[CHNOSZ-commits] r669 - in pkg/CHNOSZ: . inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 7 13:12:28 CEST 2021
Author: jedick
Date: 2021-04-07 13:12:28 +0200 (Wed, 07 Apr 2021)
New Revision: 669
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/TODO
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/equilibrate.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/species.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Fix some long lines in Rd files
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/DESCRIPTION 2021-04-07 11:12:28 UTC (rev 669)
@@ -1,6 +1,6 @@
Date: 2021-04-07
Package: CHNOSZ
-Version: 1.4.0-38
+Version: 1.4.0-39
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 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/inst/TODO 2021-04-07 11:12:28 UTC (rev 669)
@@ -28,14 +28,6 @@
- make swap.basis() work when DEW model is active
-[20210212]
-
-- Fix formatting of messages from palply() (seen with read.fasta())
-
-[20210301]
-
-- anintro.Rmd: change red to blue for sulfur basis species
-
[20210303]
- Add demo for effective equilibrium constant for diglycine on T-pH plot at
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/man/buffer.Rd 2021-04-07 11:12:28 UTC (rev 669)
@@ -42,7 +42,7 @@
}
\seealso{
- \code{link{diagram}} with \code{type} set to the name of a basis species solves for the activity of the basis species.
+ \code{\link{diagram}} with \code{type} set to the name of a basis species solves for the activity of the basis species.
}
\examples{
Modified: pkg/CHNOSZ/man/equilibrate.Rd
===================================================================
--- pkg/CHNOSZ/man/equilibrate.Rd 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/man/equilibrate.Rd 2021-04-07 11:12:28 UTC (rev 669)
@@ -11,8 +11,9 @@
\usage{
equilibrate(aout, balance = NULL, loga.balance = NULL,
- ispecies = !grepl("cr", aout$species$state), normalize = FALSE, as.residue = FALSE,
- method = c("boltzmann", "reaction"), tol = .Machine$double.eps^0.25)
+ ispecies = !grepl("cr", aout$species$state), normalize = FALSE,
+ as.residue = FALSE, method = c("boltzmann", "reaction"),
+ tol = .Machine$double.eps^0.25)
equil.boltzmann(Astar, n.balance, loga.balance)
equil.reaction(Astar, n.balance, loga.balance, tol = .Machine$double.eps^0.25)
moles(eout)
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/man/examples.Rd 2021-04-07 11:12:28 UTC (rev 669)
@@ -30,40 +30,40 @@
\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.
- \tabular{ll}{
- \code{sources} \tab Cross-check the reference list with the thermodynamic database \cr
- \code{protein.equil} \tab Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011) \cr
- \code{affinity} \tab Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001) \cr
- \code{NaCl} \tab Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
- \code{density} \tab Density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
- \code{ORP} \tab Temperature dependence of oxidation-reduction potential for redox standards \cr
- \code{findit} \tab Minimize the standard deviation of logarithms of activities of sulfur species \cr
- \code{ionize} \tab ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK \cr
- \code{buffer} \tab Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
- \code{protbuff} \tab Chemical activities buffered by thiol peroxidases or sigma factors \cr
- \code{glycinate} \tab Metal-glycinate complexes (Shock and Koretsky, 1995; Azadi et al., 2019) \cr
- \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{arsenic} \tab Another example of \code{\link{mosaic}}: Eh-pH diagram for the system As-O-H-S (Lu and Zhu, 2011) \cr
- \code{solubility} \tab Solubility of calcite (cf. Manning et al., 2013) and \CO2 (cf. Stumm and Morgan, 1996) \cr
- \code{gold} \tab Solubility of gold (Akinfiev and Zotov; 2001; Stef{\aacute}nsson and Seward, 2004; Williams-Jones et al., 2009) \cr
- \code{contour} \tab Gold solubility contours on a log fO2 - pH diagram (Williams-Jones et al., 2009) \cr
- \code{sphalerite} \tab Solubility of sphalerite (Akinfiev and Tagirov, 2014) \cr
- \code{zinc} \tab Solubilities of multiple minerals (zincite and sphalerite) \cr
- \code{dehydration} \tab \logK of dehydration reactions; SVG file contains tooltips and links \cr
- \code{Shh} \tab Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015) \cr
- \code{saturation} \tab Equilibrium activity diagram showing activity ratios and mineral saturation limits (Bowers et al., 1984) \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{potassium} \tab Comparison of thermodynamic datasets for predicting mineral stabilities (Sverjensky et al., 1991) \cr
- \code{TCA} \tab Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
- \code{aluminum} \tab Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014) \cr
- \code{carboxylase} \tab Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase \cr
- \code{AkDi} \tab Henry's constant of dissolved gases (Akinfiev and Diamond, 2003) \cr
- \code{comproportionation} \tab Gibbs energy of sulfur comproportionation (Amend et al., 2020) \cr
- \code{Pourbaix} \tab Eh-pH diagram for Fe-O-H with equisolubility lines (Pourbaix, 1974) \cr
- \code{E_coli} \tab Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016) \cr
+ \describe{
+ \item{sources}{Cross-check the reference list with the thermodynamic database}
+ \item{protein.equil}{Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011)}
+ \item{affinity}{Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001)}
+ \item{NaCl}{Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)}
+ \item{density}{Density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}})}
+ \item{ORP}{Temperature dependence of oxidation-reduction potential for redox standards}
+ \item{findit}{Minimize the standard deviation of logarithms of activities of sulfur species}
+ \item{ionize}{ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK}
+ \item{buffer}{Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995)}
+ \item{protbuff}{Chemical activities buffered by thiol peroxidases or sigma factors}
+ \item{glycinate}{Metal-glycinate complexes (Shock and Koretsky, 1995; Azadi et al., 2019)}
+ \item{mosaic}{Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965)}
+ \item{copper}{Another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001)}
+ \item{arsenic}{Another example of \code{\link{mosaic}}: Eh-pH diagram for the system As-O-H-S (Lu and Zhu, 2011)}
+ \item{solubility}{Solubility of calcite (cf. Manning et al., 2013) and \CO2 (cf. Stumm and Morgan, 1996)}
+ \item{gold}{Solubility of gold (Akinfiev and Zotov; 2001; Stef{\aacute}nsson and Seward, 2004; Williams-Jones et al., 2009)}
+ \item{contour}{Gold solubility contours on a log fO2 - pH diagram (Williams-Jones et al., 2009)}
+ \item{sphalerite}{Solubility of sphalerite (Akinfiev and Tagirov, 2014)}
+ \item{zinc}{Solubilities of multiple minerals (zincite and sphalerite)}
+ \item{dehydration}{\logK of dehydration reactions; SVG file contains tooltips and links}
+ \item{Shh}{Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015)}
+ \item{saturation}{Equilibrium activity diagram showing activity ratios and mineral saturation limits (Bowers et al., 1984)}
+ \item{adenine}{HKF regression of heat capacity and volume of aqueous adenine (Lowe et al., 2017)}
+ \item{DEW}{Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b)}
+ \item{lambda}{Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988)}
+ \item{potassium}{Comparison of thermodynamic datasets for predicting mineral stabilities (Sverjensky et al., 1991)}
+ \item{TCA}{Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016)}
+ \item{aluminum}{Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014)}
+ \item{carboxylase}{Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase}
+ \item{AkDi}{Henry's constant of dissolved gases (Akinfiev and Diamond, 2003)}
+ \item{comproportionation}{Gibbs energy of sulfur comproportionation (Amend et al., 2020)}
+ \item{Pourbaix}{Eh-pH diagram for Fe-O-H with equisolubility lines (Pourbaix, 1974)}
+ \item{E_coli}{Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016)}
}
For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos.
Modified: pkg/CHNOSZ/man/species.Rd
===================================================================
--- pkg/CHNOSZ/man/species.Rd 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/man/species.Rd 2021-04-07 11:12:28 UTC (rev 669)
@@ -7,7 +7,8 @@
}
\usage{
- species(species = NULL, state = NULL, delete = FALSE, add = FALSE, index.return = FALSE)
+ species(species = NULL, state = NULL, delete = FALSE, add = FALSE,
+ index.return = FALSE)
}
\arguments{
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2021-04-07 10:41:18 UTC (rev 668)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2021-04-07 11:12:28 UTC (rev 669)
@@ -698,7 +698,7 @@
bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
m1 <- mosaic(bases, pH = c(0, 12, res), Eh=c(-1.2, 0.75, res), T=T)
diagram(m1$A.species, lwd = 2)
-diagram(m1$A.bases, add = TRUE, col = "red1", col.names = "red1", lty = 3,
+diagram(m1$A.bases, add = TRUE, col = 4, col.names = 4, lty = 3,
italic = TRUE)
water.lines(m1$A.species, col = "blue1")
```
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