[CHNOSZ-commits] r62 - in pkg/CHNOSZ: . inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 12 16:17:44 CET 2014
Author: jedick
Date: 2014-01-12 16:17:43 +0100 (Sun, 12 Jan 2014)
New Revision: 62
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/vignettes/equilibrium.Rnw
pkg/CHNOSZ/vignettes/equilibrium.lyx
Log:
prepare for release on CRAN
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/DESCRIPTION 2014-01-12 15:17:43 UTC (rev 62)
@@ -1,6 +1,6 @@
-Date: 2014-01-11
+Date: 2014-01-12
Package: CHNOSZ
-Version: 1.0.2-3
+Version: 1.0.3
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/inst/CHECKLIST 2014-01-12 15:17:43 UTC (rev 62)
@@ -23,7 +23,7 @@
data files are uncompressed on installation? (from BuildResaveData: no)
anim.*() produce pngs / movies (ImageMagick dependency)?
-- check that dl.aa() works with current UniProt web pages
+- check that uniprot.aa() works with current UniProt web pages
- check for stale URLs in Rd files
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/inst/NEWS 2014-01-12 15:17:43 UTC (rev 62)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.0.2-3 (2014-01-11)
---------------------------------------
+CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
+------------------------------------
- Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome
Database protein_properties.tab and SGD_features.tab dated
@@ -11,13 +11,16 @@
Reference Sequence (RefSeq) release 61 (2013-09-09). Code was
adapted to deal with WP multispecies accessions.
-- read.fasta() gets new argument 'id'; when supplied, it skips reading
- the protein names from the FASTA headers.
+- read.fasta() gets new argument 'id'; when supplied, it is used for
+ the protein names in the output, in place of those read from the
+ FASTA headers.
- When reading protein names from the FASTA headers, read.fasta()
stops only at the first space, not space or underscore as before.
-- info() no longer specially sets state of "O2" or "oxygen" to gas.
+- info() no longer specially sets state of "O2" to gas. The name
+ "oxygen", or the combination ("O2", "gas"), can be used to retrieve
+ data for the gas.
- In thermo$obigt, names of gases (e.g. "oxygen") are used only for
the gaseous species; names were removed from dissolved species in
@@ -26,15 +29,13 @@
- In read.expr(), allow multiple filter specifications.
-- In revisit(), extend ranges of axes of scatter plots.
-
- revisit() has new argument loga0, a single vector of base-10
logarithms of activities of species used to calculate the base-2 log
ratio ( log2(a1/a0) ).
-- Updated tests to be compatible with testthat version 0.8. Some tests
- now check for e.g. errors *and* warnings produced by a single
- function call.
+- Updated tests to be compatible with testthat version 0.8 (in
+ development). Some tests now check for e.g. an error *and* warning
+ produced by a single function call.
CHANGES IN CHNOSZ 1.0.1 (2013-07-04)
------------------------------------
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-12 15:17:43 UTC (rev 62)
@@ -77,10 +77,6 @@
\code{\link{diagram}} causes an error while plotting stability field boundaries if the x and y resolutions are not identical.
}
-\seealso{
- The \code{TODO} file in the package installation directory contains a list of changes anticipated or considered for future releases.
-}
-
\examples{
### Getting Started
## the 'thermo' object contains thermodynamic data and is also where
Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rnw 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rnw 2014-01-12 15:17:43 UTC (rev 62)
@@ -1,12 +1,13 @@
-%% LyX 2.0.5 created this file. For more info, see http://www.lyx.org/.
+%% LyX 2.1.0beta2 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
-\documentclass[noae]{article}
+\documentclass[english,noae]{article}
\usepackage{mathpazo}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage[letterpaper]{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\usepackage{color}
+\usepackage{babel}
\usepackage{amsbsy}
\usepackage{amssymb}
\usepackage[numbers]{natbib}
@@ -130,8 +131,6 @@
-
-
\section{Reaction-matrix approach}
@@ -159,7 +158,6 @@
species("CSG",c("METVO", "METJA"))
@
-
Although the basis species are defined, the temperature is not yet
specified, so it is not immediately possible to calculate the ionization
states of the proteins. That is why the coefficient on $\mathrm{H^{+}}$
@@ -172,7 +170,6 @@
protein.info(species()$name)
@
-
Note that \texttt{affinity()} is called twice by \texttt{protein.info()};
this so that both charges and standard Gibbs energies of ionization
of the proteins can be calculated. The \texttt{Z} values in the table
@@ -188,7 +185,6 @@
a$values
@
-
Since \texttt{affinity()} returns a list with a lot of information
(such as the basis species and species definitions) the last command
was written to only print the \texttt{values} part of that list. The
@@ -267,7 +263,6 @@
e$loga.equil
@
-
Those are the logarithms of the equilibrium activities of the proteins.
Combining these values with either Eqs. (\ref{eq:A_METVO}) or (\ref{eq:A_METJA})
gives us the same value for affinity of the formation reactions per
@@ -335,7 +330,6 @@
protein.basis(species()$name, normalize=TRUE)
@
-
Let us denote by $\boldsymbol{A}_{12}$ and $\boldsymbol{A}_{13}$
the chemical affinities of Reactions \ref{react:CSG_METVO_residue}
and \ref{react:CSG_METJA_residue}. We can write
@@ -423,6 +417,8 @@
for CSG example we have been discussing.
\begin{small}
+
+<<>>=
<<protein_equil>>=
# get an error if we don't data(thermo), only in the re-building vignettes of R CMD check
data(thermo)
@@ -431,9 +427,9 @@
swap.basis("O2", "H2")
protein.equil(protein, loga.protein=-3)
@
+
\end{small}
-
The function checks (``check it!'') against the step-by-step calculations
the values of $\boldsymbol{A}^{*}$ calculated using \texttt{affinity()},
and the equilibrium activities of the proteins calculated using \texttt{equilibrate()}.
@@ -469,14 +465,13 @@
title(main="Equilibrium activities of proteins, normalized formulas")
@
-
The reaction-matrix approach described above can also be applied to
systems having conservation coefficients that differ from unity, such
as many mineral and inorganic systems, where the immobile component
has different molar coefficients in the formulas. For example, consider
a system like that described in \citep{See96}:
-\setkeys{Gin}{width=0.7\textwidth}
+\setkeys{Gin}{width=0.7\textwidth}<<>>=
<<SulfurSpeciation,fig=T>>=
basis("CHNOS+")
basis("pH",5)
@@ -491,9 +486,9 @@
diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8)
title(main="Aqueous sulfur speciation, normalized formulas")
@
+
\setkeys{Gin}{width=1.0\textwidth}
-
The first diagram is quantitatively very similar to the one shown
by Seewald, 1997, but if we use the normalized formulas, in this case
divided by $\mathrm{H_{2}S}$ in the formation reactions, the range
@@ -534,10 +529,13 @@
activities (Blood plasma proteins, ``IL'' for interleukin):
\begin{small}
+
\setkeys{Gin}{width=0.8\textwidth}
+
+<<>>=
<<Plasma, fig=T, results=hide, width=8, height=4>>=
data(thermo) # cleanup from previous plot
-basis(c("CO2", "NH3", "H2S", "H2O", "O2"), c(-3, -3, -10))
+basis(c("CO2", "NH3", "H2S", "H2O", "oxygen"), c(-3, -3, -10))
f <- system.file("extdata/abundance/AA03.csv", package="CHNOSZ")
pdat <- read.csv(f, as.is=TRUE)
iil <- grep("^IL", pdat$name)
@@ -549,17 +547,21 @@
dE <- diagram(e, main="equilibrium activities")
stopifnot(identical(dA$predominant, dE$predominant))
@
+
\setkeys{Gin}{width=1.0\textwidth}
+
\end{small}
-
Here is an example where the predominant species in the equilibrium
assemblage are \textbf{\emph{not}} identical to those calculated the
maximum affinity method, and it is not possible for the maximum affinity
method to make those curved lines!!
\begin{small}
+
\setkeys{Gin}{width=0.8\textwidth}
+
+<<>>=
<<Amino, fig=T, results=hide, width=8, height=4>>=
basis("CHNOS+")
species(aminoacids(""))
@@ -569,9 +571,9 @@
e <- equilibrate(a)
dE <- diagram(e, main="equilibrium activities")
@
+
\end{small}
-
Take-home: when making predominance diagrams, confidently use the
maximum affinity method when \texttt{normalize=TRUE} (as done here
for proteins); otherwise it is advisable to compute the equilibrium
@@ -593,7 +595,6 @@
sessionInfo()
@
-
\bibliographystyle{plainnat}
\bibliography{vig}
Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.lyx 2014-01-11 04:28:50 UTC (rev 61)
+++ pkg/CHNOSZ/vignettes/equilibrium.lyx 2014-01-12 15:17:43 UTC (rev 62)
@@ -1,5 +1,5 @@
-#LyX 2.0 created this file. For more info see http://www.lyx.org/
-\lyxformat 413
+#LyX 2.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 474
\begin_document
\begin_header
\textclass article
@@ -21,13 +21,13 @@
\font_roman palatino
\font_sans default
\font_typewriter default
+\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
-
\graphics default
\default_output_format default
\output_sync 0
@@ -48,15 +48,24 @@
\pdf_quoted_options "citecolor=black, linkcolor=black"
\papersize letterpaper
\use_geometry true
-\use_amsmath 1
-\use_esint 1
-\use_mhchem 1
-\use_mathdots 1
-\cite_engine natbib_numerical
+\use_package amsmath 1
+\use_package amssymb 1
+\use_package cancel 0
+\use_package esint 1
+\use_package mathdots 1
+\use_package mathtools 0
+\use_package mhchem 1
+\use_package stackrel 0
+\use_package stmaryrd 0
+\use_package undertilde 0
+\cite_engine natbib
+\cite_engine_type numerical
+\biblio_style plainnat
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
+\justification true
\use_refstyle 0
\branch scrap
\selected 1
@@ -377,29 +386,37 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<add_obigt>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+add_obigt
\end_layout
-\begin_layout Chunk
+\end_inset
library(CHNOSZ)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
data(thermo)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
add.obigt()
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -493,24 +510,32 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<ProteinFormation>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+ProteinFormation
\end_layout
-\begin_layout Chunk
+\end_inset
basis("CHNOS+")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
species("CSG",c("METVO", "METJA"))
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -543,19 +568,27 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<ProteinInfo>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+ProteinInfo
\end_layout
-\begin_layout Chunk
+\end_inset
protein.info(species()$name)
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -605,24 +638,32 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<ProteinAffinity>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status collapsed
+
+\begin_layout Plain Layout
+ProteinAffinity
\end_layout
-\begin_layout Chunk
+\end_inset
a <- affinity()
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
a$values
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -875,24 +916,32 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<ProteinActivities>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+ProteinActivities
\end_layout
-\begin_layout Chunk
+\end_inset
e <- equilibrate(a)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e$loga.equil
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -1138,19 +1187,27 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
\end_layout
-\begin_layout Chunk
+\end_inset
protein.basis(species()$name, normalize=TRUE)
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -1455,57 +1512,74 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+\begin_layout Plain Layout
+
\backslash
begin{small}
\end_layout
-\begin_layout Chunk
+\end_inset
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
<<protein_equil>>=
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
# get an error if we don't data(thermo), only in the re-building vignettes
of R CMD check
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
data(thermo)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
protein <- iprotein(c("CSG_METVO", "CSG_METJA"))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
basis("CHNOS+")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
swap.basis("O2", "H2")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
protein.equil(protein, loga.protein=-3)
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\begin_layout Chunk
+\begin_inset ERT
+status collapsed
+\begin_layout Plain Layout
+
\backslash
end{small}
\end_layout
@@ -1515,6 +1589,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
The function checks (
\begin_inset Quotes eld
@@ -1608,79 +1687,87 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<ProteinSpeciation,fig=T>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+ProteinSpeciation,fig=T
\end_layout
-\begin_layout Chunk
+\end_inset
organisms <- c("METSC", "METJA", "METFE", "HALJP",
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
"METVO", "METBU", "ACEKI", "GEOSE", "BACLI", "AERSA")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
proteins <- c(rep("CSG", 6), rep("SLAP", 4))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
basis("CHNOS+")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
species(proteins, organisms)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
a <- affinity(O2=c(-100, -65))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
par(mfrow=c(2, 1))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
diagram(e, ylim=c(-5, -1), legend.x=NA)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
title(main="Equilibrium activities of proteins, whole formulas")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a, normalize=TRUE)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
diagram(e, ylim=c(-5, -1), legend.x=NA)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
title(main="Equilibrium activities of proteins, normalized formulas")
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
@@ -1707,88 +1794,102 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+\begin_layout Plain Layout
+
\backslash
setkeys{Gin}{width=0.7
\backslash
textwidth}
\end_layout
-\begin_layout Chunk
+\end_inset
+
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
<<SulfurSpeciation,fig=T>>=
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
basis("CHNOS+")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
basis("pH",5)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
species(c("H2S", "S2-2", "S3-2", "S2O3-2", "S2O4-2",
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
"S3O6-2", "S5O6-2", "S2O6-2", "HSO3-", "SO2", "HSO4-"))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
a <- affinity(O2=c(-50, -15), T=325, P=350)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
par(mfrow=c(2, 1))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a, loga.balance=-2)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
title(main="Aqueous sulfur speciation, whole formulas")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a, loga.balance=-2, normalize=TRUE)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
title(main="Aqueous sulfur speciation, normalized formulas")
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\begin_layout Chunk
+\begin_inset ERT
+status open
+\begin_layout Plain Layout
+
\backslash
setkeys{Gin}{width=1.0
\backslash
@@ -1800,6 +1901,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
The first diagram is quantitatively very similar to the one shown by Seewald,
1997, but if we use the normalized formulas, in this case divided by
@@ -1913,104 +2019,139 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+\begin_layout Plain Layout
+
\backslash
begin{small}
\end_layout
-\begin_layout Chunk
+\end_inset
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
\backslash
setkeys{Gin}{width=0.8
\backslash
textwidth}
\end_layout
-\begin_layout Chunk
+\end_inset
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
<<Plasma, fig=T, results=hide, width=8, height=4>>=
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
data(thermo) # cleanup from previous plot
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
-basis(c("CO2", "NH3", "H2S", "H2O", "O2"), c(-3, -3, -10))
+basis(c("CO2", "NH3", "H2S", "H2O", "oxygen"), c(-3, -3, -10))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
f <- system.file("extdata/abundance/AA03.csv", package="CHNOSZ")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
pdat <- read.csv(f, as.is=TRUE)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
iil <- grep("^IL", pdat$name)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
species(pdat$name[iil], "HUMAN")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
a <- affinity(O2=c(-82, -78), H2O=c(-12, -2))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
par(mfrow=c(1, 2))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
dA <- diagram(a, normalize=TRUE, main="maximum affinity")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a, normalize=TRUE)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
dE <- diagram(e, main="equilibrium activities")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
stopifnot(identical(dA$predominant, dE$predominant))
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset ERT
+status open
+\begin_layout Plain Layout
+
\backslash
setkeys{Gin}{width=1.0
\backslash
textwidth}
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Chunk
+\begin_inset ERT
+status open
+\begin_layout Plain Layout
+
\backslash
end{small}
\end_layout
@@ -2020,6 +2161,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
Here is an example where the predominant species in the equilibrium assemblage
are
@@ -2036,70 +2182,96 @@
\begin_inset Branch scrap
status open
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset ERT
+status open
+\begin_layout Plain Layout
+
\backslash
begin{small}
\end_layout
-\begin_layout Chunk
+\end_inset
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
\backslash
setkeys{Gin}{width=0.8
\backslash
textwidth}
\end_layout
-\begin_layout Chunk
+\end_inset
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
<<Amino, fig=T, results=hide, width=8, height=4>>=
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
basis("CHNOS+")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
species(aminoacids(""))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
a <- affinity(O2=c(-71, -66), H2O=c(-8, 4))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
par(mfrow=c(1, 2))
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
dA <- diagram(a, main="maximum affinity")
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
e <- equilibrate(a)
\end_layout
-\begin_layout Chunk
+\begin_layout Plain Layout
dE <- diagram(e, main="equilibrium activities")
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\begin_layout Chunk
+\begin_inset ERT
+status open
+\begin_layout Plain Layout
+
\backslash
end{small}
\end_layout
@@ -2109,6 +2281,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
Take-home: when making predominance diagrams, confidently use the maximum
affinity method when
@@ -2157,19 +2334,27 @@
R session information
\end_layout
-\begin_layout Chunk
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
-<<SessionInfo>>=
+\begin_layout Plain Layout
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+SessionInfo
\end_layout
-\begin_layout Chunk
+\end_inset
sessionInfo()
\end_layout
-\begin_layout Chunk
+\end_inset
-@
+
\end_layout
\end_inset
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