[CHNOSZ-commits] r185 - in pkg/CHNOSZ: . R data demo inst inst/extdata man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 17 12:54:22 CET 2017
Author: jedick
Date: 2017-03-17 12:54:22 +0100 (Fri, 17 Mar 2017)
New Revision: 185
Removed:
pkg/CHNOSZ/inst/extdata/js/
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/data/protein.csv
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
remove sorttable.js
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-03-09 15:05:13 UTC (rev 184)
+++ pkg/CHNOSZ/DESCRIPTION 2017-03-17 11:54:22 UTC (rev 185)
@@ -1,6 +1,6 @@
-Date: 2017-03-09
+Date: 2017-03-17
Package: CHNOSZ
-Version: 1.0.8-73
+Version: 1.0.8-74
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2017-03-09 15:05:13 UTC (rev 184)
+++ pkg/CHNOSZ/R/util.data.R 2017-03-17 11:54:22 UTC (rev 185)
@@ -171,7 +171,7 @@
# list: the output of subcrt()
## first retrieve the sources table
thermo <- get("thermo")
- x <- thermo$refs
+ x <- thermo$refs[order(thermo$refs$note), ]
## show a table in the browser if 'key' is NULL
if(is.null(key)) {
# create the html links
@@ -181,49 +181,95 @@
x$citation[notlinked] <- cite[notlinked]
# remove the last (URL) component
#x$URL <- NULL
- x <- x[1:4]
- # count the times each source is listed in OBIGT.csv
- ns1 <- sapply(x$key, function(x) length(which(thermo$obigt$ref1==x)) )
- ns1.2 <- sapply(x$key, function(x) length(which(thermo$obigt$ref2==x)) )
- ns1 <- ns1 + ns1.2
- ns1[ns1==0] <- ""
- # count the times each source is listed in protein.csv
- npr <- sapply(x$key, function(x) length(which(thermo$protein$ref==x)) )
- npr[npr==0] <- ""
+ x <- x[1:5]
+ # count the number of times each source is cited in thermo$obigt
+ # e.g. if key is "Kel60" we match "Kel60 [S92]" but not "Kel60.1 [S92]"
+ # http://stackoverflow.com/questions/6713310/how-to-specify-space-or-end-of-string-and-space-or-start-of-string
+ # we also have to escape keys with "+" signs
+ ns1 <- sapply(x$key, function(x) sum(grepl(gsub("+", "\\+", paste0(x, "($|\\s)"), fixed=TRUE), thermo$obigt$ref1)) )
+ ns2 <- sapply(x$key, function(x) sum(grepl(gsub("+", "\\+", paste0(x, "($|\\s)"), fixed=TRUE), thermo$obigt$ref2)) )
+ number <- ns1 + ns2
+ number[number==0] <- ""
+ # now that we're using the sortTable() from w3schools.com, numbers are sorted like text
+ # add leading zeros to make the numbers sortable 20170317
+ # (the zeros disappear somewhere in the rendering of the page)
+ number <- formatC(number, width = 3, format = "d", flag = "0")
# append the counts to the table to be shown
- x <- c(x,list(ns1=ns1,npr=npr))
+ x <- c(list(number=number), x)
# title to display for web page
title <- "Sources of Thermodynamic Data in CHNOSZ"
### the following is adapted from print.findFn in package 'sos'
f0 <- tempfile()
File <- paste(f0, ".html", sep="")
- Dir <- dirname(File)
- js <- system.file("extdata/js", "sorttable.js", package = "CHNOSZ")
- file.copy(js, Dir)
+ #Dir <- dirname(File)
+ #js <- system.file("extdata/js", "sorttable.js", package = "CHNOSZ")
+ #file.copy(js, Dir)
## Sundar's original construction:
con <- file(File, "wt")
on.exit(close(con))
.cat <- function(...)
cat(..., "\n", sep = "", file = con, append = TRUE)
## start
- cat("<html>", file = con)
+ cat('<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+ "http://www.w3.org/TR/html4/strict.dtd">\n', file = con)
+ .cat("<html>")
.cat("<head>")
.cat("<title>", title, "</title>")
- .cat("<script src=sorttable.js type='text/javascript'></script>")
+ # sorttable.js is "Blocked for security reasons" in Gmail 20170317
+ #.cat("<script src=sorttable.js type='text/javascript'></script>")
+ # https://www.w3schools.com/howto/howto_js_sort_table.asp
+ .cat('<script type="text/javascript">
+ function sortTable(n) {
+ var table, rows, switching, i, x, y, shouldSwitch, dir, switchcount = 0;
+ table = document.getElementById("thermorefs");
+ switching = true;
+ dir = "asc";
+ while (switching) {
+ switching = false;
+ rows = table.getElementsByTagName("TR");
+ for (i = 1; i < (rows.length - 1); i++) {
+ shouldSwitch = false;
+ x = rows[i].getElementsByTagName("TD")[n];
+ y = rows[i + 1].getElementsByTagName("TD")[n];
+ if (dir == "asc") {
+ if (x.innerHTML > y.innerHTML) {
+ shouldSwitch= true;
+ break;
+ }
+ } else if (dir == "desc") {
+ if (x.innerHTML < y.innerHTML) {
+ shouldSwitch= true;
+ break;
+ }
+ }
+ }
+ if (shouldSwitch) {
+ rows[i].parentNode.insertBefore(rows[i + 1], rows[i]);
+ switching = true;
+ switchcount ++;
+ } else {
+ if (switchcount == 0 && dir == "asc") {
+ dir = "desc";
+ switching = true;
+ }
+ }
+ }
+ }
+</script>')
.cat("</head>")
### boilerplate text
+ .cat("<body>")
.cat("<h1>Listing of all entries in thermo$refs</h1>")
- .cat("<h3>Click on hyperlinked references to open URL in new window</h3>")
- .cat("<h3>Click on column headers to sort</h3>")
- .cat("<h3>Columns 'n..' give number of times each reference appears in data tables:</h3>")
- .cat("ns1: 'ref1' and 'ref2' in data/OBIGT.csv<br>")
- .cat("npr: 'ref' in data/protein.csv<br><p>")
+ .cat("<h3>Click on hyperlinked references to open URL in new window.</h3>")
+ .cat("<h3>Click on column headers to sort.</h3>")
+ .cat("<h3>Column 'number' gives number of times each reference appears in thermo$obigt.</h3>")
### start table and headers
- .cat("<table class='sortable' border='1'>\n<thead>")
+ .cat("<table id='thermorefs' border='1'>")
.cat("<tr>")
- .cat(sprintf(" <th>%s</th>\n</tr>",
- paste(names(x), collapse = "</th>\n <th>")))
- .cat("</thead>\n<tbody>")
+ #.cat(sprintf(" <th>%s</th>\n</tr>",
+ # paste(names(x), collapse = "</th>\n <th>")))
+ for(i in 1:length(x)) .cat(sprintf(' <th onclick="sortTable(%s)">%s</th>', i-1, names(x)[i]))
+ .cat("</tr>")
### now preparing the body of the table
paste.list <- c(lapply(x, as.character), sep = "</td>\n <td>")
tbody.list <- do.call("paste", paste.list)
@@ -231,7 +277,7 @@
tbody <- sub("<td><a", "<td class=link><a", tbody, useBytes = TRUE)
.cat(tbody)
### finish it!
- .cat("</tbody></table></body></html>")
+ .cat("</table></body></html>")
### end adaptation from print.findFn
# show table in browser
browseURL(File)
Modified: pkg/CHNOSZ/data/protein.csv
===================================================================
--- pkg/CHNOSZ/data/protein.csv 2017-03-09 15:05:13 UTC (rev 184)
+++ pkg/CHNOSZ/data/protein.csv 2017-03-17 11:54:22 UTC (rev 185)
@@ -144,7 +144,6 @@
TPX,AQUAE,UniProt,O66780,1,11,2,10,16,6,12,0,11,14,11,5,7,8,5,6,4,10,27,0,4
TPX,ECOLI,UniProt,P0A862,1,22,3,10,7,10,10,1,10,7,15,0,10,6,9,5,10,12,18,0,2
H-NS,PHOPR,UniProt,Q6LT83,1,14,0,9,19,2,5,1,2,14,19,3,2,4,4,9,8,7,5,1,3
-cell,ECOLI,Nei86,NA,1,488,87,229,250,176,582,90,276,326,428,146,229,210,250,281,205,241,402,54,131
PPB,ECOLI,UniProt,P00634,1,64,4,28,24,8,45,10,16,28,39,8,20,21,22,14,22,40,23,3,11
SPTA2.SH3,CHICK,UniProt,P07751,1,3,0,5,4,1,3,0,1,8,7,1,3,3,2,2,2,4,6,2,3
BARS,BACAM,UniProt,P11540,1,6,2,4,11,2,5,1,6,6,12,0,3,2,6,3,5,4,5,3,3
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-03-09 15:05:13 UTC (rev 184)
+++ pkg/CHNOSZ/data/refs.csv 2017-03-17 11:54:22 UTC (rev 185)
@@ -1,127 +1,118 @@
-key,author,year,note,citation,URL
-Kel60,"K. K. Kelley",1960,"gases Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
-Kel60.1,"K. K. Kelley",1960,larnite Cp,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
-Kel60.2,"K. K. Kelley",1960,"iron Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
-Kel60.3,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
-Pan70,"L. B. Pankratz",1970,chlorargyrite,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245
-PK70,"L. B. Pankratz and E. G. King",1970,"bornite and chalcopyrite","U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292
-HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"minerals and phase transitions","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862
-HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"litharge S, V, and Cp parameters","Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862
-RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"chlorargyrite, rutile, and titanite","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
-RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"dickite, fluorphlogopite, halloysite, and pyrope","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
-RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"iron","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
-PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4
-WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"gases GHS","J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
-WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,manganosite,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
-WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,MgSO<sub>4</sub>,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
-BH83,"T. S. Bowers and H. C. Helgeson",1983,rutile,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2
-Hel85,"H. C. Helgeson",1985,"ferrosilite and siderite","Am. J. Sci. 285, 845-855",http://dx.doi.org/10.2475/ajs.285.9.845
-JH85,"K. J. Jackson and H. C. Helgeson",1985,"Sn minerals","Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
-Nei86,"F. C. Neidhardt",1986,,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827
-SH88,"E. L. Shock and H. C. Helgeson",1988,"ionic species","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0
-CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968
-SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"inorganic neutral species","Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4
-SH90,"E. L. Shock and H. C. Helgeson",1990,"organic species","Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O
-Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication",
-SPRONS92.1,"H. C. Helgeson et al.",1992,"titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "","slop98.dat computer data file",
-SPRONS92.2,"H. C. Helgeson et al.",1992,"Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "","slop98.dat computer data file",
-SPRONS92.3,"H. C. Helgeson et al.",1992,""Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."","slop98.dat computer data file",
-Sho92,"E. L. Shock",1992,"diglycine, alanylglycine, leucylglycine, and diketopiperazine","Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V
-Sho93,"E. L. Shock",1993,"ethylacetate and acetamide","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
-Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
-SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J
-SM93,"E. L. Shock and W. B. McKinnon",1993,"CO, HCN, urea","Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185
-SS93,"M. D. Schulte and E. L. Shock",1993,aldehydes,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V
-HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"complexes of rare earth elements","Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P
-PK95,"V. B. Parker and I. L. Khodakovskii",1995,melanterite,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131
-SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8
-SK95.1,"E. L. Shock and C. M. Koretsky",1995,"alanate, glycinate and their complexes not included in later slop files.","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8
-Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496
-AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F
-DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"phenol, and cresol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"dimethylphenol isomers","Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-MS97,"T. M. McCollom and E. L. Shock",1997,"MgSO<sub>4</sub>, NaSO<sub>4</sub><sup>-</sup>, and HCl","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
-MS97.1,"T. M. McCollom and E. L. Shock",1997,"sulfur","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
-SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uraninite","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"metal complexes","Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4
-SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"zincite and litharge","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
-TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X
-HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
-HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"amino acids","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
-RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1
-SLOP98.1,"E. L. Shock et al.",1998,"zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.2,"E. L. Shock et al.",1998,"daphnite; "G<sub>f</sub> and H<sub>f</sub> from @SS93a TMM"","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.3,"E. L. Shock et al.",1998,""Corrected values based on data from @SH90 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.4,"E. L. Shock et al.",1998,""Corrected values based on data from @SSH97 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.5,"E. L. Shock et al.",1998,""Corrected values based on data from @SS93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.6,"E. L. Shock et al.",1998,""Corrected values based on data from @SK93 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.7,"E. L. Shock et al.",1998,""Corrected values based on data from @Sho95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.8,"E. L. Shock et al.",1998,""These data were used in @SK95, but were not tabulated in the paper."","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.9,"E. L. Shock et al.",1998,""Corrected values based on data from @SK95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.10,"E. L. Shock et al.",1998,""Corrected values based on data from @HSS95 "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP98.11,"E. L. Shock et al.",1998,""Data and parameters as used by @MS97. "","slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group ions and complexes","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.1,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Rh+3","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8
-MS99,"W. M. Murphy and E. L. Shock",1999,"actinides","Rev. Mineral. Geochem. 38, 221-253",http://rimg.geoscienceworld.org/content/38/1/221
-PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
-SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9
-AP01,"J. P. Amend and A. V. Plyasunov",2001,carbohydrates,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4
-AS01,"J. P. Amend and E. L. Shock",2001,"NO and N<sub>2</sub>O","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
-AS01.1,"J. P. Amend and E. L. Shock",2001,"selenium and molybdenite","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
-MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"ice polymorphs","Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
-PS01,"A. V. Plyasunov and E. L. Shock",2001,"aqueous nonelectrolytes","Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
-Ric01,"L. Richard",2001,"organic sulfur compounds","Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X
-SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"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>","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7
-MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"goethite, lepidocrocite, and maghemite GHS","Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614
-MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613
-MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z
-SR04,"M. D. Schulte and K. L. Rogers",2004,"alkane thiols","Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001
-HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride HKF parameters","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013
-LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"nucleic-acid bases, nucleosides, and nucleotides","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010
-LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"citric acid and citrate","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010
-LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008
-LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"pyridine and piperidine","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008
-DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
-DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
-DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
-MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, and rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175
-Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley",
-MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5
-SLOP07.1,"E. L. Shock et al.",2007,"corrected charge of Pu(Oxal)+2","slop07.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP07.2,"E. L. Shock et al.",2007,"high-temperature HKF parameters from @AP01","slop07.dat computer data file",http://geopig.asu.edu/?q=tools
-Ric08,"L. Richard",2008,alkenes,"personal communication",
-GM09,"K.-D. Grevel and J. Majzlan",2009,"kieserite, starkeyite, hexahydrite, and epsomite","Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005
-HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,kerogens,"Geochim. Cosmochim. Acta 73, 594-695",http://dx.doi.org/10.1016/j.gca.2008.03.004
-AML10,"M. Accornero, L. Marini and M. Lelli",2010,"metal-chromate complexes","Appl. Geochem. 25, 242-260",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010
-MA10,"L. Marini and M. Accornero",2010,"corrected values","Environ. Earth Sci. 59, 1601-1606",http://dx.doi.org/10.1007/s12665-009-0369-x
-Sch10,"M. Schulte",2010,"organic sulfides","Aquat. Geochem. 16, 621-637",http://dx.doi.org/10.1007/s10498-010-9102-3
-RG11,"L. Richard and X. Gaona",2011,"organic iodine compounds","Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030
-LD12,"D. E. LaRowe and J. M. Dick",2012,"4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
-LD12.1,"D. E. LaRowe and J. M. Dick",2012,"updated and corrected parameters for cysteine, glycine, leucine, and methionine","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
-LD12.2,"D. E. LaRowe and J. M. Dick",2012,"methionine GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
-LD12.3,"D. E. LaRowe and J. M. Dick",2012,"methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
-DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and methylphenanthrene isomers","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020
-SLOP15.1,"E. L. Shock et al.",2015,""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.2,"E. L. Shock et al.",2015,"Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.3,"E. L. Shock et al.",2015,"formaldehyde: "Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of @SS93."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.4,"E. L. Shock et al.",2015,"adipic acid and n-dodecanoate: "Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.5,"E. L. Shock et al.",2015,"n-octanoate: "Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of @Sho95."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.6,"E. L. Shock et al.",2015,""Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-SLOP15.7,"E. L. Shock et al.",2015,"heptanol, hexanol, and octanol: "Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to @SH90."","slop15.dat computer data file",http://geopig.asu.edu/?q=tools
-CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
-CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a<sub>1</sub>--a<sub>4</sub> parameters","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
-UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/
-CHNOSZ.1,"J. M. Dick",2017,"GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.2,"J. M. Dick",2017,"alanate and glycinate: GHS as used by @DLH06","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.3,"J. M. Dick",2017,"metal-amino acid complexes: GHS were recalculated by adding the differences between values from @AH97b and @DLH06 for alanate or glycinate to the properties of the complexes reported by @SK95.","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.4,"J. M. Dick",2017,pseudo-H<sub>4</sub>SiO<sub>4</sub>,"CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.5,"J. M. Dick",2017,"AuCl4- renamed to AuCl4-3","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.6,"J. M. Dick",2017,"dipeptides not included in slop files after slop98.dat","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.7,"J. M. Dick",2017,"charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99","CHNOSZ package documentation",http://chnosz.net
-CHNOSZ.8,"J. M. Dick",2017,"Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.","CHNOSZ package documentation",http://chnosz.net
+key,author,year,citation,note,URL
+Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",http://www.worldcat.org/oclc/693388901
+Kel60.1,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","larnite Cp",http://www.worldcat.org/oclc/693388901
+Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",http://www.worldcat.org/oclc/693388901
+Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",http://www.worldcat.org/oclc/693388901
+Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,http://www.worldcat.org/oclc/14154245
+PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",http://www.worldcat.org/oclc/14154292
+HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","minerals and phase transitions",http://www.worldcat.org/oclc/13594862
+HDNB78.1,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","litharge S, V, and Cp parameters",http://www.worldcat.org/oclc/13594862
+RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","chlorargyrite, rutile, and titanite",http://pubs.er.usgs.gov/publication/b1452
+RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
+RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
+PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.doi.org/10.1016/0016-7037(82)90056-4
+WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392","gases GHS",http://dx.doi.org/10.1063/1.555661
+WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",manganosite,http://dx.doi.org/10.1063/1.555661
+WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",MgSO<sub>4</sub>,http://dx.doi.org/10.1063/1.555661
+BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2
+Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845
+JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
+SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",http://dx.doi.org/10.1016/0016-7037(88)90181-0
+SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",http://dx.doi.org/10.1016/0016-7037(89)90341-4
+SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",http://dx.doi.org/10.1016/0016-7037(90)90429-O
+Joh92a,"J. W. Johnson",1992,"personal communication","steam, Cp represented by the Maier-Kelley equation",
+SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
+SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
+SPRONS92.3,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file",""Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."",
+Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",http://dx.doi.org/10.1016/0016-7037(92)90392-V
+Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",http://dx.doi.org/10.1016/0016-7037(93)90542-5
[TRUNCATED]
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svnlook diff /svnroot/chnosz -r 185
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