[CHNOSZ-commits] r677 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 12 01:20:26 CEST 2021
Author: jedick
Date: 2021-05-12 01:20:26 +0200 (Wed, 12 May 2021)
New Revision: 677
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/TODO
pkg/CHNOSZ/vignettes/multi-metal.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Update Robinson et al. (2021) citation info
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-04-26 03:52:06 UTC (rev 676)
+++ pkg/CHNOSZ/DESCRIPTION 2021-05-11 23:20:26 UTC (rev 677)
@@ -1,6 +1,6 @@
-Date: 2021-04-21
+Date: 2021-05-12
Package: CHNOSZ
-Version: 1.4.1-3
+Version: 1.4.1-4
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/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO 2021-04-26 03:52:06 UTC (rev 676)
+++ pkg/CHNOSZ/inst/TODO 2021-05-11 23:20:26 UTC (rev 677)
@@ -32,3 +32,7 @@
- Add demo for effective equilibrium constant for diglycine on T-pH plot at
high pressure (DEW model; Robinson et al., 2021)
+
+[20210426]
+
+- anintro.Rmd: Make bold Fe-bearing mineral names in first mosaic stacking diagram
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2021-04-26 03:52:06 UTC (rev 676)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2021-05-11 23:20:26 UTC (rev 677)
@@ -547,6 +547,11 @@
NaClexpr <- as.expression(bquote(NaCl == .(m_NaCl)*m))
aqexpr <- as.expression(bquote("("*aq*")"[italic(i)] == 10^.(logm_aq)*m))
+
+
+
+
+
# Setup basis species
basis(c("Cu+", "pyrite", "H2S", "oxygen", "H2O", "H+", "Cl-"))
basis("H2S", logmS)
@@ -564,6 +569,12 @@
species(c(FeCu.cr, Cu.cr))
# Add aqueous species 20210220
species(iCu.aq, logm_aq, add = TRUE)
+
+
+
+
+
+
# TODO: limitation in mosaic() when using both solid and aqueous basis species (i.e. c(Fe.cr, Fe.aq)):
# Only the activity of the first-defined basis species is used for all basis species.
# The first-defined basis species is pyrite (logact = 0), but logact < 0 for the aq Fe species.
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2021-04-26 03:52:06 UTC (rev 676)
+++ pkg/CHNOSZ/vignettes/vig.bib 2021-05-11 23:20:26 UTC (rev 677)
@@ -81,7 +81,7 @@
@Article{Dic08,
author = {Dick, Jeffrey M.},
journal = {Geochemical Transactions},
- title = {{C}alculation of the relative metastabilities of proteins using the {CHNOSZ} software package},
+ title = {Calculation of the relative metastabilities of proteins using the {CHNOSZ} software package},
year = {2008},
pages = {10},
volume = {9},
@@ -91,7 +91,7 @@
@Article{Dic09,
author = {Dick, Jeffrey M.},
journal = {BMC Systems Biology},
- title = {{C}alculation of the relative metastabilities of proteins in subcellular compartments of \emph{{S}accharomyces cerevisiae}},
+ title = {Calculation of the relative metastabilities of proteins in subcellular compartments of \emph{{S}accharomyces cerevisiae}},
year = {2009},
pages = {75},
volume = {3},
@@ -100,8 +100,8 @@
@Article{Dic14,
author = {Dick, Jeffrey M.},
- journal = {Journal of the Royal Society Interface},
- title = {{A}verage oxidation state of carbon in proteins},
+ journal = {Journal of the Royal Society, Interface},
+ title = {Average oxidation state of carbon in proteins},
year = {2014},
pages = {20131095},
volume = {11},
@@ -119,7 +119,7 @@
@Article{DLH06,
author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
journal = {Biogeosciences},
- title = {{T}emperature, pressure, and electrochemical constraints on protein speciation: {G}roup additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
+ title = {Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
year = {2006},
number = {3},
pages = {311--336},
@@ -130,7 +130,7 @@
@Article{DS11,
author = {Dick, Jeffrey M. and Shock, Everett L.},
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},
+ title = {Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring},
year = {2011},
number = {8},
pages = {e22782},
@@ -141,7 +141,7 @@
@Article{DS13,
author = {Dick, Jeffrey M. and Shock, Everett L.},
journal = {PLOS One},
- title = {{A} metastable equilibrium model for the relative abundances of microbial phyla in a hot spring},
+ title = {A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring},
year = {2013},
number = {9},
pages = {e72395},
@@ -261,7 +261,7 @@
@Article{LD12,
author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the standard molal thermodynamic properties of crystalline peptides},
+ title = {Calculation of the standard molal thermodynamic properties of crystalline peptides},
year = {2012},
pages = {70--91},
volume = {80},
@@ -445,7 +445,7 @@
}
@Article{SC10,
- author = {Shock, Everett and Canovas, Peter},
+ author = {Shock, Everett L. and Canovas, Peter},
journal = {Geofluids},
title = {{T}he potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems},
year = {2010},
@@ -736,7 +736,7 @@
@Article{Dic17,
author = {Dick, Jeffrey M.},
journal = {PeerJ},
- title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
+ title = {Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
year = {2017},
pages = {e3421},
volume = {5},
@@ -930,7 +930,8 @@
journal = {Geochimica et Cosmochimica Acta},
title = {Quantifying the extent of amide and peptide bond synthesis across conditions relevant to geologic and planetary environments},
year = {2021},
- volume = {in press},
+ pages = {318--332},
+ volume = {300},
doi = {10.1016/j.gca.2021.01.038},
}
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