[CHNOSZ-commits] r638 - in pkg/CHNOSZ: . vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 23 10:17:51 CET 2021
Author: jedick
Date: 2021-02-23 10:17:50 +0100 (Tue, 23 Feb 2021)
New Revision: 638
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/vignettes/multi-metal.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
multi-metal.Rmd: Show resolution settings at top of vignette
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-02-23 07:52:59 UTC (rev 637)
+++ pkg/CHNOSZ/DESCRIPTION 2021-02-23 09:17:50 UTC (rev 638)
@@ -1,6 +1,6 @@
Date: 2021-02-23
Package: CHNOSZ
-Version: 1.4.0-7
+Version: 1.4.0-8
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/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2021-02-23 07:52:59 UTC (rev 637)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2021-02-23 09:17:50 UTC (rev 638)
@@ -65,20 +65,41 @@
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
## logK with a thin space 20200627
logK <- "log <i>K</i>"
+## Resolution settings
+# Change this to TRUE to make high-resolution plots
+# (default is FALSE to save time in CRAN checks)
+hires <- FALSE
+res1.lo <- 150
+res1.hi <- 256
+res1 <- ifelse(hires, res1.hi, res1.lo)
+res2.lo <- 200
+res2.hi <- 400
+res2 <- ifelse(hires, res2.hi, res2.lo)
```
```{r CHNOSZ_reset, include=FALSE}
library(CHNOSZ)
reset()
-# Change this to TRUE to make high-resolution plots
-# (default is FALSE to save time in CRAN checks)
-hires <- FALSE
-res1 <- ifelse(hires, 256, 150)
-res2 <- ifelse(hires, 400, 200)
```
This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
+The plots in this vignette were made using the following resolution settings, which can be changed if desired (low resolutions are used to save time in CRAN checks):
+
+```{r res, results = "asis", echo = FALSE}
+cat("```")
+cat("\n")
+cat(paste0(ifelse(hires, "# ", ""), "res1 <- ", res1.lo))
+cat("\n")
+cat(paste0(ifelse(hires, "", "# "), "res1 <- ", res1.hi))
+cat("\n")
+cat(paste0(ifelse(hires, "# ", ""), "res2 <- ", res2.lo))
+cat("\n")
+cat(paste0(ifelse(hires, "", "# "), "res2 <- ", res2.hi))
+cat("\n")
+cat("```")
+```
+
Basic diagrams in CHNOSZ are made for reactions that are *balanced on an element* (see [Equilibrium in CHNOSZ](equilibrium.html)) and therefore represent minerals or aqueous species that all have one element, often a metal, in common.
The package documentation has many examples of diagrams for a single metal appearing in different minerals or complexed with different ligands, but a common request is to make diagrams for multiple metals.
This vignette describes some methods for constructing diagrams for multi-metal minerals and other multi-element systems.
@@ -508,7 +529,7 @@
Cu.aq <- info(iCu.aq)$name
logaCu <- -6
species(iCu.aq, logaCu, add = TRUE)
-# FIXME: limitation in mosaic() when using both solid and aqueous basis species (i.e. c(Fe.cr, Fe.aq)):
+# 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 we want logact = -4 for the aq Fe species.
# Workaround: Adjust standard Gibbs energies of aq Fe species to virtually change their activities
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2021-02-23 07:52:59 UTC (rev 637)
+++ pkg/CHNOSZ/vignettes/vig.bib 2021-02-23 09:17:50 UTC (rev 638)
@@ -83,8 +83,8 @@
journal = {Geochemical Transactions},
title = {{C}alculation of the relative metastabilities of proteins using the {CHNOSZ} software package},
year = {2008},
+ pages = {10},
volume = {9},
- pages = {10},
doi = {10.1186/1467-4866-9-10},
}
@@ -99,13 +99,13 @@
}
@Article{Dic14,
- author = {Dick, Jeffrey M.},
- journal = {Journal of the Royal Society Interface},
- title = {{A}verage oxidation state of carbon in proteins},
- year = {2014},
- volume = {11},
- pages = {20131095},
- doi = {10.1098/rsif.2013.1095},
+ author = {Dick, Jeffrey M.},
+ journal = {Journal of the Royal Society Interface},
+ title = {{A}verage oxidation state of carbon in proteins},
+ year = {2014},
+ pages = {20131095},
+ volume = {11},
+ doi = {10.1098/rsif.2013.1095},
}
@Article{Dic15,
@@ -128,14 +128,14 @@
}
@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},
- year = {2011},
- volume = {6},
- number = {8},
- pages = {e22782},
- doi = {10.1371/journal.pone.0022782},
+ 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},
+ year = {2011},
+ number = {8},
+ pages = {e22782},
+ volume = {6},
+ doi = {10.1371/journal.pone.0022782},
}
@Article{DS13,
@@ -143,9 +143,9 @@
journal = {PLOS One},
title = {{A} metastable equilibrium model for the relative abundances of microbial phyla in a hot spring},
year = {2013},
- volume = {8},
number = {9},
pages = {e72395},
+ volume = {8},
doi = {10.1371/journal.pone.0072395},
}
@@ -323,18 +323,6 @@
doi = {10.2113/gsecongeo.80.7.1965},
}
- at InProceedings{NPW_79,
- author = {Nordstrom, D. K. and Plummer, L. N. and Wigley, T. M. L. and Wolery, T. J. and Ball, J. W. and Jenne, E. A. and Bassett, R. L. and Crerar, D. A. and Florence, T. M. and Fritz, B. and Hoffman, M. and Holdren, G. R., Jr. and Lafon, G. M. and Mattigod, S. V. and McDuff, R. E. and Morel, F. and Reddy, M. M. and Sposito, G. and Thrailkill, J.},
- booktitle = {Chemical Modeling in Aqueous Systems: Speciation, Sorption, Solubility, and Kinetics},
- title = {A comparison of computerized chemical models for equilibrium calculations in aqueous systems},
- year = {1979},
- editor = {Jenne, E. A.},
- pages = {857--892},
- publisher = {American Chemical Society},
- series = {Series 93},
- url = {https://www.worldcat.org/oclc/4591313},
-}
-
@Article{Oth76,
author = {Othmer, H. G.},
journal = {Chemical Engineering Science},
@@ -461,9 +449,9 @@
journal = {Geofluids},
title = {{T}he potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems},
year = {2010},
- volume = {10},
number = {1-2},
pages = {161--192},
+ volume = {10},
af = {Shock, E.EOLEOLCanovas, P.},
doi = {10.1111/j.1468-8123.2010.00277.x},
si = {Sp. Iss. SI},
@@ -494,14 +482,14 @@
}
@Article{SHS89,
- author = {Shock, Everett L. and Helgeson, Harold C. and Sverjensky, Dimitri A.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of inorganic neutral species},
- year = {1989},
- volume = {53},
- number = {9},
- pages = {2157--2183},
- doi = {10.1016/0016-7037(89)90341-4},
+ author = {Shock, Everett L. and Helgeson, Harold C. and Sverjensky, Dimitri A.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of inorganic neutral species},
+ year = {1989},
+ number = {9},
+ pages = {2157--2183},
+ volume = {53},
+ doi = {10.1016/0016-7037(89)90341-4},
}
@Article{SOJSH92,
@@ -509,9 +497,9 @@
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},
+ volume = {88},
doi = {10.1039/FT9928800803},
}
@@ -531,9 +519,9 @@
journal = {Journal of Geophysical Research},
title = {Organic synthesis during fluid mixing in hydrothermal systems},
year = {1998},
- volume = {103},
number = {E12},
pages = {28513--28527},
+ volume = {103},
doi = {10.1029/98JE02142},
issn = {0148-0227},
}
@@ -701,17 +689,6 @@
doi = {10.1038/ncomms2998},
}
- at Article{FMM_14,
- author = {Fuchida, Shigeshi and Mizuno, Yuki and Masuda, Harue and Toki, Tomohiro and Makita, Hiroko},
- journal = {Organic Geochemistry},
- title = {Concentrations and distributions of amino acids in black and white smoker fluids at temperatures over 200 °C},
- year = {2014},
- pages = {98--106},
- volume = {66},
- doi = {10.1016/j.orggeochem.2013.11.008},
- issn = {0146-6380},
-}
-
@Article{MD98,
author = {Merino, Enrique and Dewers, Thomas},
journal = {Journal of Hydrology},
@@ -746,14 +723,14 @@
}
@Article{Ber88,
- author = {Berman, R. G.},
- journal = {Journal of Petrology},
- title = {{I}nternally-consistent thermodynamic data for minerals in the system {N}a$_2${O}--{K}$_2${O}--{C}a{O}--{M}g{O}--{F}e{O}--{F}e$_2${O}$_3$--{A}l$_2${O}$_3$--{S}i{O}$_2$--{T}i{O}$_2$--{H}$_2${O}--{CO}$_2$},
- year = {1988},
- volume = {29},
- number = {2},
- pages = {445--522},
- doi = {10.1093/petrology/29.2.445},
+ author = {Berman, R. G.},
+ journal = {Journal of Petrology},
+ title = {{I}nternally-consistent thermodynamic data for minerals in the system {N}a$_2${O}--{K}$_2${O}--{C}a{O}--{M}g{O}--{F}e{O}--{F}e$_2${O}$_3$--{A}l$_2${O}$_3$--{S}i{O}$_2$--{T}i{O}$_2$--{H}$_2${O}--{CO}$_2$},
+ year = {1988},
+ number = {2},
+ pages = {445--522},
+ volume = {29},
+ doi = {10.1093/petrology/29.2.445},
}
@Article{Dic17,
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