[CHNOSZ-commits] r521 - in pkg/CHNOSZ: . inst inst/extdata/adds man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Dec 15 05:02:06 CET 2019 

Author: jedick
Date: 2019-12-15 05:02:04 +0100 (Sun, 15 Dec 2019)
New Revision: 521

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
submit version 1.3.4 to CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/DESCRIPTION	2019-12-15 04:02:04 UTC (rev 521)
@@ -1,6 +1,6 @@
-Date: 2019-12-10
+Date: 2019-12-15
 Package: CHNOSZ
-Version: 1.3.3-17
+Version: 1.3.4
 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
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/inst/NEWS	2019-12-15 04:02:04 UTC (rev 521)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.3.3-16 (2019-12-10)
----------------------------------------
+CHANGES IN CHNOSZ 1.3.4 (2019-12-15)
+------------------------------------
 
 THERMODYNAMIC DATA
 
@@ -13,13 +13,8 @@
 - Move more carbonates from SUPCRT92 back into the default database:
   artinite, azurite.
 
-FEATURE ENHANCEMENTS
+DIAGRAMS
 
-- subcrt(): properties of minerals are now output at the listed upper
-  T limit (or transition temperature, for e.g. cr1 -> cr2). Previously,
-  properties were set to NA at, and not only above, the T limit. Thanks
-  to Evgeniy Bastrakov for the request.
-
 - Improve the handling of solids in equilibrate(). They are now excluded
   from the equilibrium calculation, but their stability fields are
   calculated using the maximum affinity method (with diagram()). Where
@@ -27,7 +22,7 @@
   to -999, and vice versa. Thanks to Feng Lai for the request and test
   case.
 
-CLEANUP
+PACKAGE CLEANUP
 
 - Remove files Sce.csv.xz and yeastgfp.csv.xz and functions yeastgfp()
   and yeast.aa(). These have been moved to the JMDplots package
@@ -38,12 +33,17 @@
 
 BUG FIXES
 
-- describe.reaction(): remove the Unicode double arrow. Unlike that, a
+- describe.reaction(): revert the Unicode double arrow. Unlike that, a
   simple equals sign is displayed correctly on all systems.
 
 - Fix bug in unexported function obigt2eos(): lambda (exponent in heat
   capacity equation) was incorrectly going through a units conversion.
 
+- subcrt(): properties of minerals are now output at the listed upper
+  T limit (or transition temperature, for e.g. cr1 -> cr2). Previously,
+  properties were set to NA at, and not only above, the T limit. Thanks
+  to Evgeniy Bastrakov for the bug report.
+
 - In mosaic(), set the activities of only aqueous basis species to the
   total activity, which is taken from the incoming basis() definition.
   This fixes a bug where activities of minerals (particularly, native

Modified: pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv	2019-12-15 04:02:04 UTC (rev 521)
@@ -241,31 +241,32 @@
 "OBIGT",1825,"diglycine-","aq","cal",-49.22,,565
 "OBIGT",1826,"triglycine+","aq","cal",,1.75,
 "OBIGT",1827,"triglycine-","aq","cal",,1.78,
-"OBIGT",1884,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",1962,"jarosite","cr","cal",,,20697
-"OBIGT",1963,"natrojarosite","cr","cal",,,17554
-"OBIGT",1971,"realgar,alpha","cr","J",,,768
-"OBIGT",1972,"realgar,beta","cr","J",,,989
-"OBIGT",1973,"orpiment","cr","J",,,-1036
-"OBIGT",1982,"dawsonite","cr","cal",,,4653
-"OBIGT",2003,"octadecane","cr","cal",-2.63,,
-"OBIGT",2004,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2005,"eicosane","cr","cal",-2.79,,
-"OBIGT",2006,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2007,"docosane","cr","cal",-2.63,,
-"OBIGT",2008,"tricosane","cr","cal",-5.22,,
-"OBIGT",2009,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2010,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2011,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2012,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2064,"carbazole","cr","cal",-43.39,,
-"OBIGT",2105,"triphenylene","cr","cal",,,541
-"OBIGT",2418,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2611,"nonacontane","liq","cal",,,635
-"OBIGT",2618,"2-methyloctane","liq","cal",10,,
-"OBIGT",3031,"5,6-dithiadecane","liq","cal",2,,
-"OBIGT",3108,"ethylene","gas","cal",-4.59,,
-"OBIGT",3118,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",1886,"hydromagnesite","cr","cal",,,-2569
+"OBIGT",1964,"jarosite","cr","cal",,,20697
+"OBIGT",1965,"natrojarosite","cr","cal",,,17554
+"OBIGT",1973,"realgar,alpha","cr","J",,,768
+"OBIGT",1974,"realgar,beta","cr","J",,,989
+"OBIGT",1975,"orpiment","cr","J",,,-1036
+"OBIGT",1984,"dawsonite","cr","J",,,19466
+"OBIGT",1986,"ferberite","cr","J",1.21,,
+"OBIGT",2005,"octadecane","cr","cal",-2.63,,
+"OBIGT",2006,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2007,"eicosane","cr","cal",-2.79,,
+"OBIGT",2008,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2009,"docosane","cr","cal",-2.63,,
+"OBIGT",2010,"tricosane","cr","cal",-5.22,,
+"OBIGT",2011,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2012,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2013,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2014,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2066,"carbazole","cr","cal",-43.39,,
+"OBIGT",2107,"triphenylene","cr","cal",,,541
+"OBIGT",2420,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2613,"nonacontane","liq","cal",,,635
+"OBIGT",2620,"2-methyloctane","liq","cal",10,,
+"OBIGT",3033,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",3110,"ethylene","gas","cal",-4.59,,
+"OBIGT",3120,"3,5-dimethylphenol","gas","cal",,,628
 "DEW",15,"BO(OH)","aq","cal",,,-1111
 "DEW",19,"CaCl+","aq","cal",,,-593
 "DEW",20,"CaCl2","aq","cal",,,-7937
@@ -324,11 +325,11 @@
 "SLOP98",145,"MnAsO4-","aq","cal",-1.45,,
 "SLOP98",169,"PdCl4-2","aq","cal",,-1.05,
 "SUPCRT92",26,"antigorite","cr","cal",,,812
-"SUPCRT92",43,"clinochlore,7a","cr","cal",,,666
-"SUPCRT92",59,"daphnite,14a","cr","cal",,,-836
-"SUPCRT92",84,"ferrosilite","cr","cal",,,694
-"SUPCRT92",85,"ferrosilite","cr2","cal",,,694
-"SUPCRT92",96,"greenalite","cr","cal",,,142507
+"SUPCRT92",41,"clinochlore,7a","cr","cal",,,666
+"SUPCRT92",57,"daphnite,14a","cr","cal",,,-836
+"SUPCRT92",82,"ferrosilite","cr","cal",,,694
+"SUPCRT92",83,"ferrosilite","cr2","cal",,,694
+"SUPCRT92",94,"greenalite","cr","cal",,,142507
 "OldAA",11,"alanate","aq","cal",-24.28,,
 "OldAA",24,"Fe(Gly)2","aq","cal",,,537
 "OldAA",50,"Fe(Ala)2","aq","cal",,,553

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/man/diagram.Rd	2019-12-15 04:02:04 UTC (rev 521)
@@ -241,7 +241,7 @@
 ### these use the maximum affinity method
 
 ## Fe-S-O at 200 deg C, after Helgeson, 1970
-basis(c("Fe", "O2", "S2"))
+basis(c("Fe", "oxygen", "S2"))
 species(c("iron", "ferrous-oxide", "magnetite",
   "hematite", "pyrite", "pyrrhotite"))
 # the calculations include the phase transitions of

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2019-12-15 04:02:04 UTC (rev 521)
@@ -1969,7 +1969,7 @@
 <span style="color:red">`add.obigt("SUPCRT92")`</span> -- This file contains data for minerals from SUPCRT92 (mostly Helgeson et al., 1978) that have been replaced by the Berman data set.
 
 <span style="color:red">`add.obigt("SLOP98")`</span> -- This file contains data from `slop98.dat` or later slop files, from Everett Shock's GEOPIG group at Arizona State University, that were previously used in CHNOSZ but have been replaced by newer data.
-This includes updates for aqueous Al species [@TS01], Au species [@PAB_14], and arsenic-bearing aqueous species and minerals, as compiled in the [SUPCRTBL package](http://www.indiana.edu/~hydrogeo/supcrtbl.html) [@ZZL_16].
+This includes updates for aqueous Al species [@TS01], Au species [@PAB_14], and arsenic-bearing aqueous species and minerals, as compiled in the SUPCRTBL package [@ZZL_16].
 Some calculations using the older data are shown in [this vignette](#complete-equilibrium-solubility).
 See [<span style="color:blue">`demo(gold)`</span>](../demo) for calculations that depend on the data for Au species that are now loaded by default in CHNOSZ.
 

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2019-12-10 06:25:40 UTC (rev 520)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2019-12-15 04:02:04 UTC (rev 521)
@@ -32,7 +32,6 @@
   volume    = {39},
   number    = {10},
   pages     = {990--1006},
-  url       = {http://www.maik.ru/cgi-perl/search.pl?type=abstract&name=geochem&number=10&year=1&page=990},
 }
 
 @Article{AH97b,

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