[CHNOSZ-commits] r438 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 13 16:46:44 CEST 2019
Author: jedick
Date: 2019-04-13 16:46:44 +0200 (Sat, 13 Apr 2019)
New Revision: 438
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/vignettes/obigt.bib
pkg/CHNOSZ/vignettes/vig.bib
Log:
EOSregress.Rd: remove non-portable characters from example code
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/DESCRIPTION 2019-04-13 14:46:44 UTC (rev 438)
@@ -1,6 +1,6 @@
Date: 2019-04-13
Package: CHNOSZ
-Version: 1.3.1-18
+Version: 1.3.1-19
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/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/inst/CHECKLIST 2019-04-13 14:46:44 UTC (rev 438)
@@ -21,6 +21,9 @@
- 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
rmarkdown/rmd/h/bootstrap/fonts/ with empty files
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2019-04-13 14:46:44 UTC (rev 438)
@@ -37,7 +37,7 @@
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
SH90.1,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","formic acid, formate, and propanoate",https://doi.org/10.1016/0016-7037(90)90429-O
BN91,"J. W. Ball and D. K. Nordstrom",1991,"User's manual for WATEQ4F, with revised thermodynamic data base and text cases for calculating speciation of major, trace, and redox elements in natural waters. USGS Open-File Report 91-183","arsenopyrite: G",https://pubs.er.usgs.gov/publication/ofr91183
-HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",bohemite,http://pubs.er.usgs.gov/publication/70016664
+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
SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2019-04-13 14:46:44 UTC (rev 438)
@@ -140,7 +140,7 @@
opar <- par(mfrow=c(2,2))
EOSplot(d, T.max=600)
title("Cp of CH4(aq), fit to 600 K")
-legend("bottomleft", pch=1, legend="Hnědkovský and Wood, 1997")
+legend("bottomleft", pch=1, legend="Hnedkovsky and Wood, 1997")
EOSplot(d, coefficients=CH4coeffs)
title("Cp from EOS parameters in database")
EOSplot(d, T.max=600, T.plot=600)
@@ -178,7 +178,7 @@
# for both HKF and the expansivity equation
# we'll fit up to a temperature limit
EOSplot(d, varHKF, T.max=663, T.plot=625)
-legend("bottomright", pch=1, legend="Hnědkovský et al., 1996")
+legend("bottomright", pch=1, legend="Hnedkovsky et al., 1996")
title("V of CH4(aq), HKF equation")
EOSplot(d, varal, T.max=663, T.plot=625)
title("V of CH4(aq), expansivity equation")
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2019-04-13 14:46:44 UTC (rev 438)
@@ -164,13 +164,13 @@
}
@Book{HGK84,
- author = {Haar, Lester and Gallagher, John S. and Kell, George S.},
- publisher = {Hemisphere Publishing Corporation},
- title = {{NBS}/{NRC} {S}team {T}ables: {T}hermodynamic and {T}ransport {P}roperties and {C}omputer {P}rograms for {V}apor and {L}iquid {S}tates of {W}ater in {SI} {U}nits},
- year = {1984},
- address = {Washington, D. C.},
- pages = {320},
- url = {http://www.worldcat.org/oclc/858456124},
+ author = {Haar, Lester and Gallagher, John S. and Kell, George S.},
+ publisher = {Hemisphere Publishing Corporation},
+ title = {{NBS}/{NRC} {S}team {T}ables: {T}hermodynamic and {T}ransport {P}roperties and {C}omputer {P}rograms for {V}apor and {L}iquid {S}tates of {W}ater in {SI} {U}nits},
+ year = {1984},
+ address = {Washington, D. C.},
+ pages = {320},
+ url = {http://www.worldcat.org/oclc/858456124},
}
@Article{HSS95,
@@ -282,7 +282,6 @@
pages = {171--187},
doi = {10.1007/s00239-014-9616-1},
issn = {0022-2844},
- language = {English},
}
@Article{LD12,
@@ -405,14 +404,14 @@
}
@Article{MVT01,
- author = {Mercury, Lionel and Vieillard, Philippe and Tardy, Yves},
- journal = {Applied Geochemistry},
- title = {{T}hermodynamics of ice polymorphs and {‘}ice-like{’} water in hydrates and hydroxides},
- year = {2001},
- volume = {16},
- number = {2},
- pages = {161--181},
- doi = {10.1016/S0883-2927(00)00025-1},
+ author = {Mercury, Lionel and Vieillard, Philippe and Tardy, Yves},
+ journal = {Applied Geochemistry},
+ title = {{T}hermodynamics of ice polymorphs and {‘}ice-like{’} water in hydrates and hydroxides},
+ year = {2001},
+ volume = {16},
+ number = {2},
+ pages = {161--181},
+ doi = {10.1016/S0883-2927(00)00025-1},
}
@Book{Pan70,
@@ -722,14 +721,14 @@
}
@Article{SK95,
- author = {Shock, Everett L. and Koretsky, Carla M.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{M}etal-organic complexes in geochemical processes: {E}stimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures},
- year = {1995},
- volume = {59},
- number = {8},
- pages = {1497--1532},
- doi = {10.1016/0016-7037(95)00058-8},
+ author = {Shock, Everett L. and Koretsky, Carla M.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{M}etal-organic complexes in geochemical processes: {E}stimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures},
+ year = {1995},
+ volume = {59},
+ number = {8},
+ pages = {1497--1532},
+ doi = {10.1016/0016-7037(95)00058-8},
}
@Article{SM93,
@@ -1124,16 +1123,16 @@
}
@Article{Kul06,
- author = {Kulik, D. A.},
- journal = {Chemical Geology},
- title = {{D}ual-thermodynamic estimation of stoichiometry and stability of solid solution end members in aqueous–solid solution systems},
- year = {2006},
- volume = {225},
- number = {3},
- pages = {189--212},
- note = {Solid solutions: from theory to experiment},
- doi = {10.1016/j.chemgeo.2005.08.014},
- issn = {0009-2541},
+ author = {Kulik, D. A.},
+ journal = {Chemical Geology},
+ title = {{D}ual-thermodynamic estimation of stoichiometry and stability of solid solution end members in aqueous--solid solution systems},
+ year = {2006},
+ volume = {225},
+ number = {3},
+ pages = {189--212},
+ note = {Solid solutions: from theory to experiment},
+ doi = {10.1016/j.chemgeo.2005.08.014},
+ issn = {0009-2541},
}
@Misc{BDat17,
@@ -1377,7 +1376,7 @@
@Article{AP14,
author = {Nikolay N. Akinfiev and Andrey V. Plyasunov},
journal = {Geochimica et Cosmochimica Acta},
- title = {{A}pplication of the {A}kinfiev–{D}iamond equation of state to neutral hydroxides of metalloids ({B}({OH})$_3$, {S}i({OH})$_4$, {A}s({OH})$_3$) at infinite dilution in water over a wide range of the state parameters, including steam conditions},
+ title = {{A}pplication of the {A}kinfiev-{D}iamond equation of state to neutral hydroxides of metalloids ({B}({OH})$_3$, {S}i({OH})$_4$, {A}s({OH})$_3$) at infinite dilution in water over a wide range of the state parameters, including steam conditions},
year = {2014},
volume = {126},
pages = {338 - 351},
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2019-04-13 06:25:07 UTC (rev 437)
+++ pkg/CHNOSZ/vignettes/vig.bib 2019-04-13 14:46:44 UTC (rev 438)
@@ -126,7 +126,7 @@
@Article{DS11,
author = {Dick, Jeffrey M. and Shock, Everett L.},
- journal = {PLoS ONE},
+ journal = {PLOS One},
title = {{C}alculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring},
year = {2011},
volume = {6},
@@ -137,7 +137,7 @@
@Article{DS13,
author = {Dick, Jeffrey M. and Shock, Everett L.},
- journal = {PLoS ONE},
+ journal = {PLOS One},
title = {{A} metastable equilibrium model for the relative abundances of microbial phyla in a hot spring},
year = {2013},
volume = {8},
@@ -233,7 +233,6 @@
pages = {171--187},
doi = {10.1007/s00239-014-9616-1},
issn = {0022-2844},
- language = {English},
}
@Article{LD12,
@@ -451,14 +450,14 @@
}
@Article{SOJSH92,
- author = {Shock, Everett L. and Oelkers, Eric H. and Johnson, James W. and Sverjensky, Dimitri A. and Helgeson, Harold C.},
- journal = {Journal of the Chemical Society, Faraday Transactions},
- title = {{C}alculation of the thermodynamic properties of aqueous species at high pressures and temperatures: {E}ffective electrostatic radii, dissociation constants, and standard partial molal properties to 1000 °{C} and 5 kbar},
- year = {1992},
- volume = {88},
- number = {6},
- pages = {803--826},
- doi = {10.1039/FT9928800803},
+ author = {Shock, Everett L. and Oelkers, Eric H. and Johnson, James W. and Sverjensky, Dimitri A. and Helgeson, Harold C.},
+ journal = {Journal of the Chemical Society, Faraday Transactions},
+ title = {{C}alculation of the thermodynamic properties of aqueous species at high pressures and temperatures: {E}ffective electrostatic radii, dissociation constants, and standard partial molal properties to 1000 °{C} and 5 kbar},
+ year = {1992},
+ volume = {88},
+ number = {6},
+ pages = {803--826},
+ doi = {10.1039/FT9928800803},
}
@Article{SS98,
@@ -629,15 +628,15 @@
}
@Article{MD98,
- author = {Merino, Enrique and Dewers, Thomas},
- journal = {Journal of Hydrology},
- title = {{I}mplications of replacement for reaction–transport modeling},
- year = {1998},
- volume = {209},
- number = {1–4},
- pages = {137--146},
- doi = {10.1016/S0022-1694(98)00150-4},
- issn = {0022-1694},
+ author = {Merino, Enrique and Dewers, Thomas},
+ journal = {Journal of Hydrology},
+ title = {{I}mplications of replacement for reaction--transport modeling},
+ year = {1998},
+ volume = {209},
+ number = {1-4},
+ pages = {137--146},
+ doi = {10.1016/S0022-1694(98)00150-4},
+ issn = {0022-1694},
}
@TechReport{Wol92,
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