[CHNOSZ-commits] r285 - in pkg/CHNOSZ: . R inst/extdata/cpetc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 10 05:03:11 CET 2017
Author: jedick
Date: 2017-11-10 05:02:50 +0100 (Fri, 10 Nov 2017)
New Revision: 285
Added:
pkg/CHNOSZ/inst/extdata/cpetc/bluered.txt
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/util.plot.R
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/findit.Rd
pkg/CHNOSZ/man/nonideal.Rd
Log:
ZC.col(): use precomputed palette; remove Imports:colorspace from DESCRIPTION
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/DESCRIPTION 2017-11-10 04:02:50 UTC (rev 285)
@@ -1,12 +1,12 @@
-Date: 2017-11-09
+Date: 2017-11-10
Package: CHNOSZ
-Version: 1.1.0-82
+Version: 1.1.0-83
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Depends: R (>= 3.1.0)
Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
-Imports: grDevices, graphics, stats, utils, colorspace
+Imports: grDevices, graphics, stats, utils
Description: An integrated set of tools for thermodynamic calculations in geochemistry and
compositional biology. Thermodynamic properties are taken from a database for minerals
and inorganic and organic aqueous species including biomolecules, or from amino acid
Modified: pkg/CHNOSZ/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/NAMESPACE 2017-11-10 04:02:50 UTC (rev 285)
@@ -75,7 +75,4 @@
"uniroot", "median")
importFrom("utils", "browseURL", "capture.output", "combn", "demo",
"example", "head", "installed.packages", "read.csv", "tail",
- "write.csv", "write.table")
-
-# Imports from other packages
-importFrom("colorspace", "diverge_hcl")
+ "write.csv", "write.table", "read.table")
Modified: pkg/CHNOSZ/R/util.plot.R
===================================================================
--- pkg/CHNOSZ/R/util.plot.R 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/R/util.plot.R 2017-11-10 04:02:50 UTC (rev 285)
@@ -179,7 +179,10 @@
z <- z * 999/diff(range(z))
z <- round(z - min(z)) + 1
# diverging (blue - light grey - red) palette
- dcol <- colorspace::diverge_hcl(1000, c = 100, l = c(50, 90), power = 1)
+ # dcol <- colorspace::diverge_hcl(1000, c = 100, l = c(50, 90), power = 1)
+ # use precomputed values
+ file <- system.file("extdata/cpetc/bluered.txt", package = "CHNOSZ")
+ dcol <- read.table(file, as.is=TRUE)[[1]]
# reverse the palette so red is at lower ZC (more reduced)
rev(dcol)[z]
}
Added: pkg/CHNOSZ/inst/extdata/cpetc/bluered.txt
===================================================================
--- pkg/CHNOSZ/inst/extdata/cpetc/bluered.txt (rev 0)
+++ pkg/CHNOSZ/inst/extdata/cpetc/bluered.txt 2017-11-10 04:02:50 UTC (rev 285)
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Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/berman.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -102,7 +102,7 @@
\references{
Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{http://www.worldcat.org/oclc/474880901}
-Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O–K{\s2}O–CaO–MgO–FeO–Fe{\s2}O{\s3}–Al{\s2}O{\s3}–SiO{\s2}–TiO{\s2}–H{\s2}O–CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. \emph{Am. J. Sci.} \bold{278-A}, 1--229. \url{http://www.worldcat.org/oclc/13594862}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/diagram.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -136,7 +136,7 @@
\section{Activity Coefficients}{
The wording in this page and names of variables in functions refer exclusively to \samp{activities} of aqueous species.
-However, if activity coefficients are calculated (using the \code{IS} argument in \code{\link{affinity}}), then these variables are effectively transformed to molalities (see \code{tests/testthat/test-logmolality.R}).
+However, if activity coefficients are calculated (using the \code{IS} argument in \code{\link{affinity}}), then these variables are effectively transformed to molalities (see \code{tests/testthat/} \code{test-logmolality.R}).
So that the labels on diagrams are adjusted accordingly, \code{\link{diagram}} sets the \code{use.molality} argument of \code{\link{axis.label}} to TRUE if \code{IS} was supplied as an argument to \code{\link{affinity}}.
The labeling as molality takes effect even if \code{IS} is set to 0; this way, by including (or not) the \code{IS = 0} argument to \code{affinity}, the user decides whether to label aqueous species variables as molality (or activity) for calculations at zero ionic strength (where molality = activity).
}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/examples.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -26,11 +26,9 @@
\code{examples} runs all the examples in the documentation for the package.
\code{\link{example}} is called for each topic with \code{ask} set to \code{FALSE} (so all of the figures are shown without prompting the user).
-\code{demos} is a function to run other examples that are provided as \code{\link{demo}s}.
-\code{\link{demo}} is called with settings to not echo the source code and to not ask before making each plot.
+\code{demos} runs all the \code{\link{demo}s} in the package.
The demo(s) to run is/are specified by \code{which}; the default is to run them in the order of the list below.
-Demos that are displayed on the CHNOSZ website (\url{http://chnosz.net/demos}) are indicated with an asterisk.
-See the comments in the source code for more information about each demo.
+(Demos that are displayed on the CHNOSZ website (\url{http://chnosz.net/demos}) are indicated with an asterisk.)
\tabular{ll}{
\code{sources} \tab Cross-check the reference list with the thermodynamic database \cr
@@ -48,12 +46,12 @@
\code{mosaic} \tab * Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
\code{copper} \tab * Another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
\code{solubility} \tab * Solubility of calcite (cf. Manning et al., 2013) or \CO2 (cf. Stumm and Morgan, 1996) \cr
- \code{wjd} \tab * Gibbs energy minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast \cr
+ \code{wjd} \tab * \eqn{G}{G} minimization: prebiological atmospheres (Dayhoff et al., 1964) and cell periphery of yeast \cr
\code{dehydration} \tab * \logK of dehydration reactions; SVG file contains tooltips and links \cr
\code{bugstab} \tab * Formation potential of microbial proteins in colorectal cancer (Dick, 2016) \cr
\code{Shh} \tab * Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015) \cr
\code{activity_ratios} \tab * Mineral stability plots with activity ratios on the axes \cr
- \code{adenine} \tab * HKF parameters regressed from heat capacity and volume of aqueous adenine (Lowe et al., 2017) \cr
+ \code{adenine} \tab * HKF regression of heat capacity and volume of aqueous adenine (Lowe et al., 2017) \cr
\code{DEW} \tab * Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b) \cr
\code{lambda} \tab * Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988) \cr
\code{TCA} \tab * Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
@@ -81,7 +79,7 @@
Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. \emph{FEMS Microbiol. Rev.} \bold{25}, 175--243. \url{https://doi.org/10.1016/S0168-6445(00)00062-0}
-Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O–K{\s2}O–CaO–MgO–FeO–Fe{\s2}O{\s3}–Al{\s2}O{\s3}–SiO{\s2}–TiO{\s2}–H{\s2}O–CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
Canovas, P. A., III and Shock, E. L. (2016) Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle. \emph{Geochim. Cosmochim. Acta} \bold{195}, 293--322. \url{https://doi.org/10.1016/j.gca.2016.08.028}
@@ -120,10 +118,6 @@
\dontshow{opar <- par(no.readonly=TRUE)}
demos(c("ORP", "NaCl"))
\dontshow{par(opar)}
-\dontrun{
-# use the following to run examples in all help topics
-examples()}
}
-
\concept{Other tools}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/extdata.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -43,6 +43,7 @@
\item \code{SC10_Rainbow.csv} Values of temperature (\degC, pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. See the vignette \code{anintro.Rmd} for an example that uses this file.
\item \code{SS98_Fig5a.csv}, \code{SS98_Fig5b.csv} Values of logarithm of fugacity of \O2 and pH as a function of temperature for mixing of seawater and hydrothermal fluid, digitized from Figs. 5a and b of Shock and Schulte, 1998. See the vignette \code{anintro.Rmd} for an example that uses this file.
\item \code{rubisco.csv} UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See the vignette \code{anintro.Rmd} for an example that uses this file.
+ \item \code{bluered.txt} Blue - light grey - red color palette, computed using \CRANpkg{colorspace}\code{::diverge_hcl(1000,} \code{c = 100, l = c(50, 90), power = 1)}. This is used by \code{\link{ZC.col}}.
}
Files in \code{fasta} contain protein sequences:
@@ -111,7 +112,7 @@
\references{
Bazarkina, E. F., Zotov, A. V. and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1–1000 bar and 25°C. \emph{Geol. Ore Deposits} \bold{52}, 167--178. \url{https://doi.org/10.1134/S1075701510020054}
-Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O–K{\s2}O–CaO–MgO–FeO–Fe{\s2}O{\s3}–Al{\s2}O{\s3}–SiO{\s2}–TiO{\s2}–H{\s2}O–CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. \emph{Science} \bold{146}, 1461--1464. \url{https://doi.org/10.1126/science.146.3650.1461}
@@ -133,8 +134,6 @@
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. \emph{Nature} \bold{425}(6959), 686--691. \url{https://doi.org/10.1038/nature02026}
-HAMAP system. HAMAP FTP directory, \url{ftp://ftp.expasy.org/databases/hamap/}
-
Hnědkovský, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. \emph{J. Chem. Thermodyn.} \bold{28}, 125--142. \url{https://doi.org/10.1006/jcht.1996.0011}
Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{https://doi.org/10.1006/jcht.1997.0192}
Modified: pkg/CHNOSZ/man/findit.Rd
===================================================================
--- pkg/CHNOSZ/man/findit.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/findit.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -50,16 +50,16 @@
These settings have been selected to be able to run the function quickly in the higher dimensions.
Detailed studies of a system might have to use more iterations and/or higher resolutions.
- \tabular{rrrrr}{
- \code{nd} \tab \code{niter} \tab \code{res} \tab grid points (\code{res^nd}) \tab \code{rat} \cr
- 1 \tab 4 \tab 128 \tab 128 \tab 0.7 \cr
- 2 \tab 6 \tab 64 \tab 4096 \tab 0.7 \cr
- 3 \tab 6 \tab 16 \tab 4096 \tab 0.8 \cr
- 4 \tab 8 \tab 8 \tab 4096 \tab 0.9 \cr
- 5 \tab 12 \tab 6 \tab 7776 \tab 0.9 \cr
- 6 \tab 12 \tab 4 \tab 4096 \tab 0.95 \cr
- 7 \tab 12 \tab 4 \tab 16384 \tab 0.95 \cr
- }
+\tabular{rrrrr}{
+ \code{nd} \tab \code{niter} \tab \code{res} \tab grid points (\code{res^nd}) \tab \code{rat} \cr
+ 1 \tab 4 \tab 128 \tab 128 \tab 0.7 \cr
+ 2 \tab 6 \tab 64 \tab 4096 \tab 0.7 \cr
+ 3 \tab 6 \tab 16 \tab 4096 \tab 0.8 \cr
+ 4 \tab 8 \tab 8 \tab 4096 \tab 0.9 \cr
+ 5 \tab 12 \tab 6 \tab 7776 \tab 0.9 \cr
+ 6 \tab 12 \tab 4 \tab 4096 \tab 0.95 \cr
+ 7 \tab 12 \tab 4 \tab 16384 \tab 0.95 \cr
+}
The function performs \code{niter} iterations.
At first, the limits of the parameters given in \code{lims} define the extent of a \eqn{nd}-dimensional box around the space of interest.
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2017-11-09 13:22:52 UTC (rev 284)
+++ pkg/CHNOSZ/man/nonideal.Rd 2017-11-10 04:02:50 UTC (rev 285)
@@ -8,7 +8,8 @@
}
\usage{
- nonideal(species, speciesprops, IS, T, P, A_DH, B_DH, method=get("thermo")$opt$nonideal)
+ nonideal(species, speciesprops, IS, T, P, A_DH, B_DH,
+ method=get("thermo")$opt$nonideal)
Bdot(TC, P, showsplines = "")
}
@@ -74,11 +75,13 @@
lty <- 1:3
species <- c("H2PO4-", "HADP-2", "HATP-3", "ATP-4")
col <- rainbow(4)
-thermo.plot.new(xlim = range(IS), ylim = c(0, 1), xlab = axis.label("IS"), ylab = "gamma")
+thermo.plot.new(xlim = range(IS), ylim = c(0, 1),
+ xlab = axis.label("IS"), ylab = "gamma")
for(j in 1:3) {
# use subcrt to generate speciesprops
speciesprops <- subcrt(species, T = rep(T[j], length(IS)))$out
- # use nonideal to calculate loggamma; this also adjusts G, H, S, Cp, but we don't use them here
+ # use nonideal to calculate loggamma; this also adjusts G, H, S, Cp,
+ # but we don't use them here
nonidealprops <- nonideal(species, speciesprops, IS = IS, T = convert(T[j], "K"))
for(i in 1:4) lines(IS, 10^(nonidealprops[[i]]$loggam), lty=lty[j], col=col[i])
}
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