[CHNOSZ-commits] r626 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Nov 10 15:38:12 CET 2020 

Author: jedick
Date: 2020-11-10 15:38:12 +0100 (Tue, 10 Nov 2020)
New Revision: 626

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Change some usgs.gov URLs to DOIs


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-11-10 14:25:43 UTC (rev 625)
+++ pkg/CHNOSZ/DESCRIPTION	2020-11-10 14:38:12 UTC (rev 626)
@@ -1,6 +1,6 @@
 Date: 2020-11-10
 Package: CHNOSZ
-Version: 1.3.6-98
+Version: 1.3.6-99
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2020-11-10 14:25:43 UTC (rev 625)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2020-11-10 14:38:12 UTC (rev 626)
@@ -102,7 +102,7 @@
 
       \item \samp{inorganic_cr.csv}: Add wustite, manganese, and Mn oxides
       (manganosite, pyrolusite, bixbyite, and hausmannite) from
-      \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
+      \href{https://doi.org/10.3133/b2131}{Robie and Hemingway,
         1995}.
 
       \item \samp{inorganic_cr.csv}: Add amorphous Mn(OH)\s{2} from
@@ -118,13 +118,13 @@
       Co-pentlandite (Co\s{9}S\s{8}) from
       \href{https://www.worldcat.org/oclc/801856147}{Vaughan and Craig, 1978}
       and cattierite (CoS\s{2}) and cobalt from
-      \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
+      \href{https://doi.org/10.3133/b2131}{Robie and Hemingway,
         1995}.
 
       \item Add GHS and Cp at 25 \degC for almandine, dickite, fluorphlogopite,
       glaucophane, grunerite, halloysite, larnite, pyrope (\samp{SUPCRT92.csv})
       and bromellite (\samp{inorganic_cr.csv}) from
-      \href{https://pubs.er.usgs.gov/publication/b2131}{Robie and Hemingway,
+      \href{https://doi.org/10.3133/b2131}{Robie and Hemingway,
         1995}.
 
       \item \samp{inorganic_cr.csv}: Correct formulas for number of \H2O in

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-11-10 14:25:43 UTC (rev 625)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2020-11-10 14:38:12 UTC (rev 626)
@@ -8,10 +8,10 @@
 HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","data for minerals and phase transitions",https://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",https://www.worldcat.org/oclc/13594862
 HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862
-RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://pubs.er.usgs.gov/publication/b1452
-RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://pubs.er.usgs.gov/publication/b1452
-RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://pubs.er.usgs.gov/publication/b1452
-RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://pubs.er.usgs.gov/publication/b1452
+RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://doi.org/10.3133/b1452
+RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452
+RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452
+RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452
 VC78,"D. J. Vaughan and J. R. Craig",1978,"Mineral Chemistry of Metal Sulfides","linnaeite and Co-pentlandite",https://www.worldcat.org/oclc/801856147
 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://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, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
@@ -58,15 +58,15 @@
 HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
 PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
 PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","manganese, manganosite, pyrolusite, bixbyite, hausmannite, heubnerite, cattierite, cobalt, and wustite",https://pubs.er.usgs.gov/publication/b2131
-RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://pubs.er.usgs.gov/publication/b2131
-RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://pubs.er.usgs.gov/publication/b2131
-RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://pubs.er.usgs.gov/publication/b2131
-RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
-RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://pubs.er.usgs.gov/publication/b2131
-RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://pubs.er.usgs.gov/publication/b2131
-RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://pubs.er.usgs.gov/publication/b2131
-RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","linnaeite V",https://pubs.er.usgs.gov/publication/b2131
+RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","manganese, manganosite, pyrolusite, bixbyite, hausmannite, heubnerite, cattierite, cobalt, and wustite",https://doi.org/10.3133/b2131
+RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/b2131
+RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://doi.org/10.3133/b2131
+RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131
+RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
+RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://doi.org/10.3133/b2131
+RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
+RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","gypsum GHS",https://doi.org/10.3133/b2131
+RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","linnaeite V",https://doi.org/10.3133/b2131
 SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
 SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes with metals. Values are taken from slop98.dat, which notes corrected values for some species.",https://doi.org/10.1016/0016-7037(95)00058-8
 Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
@@ -187,7 +187,7 @@
 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>",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

Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib	2020-11-10 14:25:43 UTC (rev 625)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib	2020-11-10 14:38:12 UTC (rev 626)
@@ -605,7 +605,7 @@
   title     = {{T}hermodynamic {P}roperties of {M}inerals and {R}elated {S}ubstances at 298.15 {K} and 1 {B}ar ($10^5$ {P}ascals) {P}ressure and at {H}igher {T}emperatures},
   year      = {1978},
   series    = {Bulletin 1452},
-  url       = {https://pubs.er.usgs.gov/publication/b1452},
+  doi       = {10.3133/b1452},
 }
 
 @Article{SS98a,
@@ -1234,11 +1234,11 @@
 @Article{HRA91,
   author    = {Hemingway, B. S. and Robie, R. A. and Apps, J. A.},
   journal   = {American Mineralogist},
-  title     = {{R}evised values for the thermodynamic properties of boehmite, {A}l{O}({OH}) , and related species and phases in the system {A}l-{H}-{O}},
+  title     = {{R}evised values for the thermodynamic properties of boehmite, {A}l{O}({OH}), and related species and phases in the system {A}l-{H}-{O}},
   year      = {1991},
-  volume    = {76},
   number    = {3-4},
   pages     = {445--457},
+  volume    = {76},
   url       = {https://pubs.er.usgs.gov/publication/70016664},
 }

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