[CHNOSZ-commits] r391 - in pkg/CHNOSZ: . demo inst man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Feb 9 09:19:06 CET 2019 

Author: jedick
Date: 2019-02-09 09:18:42 +0100 (Sat, 09 Feb 2019)
New Revision: 391

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/00Index
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/add.obigt.Rd
   pkg/CHNOSZ/man/affinity.Rd
   pkg/CHNOSZ/man/basis.Rd
   pkg/CHNOSZ/man/berman.Rd
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Rd files: fix truncated lines in PDF


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-09 08:18:42 UTC (rev 391)
@@ -1,6 +1,6 @@
 Date: 2019-02-09
 Package: CHNOSZ
-Version: 1.1.3-99
+Version: 1.1.3-100
 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/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/demo/00Index	2019-02-09 08:18:42 UTC (rev 391)
@@ -10,7 +10,7 @@
 buffer          Minerals and aqueous species as buffers of hydrogen fugacity
 protbuff        Chemical activities buffered by thiol peroxidases or sigma factors
 yeastgfp        Subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
-glycinate       Divalent and monovalent metal-glycinate complexes
+glycinate       Metal-glycinate complexes
 mosaic          Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species
 copper          Another example of mosaic(): complexation of copper with glycine species
 solubility      Solubility of calcite and CO2(gas) as a function of pH

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-02-09 08:18:42 UTC (rev 391)
@@ -24,7 +24,7 @@
   try both qpdf and ghostscript to compact vignettes:
   R CMD build --compact-vignettes=both chnosz/
 
-- check reverse dependencies: ecipex and canprot packages
+- check reverse dependencies on CRAN: LipidMS, canprot, ecipex, iemisc as of 2019-02-09
 
 - vignettes/obigt.bib: check correct year for CHNOSZ reference
 

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/inst/NEWS	2019-02-09 08:18:42 UTC (rev 391)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.1.3-93 (2019-02-08)
----------------------------------------
+CHANGES IN CHNOSZ 1.1.3-100 (2019-02-09)
+----------------------------------------
 
 BUG FIXES
 
@@ -19,8 +19,8 @@
   reactions, and the user hasn't provided balance coefficients, stop
   with an error instead of setting the balance cofficients to 1.
   Thanks to Shuang Kong for an example calculation and Tucker Ely for
-  a previous request to produce an error here. The affected code is in
-  balance(), an unexported function used in equilibrate() and
+  a previous suggestion to produce an error here. The affected code is
+  in balance(), an unexported function used in equilibrate() and
   diagram() (and now also solubility()).
 
 NEW FEATURE: SOLUBILITY CALCULATIONS

Modified: pkg/CHNOSZ/man/add.obigt.Rd
===================================================================
--- pkg/CHNOSZ/man/add.obigt.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/add.obigt.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -118,7 +118,8 @@
 add.obigt("OldAA")
 DLH06 <- subcrt(c("[AABB]", "[UPBB]", "H2O"), c(-1, 1, 1), T = seq(0, 300, 10))
 xlab <- axis.label("T"); ylab <- axis.label("DG", prefix="k")
-plot(Kit14$out$T, Kit14$out$G/1000, type = "l", ylim = c(10, 35), xlab = xlab, ylab = ylab)
+plot(Kit14$out$T, Kit14$out$G/1000, type = "l", ylim = c(10, 35),
+     xlab = xlab, ylab = ylab)
 lines(DLH06$out$T, DLH06$out$G/1000, lty = 2)
 legend("topleft", c("Dick et al., 2006", "Kitadai, 2014"), lty = c(2, 1))
 title(main = "AABB = UPBB + H2O; after Figure 9 of Kitadai, 2014")

Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/affinity.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -7,8 +7,9 @@
 }
 
 \usage{
-  affinity(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rhomin = FALSE,
-    return.buffer=FALSE, return.sout=FALSE, balance="PBB", iprotein=NULL, loga.protein=-3)
+  affinity(..., property = NULL, sout = NULL, exceed.Ttr = FALSE,
+    exceed.rhomin = FALSE, return.buffer = FALSE, return.sout = FALSE,
+    balance = "PBB", iprotein = NULL, loga.protein = -3)
 }
 
 \arguments{

Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/basis.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -33,11 +33,9 @@
 
 Whenever \code{basis} is called with NULL values of both \code{state} and \code{logact}, the new set of species, if they are a valid basis set, completely replaces any existing basis definition.
 If this occurs, any existing species definition (created by the \code{species} function) is deleted.
-Call \code{basis} with \code{delete} set to TRUE or \code{species} set to \samp{""} to clear the basis definition.
-This also deletes the \code{\link{species}} list, if any.
+Call \code{basis} with \code{delete} set to TRUE or \code{species} set to \samp{""} to clear the basis definition and that of the \code{\link{species}}, if present.
 
 If the value of \code{basis} is one of the keywords in the following table, the corresponding set of basis species is loaded, and their activities are given preset values.
-This approach is used by many of the examples in the package.
 The basis species identified by these keywords are aqueous except for \H2O (liq), \O2 (gas) and \Fe2O3 (hematite).
 
   \tabular{ll}{

Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/berman.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -126,7 +126,8 @@
 # and not coesite or some other phase of SiO2
 iSiO2 <- rownames(basis()) == "SiO2"
 stopifnot(info(basis()$ispecies[iSiO2])$name == "quartz")
-# Berman's dataset doesn't have the upper temperature limits, so we don't need exceed.Ttr here
+# Berman's dataset doesn't have the upper temperature limits,
+# so we don't need exceed.Ttr here
 a <- affinity(`K+` = c(0, 5, res), T = c(200, 650, res), P = 1000, exceed.rhomin = TRUE)
 diagram(a, add = TRUE, names = NULL, col = "blue", lwd = 1.5)
 # the list of references:

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/diagram.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -14,25 +14,26 @@
     eout,
     # type plot
     type = "auto", alpha = FALSE, normalize = FALSE,
-    as.residue = FALSE, balance=NULL, groups=as.list(1:length(eout$values)),
+    as.residue = FALSE, balance = NULL, groups = as.list(1:length(eout$values)),
     # figure size and sides for axis tick marks
-    xrange=NULL, mar=NULL, yline=par("mgp")[1]+0.3, side=1:4,
+    xrange = NULL, mar = NULL, yline = par("mgp")[1]+0.3, side = 1:4,
     # axis limits and labels
-    ylog=TRUE, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
+    ylog = TRUE, xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL,
     # character sizes
-    cex=par("cex"), cex.names=1, cex.axis=par("cex"),
+    cex = par("cex"), cex.names = 1, cex.axis = par("cex"),
     # line styles
-    lty=NULL, lwd=par("lwd"), dotted=NULL, spline.method = NULL, contour.method = "edge",
+    lty = NULL, lwd = par("lwd"), dotted = NULL, spline.method = NULL,
+    contour.method = "edge",
     # colors
-    col=par("col"), col.names=par("col"), fill=NULL,
-    fill.NA="slategray1", limit.water=TRUE,
+    col = par("col"), col.names = par("col"), fill = NULL,
+    fill.NA = "slategray1", limit.water = TRUE,
     # field and line labels
-    names=NULL, format.names=TRUE, bold = FALSE, italic = FALSE, 
-    font = par("font"), family = par("family"), adj=0.5, dy=0, srt=0,
+    names = NULL, format.names = TRUE, bold = FALSE, italic = FALSE, 
+    font = par("font"), family = par("family"), adj = 0.5, dy = 0, srt = 0,
     # title and legend
-    main=NULL, legend.x=NA,
+    main = NULL, legend.x = NA,
     # plotting controls
-    add=FALSE, plot.it=TRUE, tplot=TRUE, ...)
+    add = FALSE, plot.it = TRUE, tplot = TRUE, ...)
   strip(affinity, ispecies = NULL, col = NULL, ns = NULL, 
     xticks = NULL, ymin = -0.2, xpad = 1, cex.names = 0.7)
   find.tp(x)

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/man/examples.Rd	2019-02-09 08:18:42 UTC (rev 391)
@@ -28,37 +28,36 @@
 
 \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.)
 
   \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{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{revisit} \tab Coefficient of variation of metastable equilibrium activities of proteins \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{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{yeastgfp} \tab * Subcellular locations: \logfO2 - \logaH2O and \loga - \logfO2 diagrams (Dick, 2009) \cr
-    \code{glycinate} \tab * Divalent and monovalent metal-glycinate complexes (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{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{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{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{TCA} \tab * Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
-    \code{go-IU} \tab * Diagrams using thermodynamic data in the SUPCRTBL compilation (Zimmer et al., 2016) \cr
-    \code{carboxylase} \tab * Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase \cr
+    \code{yeastgfp} \tab Subcellular locations: \logfO2 - \logaH2O and \loga - \logfO2 diagrams (Dick, 2009) \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{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{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{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{TCA} \tab Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
+    \code{go-IU} \tab Diagrams using thermodynamic data in the SUPCRTBL compilation (Zimmer et al., 2016) \cr
+    \code{carboxylase} \tab Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase \cr
     \code{bison} \tab Average oxidation state of carbon in proteins for phyla at Bison Pool (Dick and Shock, 2013) \cr
   }
 
@@ -119,6 +118,8 @@
 
 Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. \emph{Orig. Life Evol. Biosph.} \bold{25}, 161--173. \url{https://doi.org/10.1007/BF01581580}
 
+Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. \emph{Geochim. Cosmochim. Acta} \bold{59}, 1497--1532. \url{https://doi.org/10.1016/0016-7037(95)00058-8}
+
 Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 \degC and 5 kbar. \emph{J. Chem. Soc. Faraday Trans.} \bold{88}, 803--826. \url{https://doi.org/10.1039/FT9928800803}
 
 Stef{\aacute}nsson, A. and Seward, T. M. (2004) Gold(I) complexing in aqueous sulphide solutions to 500\degC at 500 bar. \emph{Geochim. Cosmochim. Acta} \bold{68}, 4121--4143. \url{https://doi.org/10.1016/j.gca.2004.04.006}

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2019-02-09 05:52:58 UTC (rev 390)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2019-02-09 08:18:42 UTC (rev 391)
@@ -2197,7 +2197,7 @@
 
 # Document history
 
-* 2010-09-30 Initial version.
+* 2010-09-30 Initial version (titled "Getting started with CHNOSZ").
 <!--
 * 2011-08-15 Add <span style="color:green">`browse.refs()`</span>; modifying database hint changed to <span style="color:blue">`help(thermo)`</span>.
 ```{marginfigure}

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