[CHNOSZ-commits] r144 - in pkg/CHNOSZ: . R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 12 03:14:49 CET 2017
Author: jedick
Date: 2017-02-12 03:14:49 +0100 (Sun, 12 Feb 2017)
New Revision: 144
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/revisit.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/eos-regress.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
anintro.Rmd: comment "csl: elementa.csl" for building on R-Forge
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-12 02:14:49 UTC (rev 144)
@@ -1,6 +1,6 @@
-Date: 2017-02-11
+Date: 2017-02-12
Package: CHNOSZ
-Version: 1.0.8-33
+Version: 1.0.8-34
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/revisit.R
===================================================================
--- pkg/CHNOSZ/R/revisit.R 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/R/revisit.R 2017-02-12 02:14:49 UTC (rev 144)
@@ -172,7 +172,7 @@
xlab <- "loga2"
if(is.null(xlim)) xlim <- extendrange(loga2)
if(is.null(ylim)) ylim <- extendrange(loga1)
- plot(loga2, loga1, xlab=xlab, ylab=ylab, pch=pch, col=col, xlim=xlim, ylim=ylim)
+ plot(loga2, loga1, xlab=xlab, ylab=ylab, pch=pch, col=col, xlim=xlim, ylim=ylim, cex=cex)
# add a 1:1 line
lines(range(loga2), range(loga2), col="grey")
# add a lowess line
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-12 02:14:49 UTC (rev 144)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-33 (2017-02-11)
+CHANGES IN CHNOSZ 1.0.8-34 (2017-02-12)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-12 02:14:49 UTC (rev 144)
@@ -20,7 +20,9 @@
\usepackage[utf8]{inputenc}
bibliography: vig.bib
link-citations: yes
-csl: elementa.csl
+# The custom CSL file gives a build error on R-Forge (2017-02-12):
+# pandoc-citeproc: error while parsing the XML string
+#csl: elementa.csl
---
```{r options, include=FALSE}
@@ -46,7 +48,8 @@
dpi <- 72
# use pngquant to optimize PNG images
knit_hooks$set(pngquant = hook_pngquant)
-pngquant <- "--speed=1 --quality=0-50"
+# pngquant isn't available on R-Forge ...
+if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL else pngquant <- "--speed=1 --quality=0-50"
# some frequently used HTML expressions
logfO2 <- "log<i>f</i><sub>O<sub>2</sub></sub>"
# use lowercase here because these tend to be variable names in the examples
@@ -56,7 +59,7 @@
# http://stackoverflow.com/questions/23852753/knitr-with-gridsvg
# Set up a chunk hook for manually saved plots.
knit_hooks$set(custom.plot = hook_plot_custom)
-# hook to change <img /> to <embed /> - required for interactive SVG
+# hook to change <img /> to <embed /> -- required for interactive SVG
hook_plot <- knit_hooks$get("plot")
knit_hooks$set(plot = function(x, options) {
x <- hook_plot(x, options)
@@ -921,7 +924,7 @@
Caveat: these plots demonstrate some possibilities in CHNOSZ and are not necessarily realistic portrayals of this system.
It does seem odd to balance on a fugacious component like `r o2` or `r h2o`.
Unlike different choices of basis species, which are thermodynamically equivalent (see the example above for a mineral system), the choice of balance reflects extra-thermodynamic factors.
-For instance, the widespread rule of thumb for balancing mineral reactions on a component is unrealistic for processes where volume is conserved [@MC11].
+For instance, the widespread rule of thumb for balancing mineral reactions on a component is unrealistic for processes where volume is conserved [@MD98].
Any choice of balancing constraints may oversimplify the physical or biological context for reactions of organic species or biomolecules.
While choosing an inappropriate balance leads to infeasible models, consideration of the possibilities might give insight into the conditions affecting the dynamics of some systems.
Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-02-12 02:14:49 UTC (rev 144)
@@ -19,7 +19,7 @@
\usepackage[utf8]{inputenc}
bibliography: vig.bib
link-citations: yes
-csl: elementa.csl
+#csl: elementa.csl
---
```{r setup, include=FALSE}
@@ -28,7 +28,8 @@
options(htmltools.dir.version = FALSE)
# use pngquant to optimize PNG images
knitr::knit_hooks$set(pngquant = knitr::hook_pngquant)
-pngquant <- "--speed=1 --quality=0-50"
+# pngquant isn't available on R-Forge ...
+if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL else pngquant <- "--speed=1 --quality=0-50"
```
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2017-02-11 18:37:23 UTC (rev 143)
+++ pkg/CHNOSZ/vignettes/vig.bib 2017-02-12 02:14:49 UTC (rev 144)
@@ -115,14 +115,14 @@
}
@Article{GHB_03,
- author = {Ghaemmaghami, Sina and Huh, Won-Ki and Bower, Kiowa and Howson, Russell W. and Belle, Archana and Dephoure, Noah and O'Shea, Erin K. and Weissman, Jonathan S.},
- journal = {Nature},
- title = {Global analysis of protein expression in yeast},
- year = {2003},
- volume = {425},
- number = {6959},
- pages = {737--741},
- doi = {10.1038/nature02046},
+ author = {Ghaemmaghami, Sina and Huh, Won-Ki and Bower, Kiowa and Howson, Russell W. and Belle, Archana and Dephoure, Noah and O'Shea, Erin K. and Weissman, Jonathan S.},
+ journal = {Nature},
+ title = {Global analysis of protein expression in yeast},
+ year = {2003},
+ volume = {425},
+ number = {6959},
+ pages = {737--741},
+ doi = {10.1038/nature02046},
}
@Incollection{Hel70c,
@@ -182,19 +182,6 @@
doi = {10.2138/rmg.2013.75.5},
}
- at Article{MC11,
- author = {Merino, Enrique and Canals, Àngels},
- journal = {American Journal of Science},
- title = {Self-accelerating dolomite-for-calcite replacement: Self-organized dynamics of burial dolomitization and associated mineralization},
- year = {2011},
- volume = {311},
- number = {7},
- pages = {573--607},
- doi = {10.2475/07.2011.01},
- sn = {0002-9599},
- z9 = {0},
-}
-
@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.},
title = {A comparison of computerized chemical models for equilibrium calculations in aqueous systems},
@@ -458,3 +445,15 @@
doi = {10.1038/ncomms2998},
}
+ at Article{MD98,
+ author = {Merino, Enrique and Dewers, Thomas},
+ journal = {Journal of Hydrology},
+ title = {Implications 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},
+}
+
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