.residue - loga.residue # 0.446, after Eq. 16
# A-star of the residue in natural log units (A/RT)
log(10) * Astar.residue # 0.4359, after Eq. 23
+# forget about the old [Met] group for whatever comes next
+data(thermo)
Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/demo/sources.R 2017-02-22 16:46:33 UTC (rev 170)
@@ -6,13 +6,8 @@
# sources in the primary thermodynamic database
os1 <- thermo$obigt$ref1
os2 <- thermo$obigt$ref2
-# sources also in the supplemental database (OBIGT-2.csv)
-add.obigt()
-os3 <- thermo$obigt$ref1
-os4 <- thermo$obigt$ref2
-data(thermo)
# all of the thermodynamic data sources - some of them might be NA
-obigt.source <- unique(c(os1,os2,os3,os4))
+obigt.source <- unique(c(os1,os2))
obigt.source <- obigt.source[!is.na(obigt.source)]
# sources of protein compositions
protein.source <- thermo$protein$ref
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-22 16:46:33 UTC (rev 170)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-59 (2017-02-22)
+CHANGES IN CHNOSZ 1.0.8-60 (2017-02-22)
---------------------------------------
DOCUMENTATION:
@@ -76,30 +76,35 @@
- Add syslab() and ratlab() to make formatted expressions for
sets of thermodynamic components and activity ratios.
-NEW DATA:
+NEW AND OLD DATA:
+- Split OBIGT.csv and OBIGT-2.csv into multiple files according to
+ author names. All files are now under extdata/OBIGT/.
+
- Canovas_aq.csv: Add data for citric acid cycle metabolites from Canovas and
Shock, 2016.
- CHNOSZ_aq.csv: Add H4SiO4 pseudospecies (pseudo-H4SiO4); see calculations
in eos-regress.Rmd.
-- OBIGT-2.csv: Rename H4SiO4 to H4SiO4_Ste01 (Steffánson, 2001).
+- Remove superseded data previously in OBIGT-2.csv: citric acid cycle
+ metabolites from Dalla-Betta and Schulte, 2009.
-- extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a,
- SS98_Fig5b, PM90 (all used by anintro.Rmd).
+- Remove superseded data previously in OBIGT-2.csv: methionine and [Met]
+ from Dick et al., 2006. Examples that require the old group additivity
+ parameters can modify the database using:
+ `mod.obigt("[Met]", G=-35245, H=-59310)`.
-DATA CHANGES:
+- Move two datasets that conflict with the primary database, but are
+ used in tests, examples, or vignettes, from OBIGT-2.csv to
+ extdata/thermo (Ste01.csv and BZA10.csv).
-- Split OBIGT.csv into multiple files according to author names.
+- Remove other conflicting datasets previously in OBIGT-2.csv, including
+ aluminum species from Tagirov and Schott, 2001.
-- OBIGT-2.csv: remove data for citric acid cycle metabolites from
- Dalla-Betta and Schulte, 2009; thioester species have been kept.
+- extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a,
+ SS98_Fig5b, PM90 (all used by anintro.Rmd).
-- OBIGT-2.csv: remove data for methionine and [Met] from Dick et al.,
- 2006. Examples that require the old group additivity parameters
- modify the database using: `mod.obigt("[Met]", G=-35245, H=-59310)`.
-
BUG FIXES:
- Correct charge (-2) of NAD(red)-2 in LaRowe_aq.csv. Thanks to Peter
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-02-22 13:06:35 UTC (rev 169)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv 2017-02-22 16:46:33 UTC (rev 170)
@@ -234,3 +234,8 @@
wollastonite,Wo,CaSiO3,cr,HDN+78,SH88,15.Mar.90,-369225,-389590,19.6,NA,39.93,26.64,3.6,-6.52,0,0,0,0,1400
wurtzite,Wur,ZnS,cr,HDN+78,NA,5.May.78,-44810,-45850,14.064,NA,23.846,11.82,1.16,-1.04,0,0,0,0,1300
zoisite,Zo,Ca2Al3Si3O12(OH),cr,HDN+78,SH88,15.Mar.90,-1549179,-1643691,70.74,NA,135.9,106.118,25.214,-27.145,0,0,0,0,700
+berndtite,Brn,SnS2,cr,JH85b,NA,5.May.78,-34750,-36700,20.9,NA,40.96,15.51,4.2,0,0,0,0,0,1000
+cassiterite,Cst,SnO2,cr,JH85b,NA,5.May.78,-124260,-138800,12.5,NA,21.55,17.246,2.8026,-4.9001,0,0,0,0,1500
+romarchite,Sn-Ox,SnO,cr,JH85b,NA,5.May.78,-61459,-68340,13.66,NA,20.895,9.55,3.5,0,0,0,0,0,1237
+tin,Sn,Sn,cr1,JH85b,NA,Aug.85,0,0,12.24,NA,16.289,4.42,6.3,0,0,0,0,0,505.06
+tin,Sn,Sn,cr2,JH85b,NA,Aug.85,679.802,1607.605,15.3519,NA,16.289,7.3,0,0,0,0,0,0,3000
Added: pkg/CHNOSZ/inst/extdata/OBIGT/Marini_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Marini_aq.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Marini_aq.csv 2017-02-22 16:46:33 UTC (rev 170)
@@ -0,0 +1,98 @@
+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
+NaH2AsO4,NA,NaH2AsO4,aq,MA07,MA10,12.Sep.07,-240179,-272608,41.2,37.8,41.1,7.3772,10.2352,1.1421,-3.2022,27.9202,4.6622,-0.038,0
+KH2AsO4,NA,KH2AsO4,aq,MA07,MA10,12.Sep.07,-244935,-274352,54.5,21.9,52.4,8.9277,14.0226,-0.484,-3.3587,18.6125,1.4173,-0.038,0
+MgH2AsO4+,NA,MgH2AsO4+,aq,MA07,MA10,12.Sep.07,-290910,-332717,-10.4,50.7,18.3,4.5105,3.2335,4.1483,-2.9127,42.265,7.2899,0.7009,1
+CaH2AsO4+,NA,CaH2AsO4+,aq,MA07,MA10,12.Sep.07,-314170,-348007,18.5,45.8,22.2,4.8949,4.1724,3.7452,-2.9515,35.3597,6.2862,0.2639,1
+SrH2AsO4+,NA,SrH2AsO4+,aq,MA07,MA10,12.Sep.07,-315896,-347841,27.3,40.1,22.9,4.9488,4.3041,3.6887,-2.957,30.8142,5.1312,0.1301,1
+MnH2AsO4+,NA,MnH2AsO4+,aq,MA07,MA10,12.Sep.07,-236482,-270828,14.5,53.5,23.3,5.0617,4.5799,3.5702,-2.9684,40.4264,7.8583,0.3244,1
+FeH2AsO4+,NA,FeH2AsO4+,aq,MA07,MA10,12.Sep.07,-205693,-243719,1,44.9,17.6,4.3531,2.849,4.3134,-2.8968,37.3097,6.1166,0.5283,1
+CoH2AsO4+,NA,CoH2AsO4+,aq,MA07,MA10,12.Sep.07,-193388,-232357,-1.5,45.2,13.9,3.8628,1.6516,4.8275,-2.8473,37.7921,6.1625,0.5664,1
+NiH2AsO4+,NA,NiH2AsO4+,aq,MA07,MA10,12.Sep.07,-193146,-233785,-7.1,36.4,10,3.358,0.4185,5.3569,-2.7963,33.4496,4.375,0.6516,1
+CuH2AsO4+,NA,CuH2AsO4+,aq,MA07,MA10,12.Sep.07,-166866,-204382,4.1,49.9,14.9,3.9712,1.9164,4.7138,-2.8583,39.7683,7.1249,0.4813,1
+ZnH2AsO4+,NA,ZnH2AsO4+,aq,MA07,MA10,12.Sep.07,-215927,-255372,-0.3,50.7,15.3,4.0397,2.0836,4.642,-2.8652,40.8741,7.2945,0.5485,1
+PbH2AsO4+,NA,PbH2AsO4+,aq,MA07,MA10,12.Sep.07,-187896,-215577,44.7,34.1,25,5.1359,4.7611,3.4924,-2.9759,24.9084,3.9167,-0.1328,1
+AlH2AsO4+2,NA,AlH2AsO4+2,aq,MA07,MA10,12.Sep.07,-299978,-350717,-57,34.9,-7.1,1.4491,-4.244,7.3587,-2.6036,44.5413,4.0694,1.9508,2
+FeH2AsO4+2,NA,FeH2AsO4+2,aq,MA07,MA10,12.Sep.07,-189949,-235535,-39.9,66.2,1.1,2.4901,-1.7013,6.267,-2.7087,60.4374,10.4402,1.6927,2
+NaHAsO4-,NA,NaHAsO4-,aq,MA07,MA10,12.Sep.07,-234025,-272938,19.4,11,16.4,4.464,3.12,4.197,-2.908,24.8601,-0.79,1.3274,-1
+KHAsO4-,NA,KHAsO4-,aq,MA07,MA10,12.Sep.07,-238754,-275247,30.7,3.9,26.1,5.7282,6.2078,2.8713,-3.0357,19.1455,-2.2322,1.1561,-1
+MgHAsO4,NA,MgHAsO4,aq,MA07,MA10,12.Sep.07,-282655,-326456,-17.1,-3.4,-0.5,1.6885,-3.6591,7.1076,-2.6278,3.8675,-3.7233,-0.038,0
+CaHAsO4,NA,CaHAsO4,aq,MA07,MA10,12.Sep.07,-306038,-344341,3.5,-5.6,2,2.0228,-2.8426,6.757,-2.6615,2.5879,-4.1694,-0.038,0
+SrHAsO4,NA,SrHAsO4,aq,MA07,MA10,12.Sep.07,-307750,-344917,9.8,-8.1,2.4,2.0851,-2.6905,6.6917,-2.6678,1.1155,-4.6827,-0.038,0
+MnHAsO4,NA,MnHAsO4,aq,MA07,MA10,12.Sep.07,-229564,-268033,0.7,-2.1,2.7,2.1148,-2.618,6.6606,-2.6708,4.592,-3.4707,-0.038,0
+FeHAsO4,NA,FeHAsO4,aq,MA07,MA10,12.Sep.07,-196961,-237958,-8.9,-5.9,-0.9,1.6263,-3.8112,7.1729,-2.6215,2.3717,-4.2448,-0.038,0
+CoHAsO4,NA,CoHAsO4,aq,MA07,MA10,12.Sep.07,-187516,-229240,-10.7,-5.8,-3.2,1.3102,-4.5832,7.5044,-2.5896,2.4302,-4.2244,-0.038,0
+NiHAsO4,NA,NiHAsO4,aq,MA07,MA10,12.Sep.07,-185083,-227995,-14.7,-9.7,-5.7,0.9749,-5.4021,7.8559,-2.5557,0.1514,-5.0188,-0.038,0
+CuHAsO4,NA,CuHAsO4,aq,MA07,MA10,12.Sep.07,-160044,-200797,-6.7,-3.7,-2.6,1.3964,-4.3727,7.414,-2.5983,3.6572,-3.7966,-0.038,0
+ZnHAsO4,NA,ZnHAsO4,aq,MA07,MA10,12.Sep.07,-209827,-252128,-9.9,-3.4,-2.4,1.4251,-4.3025,7.3838,-2.6012,3.8733,-3.7213,-0.038,0
+PbHAsO4,NA,PbHAsO4,aq,MA07,MA10,12.Sep.07,-180119,-214509,22.2,-10.7,3.7,2.2585,-2.267,6.5099,-2.6853,-0.4328,-5.2225,-0.038,0
+AlHAsO4+,NA,AlHAsO4+,aq,MA07,MA10,12.Sep.07,-295884,-343378,-46.1,-37.3,-8.2,1.0572,-5.2011,7.7697,-2.564,-4.1613,-10.6336,1.242,1
+FeHAsO4+,NA,FeHAsO4+,aq,MA07,MA10,12.Sep.07,-188188,-232211,-34.7,-23.4,-4.9,1.4545,-4.2306,7.353,-2.6042,2.37,-7.8022,1.0694,1
+NaAsO4-2,NA,NaAsO4-2,aq,MA07,MA10,12.Sep.07,-223700,-253943,48.5,-38.4,-17,0.2824,-7.0935,8.5822,-2.4858,6.8433,-10.8648,2.5085,-2
+KAsO4-2,NA,KAsO4-2,aq,MA07,MA10,12.Sep.07,-228428,-249049,84,-45.5,-9.64,1.1121,-5.0669,7.712,-2.5696,-2.2416,-12.307,1.9714,-2
+MgAsO4-,NA,MgAsO4-,aq,MA07,MA10,12.Sep.07,-271474,-307316,9.64,-55,-25.98,-1.3284,-11.0278,10.2713,-2.3232,-12.33,-14.2311,1.3662,-1
+CaAsO4-,NA,CaAsO4-,aq,MA07,MA10,12.Sep.07,-294913,-323114,37.4,-57.2,-25.5,-1.3685,-11.1259,10.3134,-2.3191,-17.4821,-14.6772,1.0531,-1
+SrAsO4-,NA,SrAsO4-,aq,MA07,MA10,12.Sep.07,-296243,-323239,43.9,-59.7,-25.41,-1.3889,-11.1758,10.3349,-2.317,-19.8655,-15.1905,0.9562,-1
+MnAsO4-,NA,MnAsO4-,aq,MA07,MA10,12.Sep.07,-218289,-247805,30.7,-53.7,-25.37,-1.2541,-10.8464,10.1934,-2.3307,-14.5434,-13.9785,1.339,-1
+FeAsO4-,NA,FeAsO4-,aq,MA07,MA10,12.Sep.07,-186668,-218541,21.7,-57.5,-26.07,-1.3653,-11.1181,10.3101,-2.3194,-15.504,-14.7525,1.2932,-1
+CoAsO4-,NA,CoAsO4-,aq,MA07,MA10,12.Sep.07,-177190,-210481,17.6,-57.4,-26.53,-1.4073,-11.2205,10.3541,-2.3152,-14.8722,-14.7322,1.3555,-1
+NiAsO4-,NA,NiAsO4-,aq,MA07,MA10,12.Sep.07,-176304,-211320,11.8,-61.3,-27.01,-1.4432,-11.3083,10.3918,-2.3116,-16.3404,-15.5266,1.4434,-1
+CuAsO4-,NA,CuAsO4-,aq,MA07,MA10,12.Sep.07,-151743,-183607,23.1,-55.3,-26.4,-1.4178,-11.2463,10.3651,-2.3141,-14.418,-14.3044,1.2716,-1
+ZnAsO4-,NA,ZnAsO4-,aq,MA07,MA10,12.Sep.07,-200121,-233853,18.9,-55,-26.36,-1.3907,-11.1799,10.3366,-2.3169,-13.6104,-14.229,1.3358,-1
+PbAsO4-,NA,PbAsO4-,aq,MA07,MA10,12.Sep.07,-169793,-194437,54.9,-62.3,-25.16,-1.4108,-11.2291,10.3577,-2.3148,-22.9414,-15.7303,0.7904,-1
+AlAsO4,NA,AlAsO4,aq,MA07,MA10,12.Sep.07,-285558,-330011,-35.9,-60.2,-9.75,0.418,-6.7624,8.44,-2.4995,-29.3427,-15.3014,-0.038,0
+FeAsO4,NA,FeAsO4,aq,MA07,MA10,12.Sep.07,-177862,-218546,-23.5,-84.8,-13.09,-0.0391,-7.8787,8.9193,-2.4533,-43.7161,-20.3124,-0.038,0
+NaH2AsO3,NA,NaH2AsO3,aq,MA07,MA10,12.Sep.07,-203270,-228832,39.7,28.4,32.7,6.2236,7.4178,2.3518,-3.0857,22.4338,2.7495,-0.038,0
+AgH2AsO3,NA,AgH2AsO3,aq,MA07,MA10,12.Sep.07,-123526,-147071,44.3,25.8,33,6.2709,7.5332,2.3022,-3.0905,20.9088,2.2178,-0.038,0
+MgH2AsO3+,NA,MgH2AsO3+,aq,MA07,MA10,12.Sep.07,-251410,-286183,-11.3,41.3,9.9,3.3617,0.4276,5.353,-2.7967,36.9078,5.3772,0.7149,1
+CaH2AsO3+,NA,CaH2AsO3+,aq,MA07,MA10,12.Sep.07,-274922,-301872,17.1,36.4,13.8,3.7486,1.3726,4.9473,-2.8358,30.0706,4.3735,0.2853,1
+SrH2AsO3+,NA,SrH2AsO3+,aq,MA07,MA10,12.Sep.07,-275601,-300702,25.8,30.7,14.5,3.8032,1.506,4.89,-2.8413,25.5459,3.2185,0.1538,1
+BaH2AsO3+,NA,BaH2AsO3+,aq,MA07,MA10,12.Sep.07,-276315,-297936,40.1,25.6,19.9,4.4634,3.1185,4.1977,-2.908,20.5926,2.1872,-0.0628,1
+CuH2AsO3+,NA,CuH2AsO3+,aq,MA07,MA10,12.Sep.07,-134368,-164924,3,40.5,6.5,2.8237,-0.8865,5.9172,-2.7424,34.4453,5.2122,0.499,1
+PbH2AsO3+,NA,PbH2AsO3+,aq,MA07,MA10,12.Sep.07,-153138,-174063,42.8,24.7,16.5,3.9918,1.9667,4.6922,-2.8603,19.6811,2.0039,-0.1047,1
+AlH2AsO3+2,NA,AlH2AsO3+2,aq,MA07,MA10,12.Sep.07,-266611,-309612,-55.5,25.5,-15.6,0.2882,-7.0795,8.5761,-2.4864,38.8545,2.1567,1.929,2
+FeH2AsO3+2,NA,FeH2AsO3+2,aq,MA07,MA10,12.Sep.07,-154392,-192413,-39.1,56.8,-7.3,1.3321,-4.5295,7.4813,-2.5918,54.8314,8.5274,1.6797,2
+LiCrO4-,NA,LiCrO4-,aq,AML10,NA,03.Jul.10,-246189,-276987,23.021,-1.86,25.17,5.6394,5.9909,2.9644,-3.0267,16.8298,-3.4143,1.2728,-1
+NaCrO4-,NA,NaCrO4-,aq,AML10,NA,03.Jul.10,-239025,-266828,38.364,-3.93,24.95,5.5308,5.7256,3.0783,-3.0157,13.4846,-3.8343,1.0404,-1
+KCrO4-,NA,KCrO4-,aq,AML10,NA,03.Jul.10,-243870,-269706,48.161,-16.63,33.98,6.7157,8.6197,1.8358,-3.1354,4.6973,-6.4214,0.8921,-1
+NH4CrO4-,NA,NH4CrO4-,aq,AML10,NA,03.Jul.10,-195220,-241227,50.414,1.05,43.22,7.9692,11.6814,0.5212,-3.2619,14.7104,-2.8209,0.858,-1
+BeCrO4,NA,BeCrO4,aq,AML10,NA,03.Jul.10,-268795,-304575,-14.001,-27.06,7.24,2.7431,-1.0832,6.0017,-2.7343,-9.9664,-8.5462,-0.038,0
+MgCrO4,NA,MgCrO4,aq,AML10,NA,03.Jul.10,-286677,-324405,-14.995,-26.44,6.66,2.6638,-1.277,6.0849,-2.7263,-9.6061,-8.4206,-0.038,0
+CaCrO4,NA,CaCrO4,aq,AML10,NA,03.Jul.10,-310665,-342487,6.948,-30.19,10.48,3.1862,-0.0009,5.537,-2.779,-11.7978,-9.1847,-0.038,0
+SrCrO4,NA,SrCrO4,aq,AML10,NA,03.Jul.10,-313068,-343782,13.152,-32.76,10.36,3.1693,-0.0424,5.5548,-2.7773,-13.2959,-9.707,-0.038,0
+BaCrO4,NA,BaCrO4,aq,AML10,NA,03.Jul.10,-312583,-340842,24.015,-35.77,14.65,3.7566,1.3921,4.9389,-2.8366,-15.0586,-10.3215,-0.038,0
+RaCrO4,NA,RaCrO4,aq,AML10,NA,03.Jul.10,-313122,-338458,35.729,-38.45,14.92,3.7932,1.4816,4.9005,-2.8403,-16.6254,-10.8678,-0.038,0
+MnCrO4,NA,MnCrO4,aq,AML10,NA,03.Jul.10,-233415,-265560,3.57,-24.78,10.63,3.2071,0.0501,5.5151,-2.7811,-8.6346,-8.0819,-0.038,0
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 170
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