[CHNOSZ-commits] r81 - in pkg/CHNOSZ: . R inst inst/tests man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 14 11:07:47 CEST 2015
Author: jedick
Date: 2015-05-14 11:07:47 +0200 (Thu, 14 May 2015)
New Revision: 81
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/findit.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/tests/test-diagram.R
pkg/CHNOSZ/man/findit.Rd
pkg/CHNOSZ/vignettes/anintro.Rnw
pkg/CHNOSZ/vignettes/anintro.lyx
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
pkg/CHNOSZ/vignettes/vig.bib
Log:
fixes for hotspring.Rnw and anintro.Rnw
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/DESCRIPTION 2015-05-14 09:07:47 UTC (rev 81)
@@ -1,6 +1,6 @@
-Date: 2015-03-10
+Date: 2015-05-14
Package: CHNOSZ
-Version: 1.0.3-18
+Version: 1.0.3-19
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/R/diagram.R 2015-05-14 09:07:47 UTC (rev 81)
@@ -153,6 +153,9 @@
dim(predominant) <- dim(pv[[1]])
}
+ # a warning about that we can only show properties of the first species on a 2-D diagram
+ if(nd==2 & length(plotvals) > 1 & identical(predominant, NA)) warning("showing only first species in 2-D property diagram")
+
## where we'll put extra output for predominance diagrams (lx, ly, is)
out2D <- list()
@@ -411,7 +414,6 @@
# colors and curves (predominance), or contours (properties)
if(identical(predominant, NA)) {
zs <- plotvals[[1]]
- if(length(plotvals) > 1) warning("showing only first species in 2-D property diagram")
contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex)
pn <- list(lx=NULL, ly=NULL, is=NULL)
} else {
Modified: pkg/CHNOSZ/R/findit.R
===================================================================
--- pkg/CHNOSZ/R/findit.R 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/R/findit.R 2015-05-14 09:07:47 UTC (rev 81)
@@ -214,7 +214,7 @@
}
# to plot results from findit()
-plot.findit <- function(x,which=NULL,mar=c(3.5,5,2,2),xlab="iteration",...) {
+plot_findit <- function(x,which=NULL,mar=c(3.5,5,2,2),xlab="iteration",...) {
# show the values of the test statistic and of the
# chemical variables at each iteration
l <- length(x$value)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/inst/NEWS 2015-05-14 09:07:47 UTC (rev 81)
@@ -1,37 +1,49 @@
-CHANGES IN CHNOSZ 1.0.3-18 (2015-03-10)
+CHANGES IN CHNOSZ 1.0.3-19 (2015-05-14)
---------------------------------------
-- Add files with average amino acid compositions of proteins from Bison
- Pool grouped according to annotation keyword (DS11.csv) (moved here
- from main protein.csv) or phylum assignment (DS13.csv).
+NEW FEATURES:
-- Convert hotspring.Rnw to use knitr, and add example calculations of
- relative abundances of microbial phyla from Dick and Shock, 2013.
+- Add mosaic() function for affinity calculations with changing basis
+ species. See also new 'mosaic.R' demo.
-- In energy(), add missing 'IS' argument in call to subcrt(). Thanks to
- Grayson Boyer for the bug report.
+- Add thermo$opt$varP option as a flag for subcrt() to calculate Gibbs
+ energies of gases using a variable-pressure standard state.
-- In nonideal(), skip proton and electron. Add test for calculations
- at constant and variable IS to test-util.affinity.R.
+- Add 'solubility.R' demo, and calcite solubility plot to anintro.Rnw.
-- diagram() returns 'lx', 'ly' and 'is' for calculated positions of
- labels and indices of those species in predominance diagrams,
- including when the labels aren't plotted (by setting names=FALSE).
+DATA CONSISTENCY:
- Move aqueous Ti(OH)4 and H4SiO4 to OBIGT-2.csv.
-- Add warning about data and examples to CHNOSZ-package.Rd.
+- Add warning about data consistency and use of examples to
+ CHNOSZ-package.Rd and anintro.Rnw.
-- water.lines() gets 'O2state' argument for state of O2.
+OTHER CHANGES:
-- Add mosaic() function for affinity calculations with changing basis
- species.
-
- When making filled color diagrams, diagram() calls image() with
useRaster=TRUE. This speeds up plotting, eliminates artifacts at
some resolutions (i.e. blank lines), and greatly reduces the size
of PDF files.
+- diagram() returns 'lx', 'ly' and 'is' for calculated positions of
+ labels and indices of those species in predominance diagrams,
+ including when the labels aren't plotted (by setting names=FALSE).
+
+- In energy(), add missing 'IS' argument in call to subcrt(). Thanks to
+ Grayson Boyer for the bug report.
+
+- In nonideal(), skip proton and electron. Add test for calculations
+ at constant and variable IS to test-util.affinity.R.
+
+- Modify hotspring.Rnw to use knitr, and add example calculations of
+ relative abundances of microbial phyla from Dick and Shock, 2013.
+
+- Add files with average amino acid compositions of proteins from Bison
+ Pool grouped according to annotation keyword (DS11.csv) (moved here
+ from protein.csv) or phylum assignment (DS13.csv).
+
+- water.lines() gets 'O2state' argument to specify state of O2.
+
- Add 'as.residue' argument to diagram(), to divide reactions by
balance coefficients without rescaling to whole species formulas
(cf. 'normalize' argument which uses rescaling).
@@ -45,13 +57,9 @@
- In test-diagram.R, test that same diagrams are produced using
'as.residue' in equilibrate() or diagram().
-- Add 'tplot' argument to diagram().
+- Add 'tplot' argument to diagram() (set to FALSE to use R's default
+ plot set-up).
-- Add thermo$opt$varP option as a flag for subcrt() to calculate Gibbs
- energies of gases using a variable-pressure standard state.
-
-- Add 'solubility.R' demo and calcite solubility plot to anintro.Rnw.
-
CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
------------------------------------
Modified: pkg/CHNOSZ/inst/tests/test-diagram.R
===================================================================
--- pkg/CHNOSZ/inst/tests/test-diagram.R 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/inst/tests/test-diagram.R 2015-05-14 09:07:47 UTC (rev 81)
@@ -82,5 +82,5 @@
a <- affinity(T=c(0, 200, 6), O2=c(-90, -60, 5))
# TODO: fix plot.line() function in diagram() so that the plot can be made
#expect_equal(diagram(a), diagram(a, plot.it=FALSE))
- expect_warning(diagram(a, what="CO2"), "showing only first species in 2-D property diagram")
+ expect_warning(diagram(a, what="CO2", plot.it=FALSE), "showing only first species in 2-D property diagram")
})
Modified: pkg/CHNOSZ/man/findit.Rd
===================================================================
--- pkg/CHNOSZ/man/findit.Rd 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/man/findit.Rd 2015-05-14 09:07:47 UTC (rev 81)
@@ -1,6 +1,6 @@
\name{findit}
\alias{findit}
-\alias{plot.findit}
+\alias{plot_findit}
\title{Gridded Search to Optimize Objective Functions}
\description{
Use a gridded search to find a combination of one or more of chemical activities of basis species, temperature and/or pressure that maximize or minimize a objective function of the metastable equilibrium chemical activities of the species of interest.
@@ -62,7 +62,7 @@
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. The value of \code{objective} is calculated at each of the \eqn{res^{nd}}{res^nd} grid points and and optimum value located (see \code{\link{revisit}} and \code{\link{optimal.index}}). In the next iteration the new search box is centered on the location of the optimum value, and the edges are shrunk so their length is \code{rat} * the length in the previous step. If the limits of any of the parameters extend beyond those in \code{lims}, they are pushed in to fit (preserving the difference between them).
- \code{plot.findit} plots the values of the parameters and the objective function as a function of the number of iterations.
+ \code{plot_findit} plots the values of the parameters and the objective function as a function of the number of iterations.
}
Modified: pkg/CHNOSZ/vignettes/anintro.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rnw 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/vignettes/anintro.Rnw 2015-05-14 09:07:47 UTC (rev 81)
@@ -82,7 +82,7 @@
demonstrate basic usage to new users.
-\section{Outline of workflow}
+\subsection{Outline of workflow}
CHNOSZ is made up of a set of functions and supporting datasets. The
major components of the package are shown in the figure below, which
@@ -120,7 +120,7 @@
or others with whom you might share your scripts.
-\section{Installing and loading CHNOSZ}
+\subsection{Installing and loading CHNOSZ}
If you have just installed R, and you are online, installing the CHNOSZ
package should be as simple as selecting ``Install packages from
@@ -154,6 +154,30 @@
\section{Thermodynamic database}
+\subsection{Warning about internal consistency of thermodynamic data}
+
+All thermodynamic data and examples are provided on an as-is basis.
+It is up to you to check not only the accuracy of the data, but also
+\emph{the suitability of the data AND computational techniques} for
+your problem. By combining data taken from different sources, it is
+possible to build an inconsistent and/or nonsensical calculation.
+An attempt has been made to provide a primary database (OBIGT.csv)
+that is internally consistent, but no guarantee can be made. Where
+possible, data with known or suspected inconsistencies have been placed
+into a secondary database (OBIGT-2.csv) that should be regarded as
+experimental. If there is any doubt about the accuracy or suitability
+of data for a particular problem, please \emph{consult the primary
+sources} (which can be located using \texttt{browse.refs()}; see Section
+\ref{sub:thermo_refs}). Do not assume that by adding any species
+to your calculation (or to any of the examples), you will necessarily
+obtain a reasonable answer. Do not assume that the examples are correct,
+or that they can be applied to your problem. As with the data, please
+\emph{compare the construction and output of the examples to the primary
+sources}, cited in the reference list in each help page. Examples
+without a reference (and some with references) demonstrate experimental
+features of CHNOSZ.
+
+
\subsection{\texttt{info()} part I}
So you want to know what are the standard molal thermodynamic properties
@@ -195,7 +219,7 @@
@
-\subsection{\texttt{thermo\$refs}}
+\subsection{\texttt{\label{sub:thermo_refs}thermo\$refs}}
The thermodynamic data and other parameters used by the functions,
as well as system definitions provided by the user in an interactive
@@ -552,7 +576,6 @@
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<demo_solubility, results=hide, fig=TRUE>>=
demo("solubility", ask=FALSE)
@
@@ -619,7 +642,6 @@
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<CSG_diagram,fig=T,width=4,height=4>>=
e <- equilibrate(a, normalize=TRUE)
diagram(e, legend.x="bottomleft", ylim=c(-6, -2))
@@ -643,7 +665,6 @@
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<PredominanceDiagram,fig=T,width=4,height=4>>=
species(c("SLAP_ACEKI", "SLAP_GEOSE", "SLAP_BACLI", "SLAP_AERSA"))
basis(c("NH3", "H2S"), c(-1, -10))
@@ -685,7 +706,6 @@
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<Bowers,fig=T,width=4,height=4>>=
basis(c("HCl","H2O","Ca+2","CO2","Mg+2","SiO2","O2","H+"),
c(999,0,999,999,999,999,999,-7))
@@ -796,13 +816,12 @@
soils \citep{BKM60} and hot springs in Yellowstone ($+$) \citep{SWM+05}
and Iceland ($\blacktriangle$) \citep{SA02}. The symbols identifying
the latter two sources were swapped in the figure caption of \citet{DLH06}.
-Finally legends are draws to identify the lines and symbols. The \texttt{describe.property()}
+Finally legends are drawn to identify the lines and symbols. The \texttt{describe.property()}
function of CHNOSZ is used to generate the temperature notation (italic
$T$, and degree sign in the units).
\setkeys{Gin}{width=0.5\textwidth}
-\selectlanguage{english}%
<<amylaseplot, fig=TRUE, results=hide, width=5, height=5>>=
basis("CHNOSe")
basis(c("NH3", "H2S"), c(-6, -3))
@@ -842,7 +861,6 @@
\setkeys{Gin}{width=0.7\textwidth}
-\selectlanguage{english}%
<<yeastplot, fig=TRUE, results=hide, width=7, height=5>>=
locations <- yeastgfp()
gfp <- yeastgfp(locations)
@@ -966,7 +984,6 @@
\begin{small}
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<revisit_alpha, fig=T, results=hide, width=6, height=4>>=
basis(c("CO2", "O2"), c(r$x, r$y))
a <- affinity()
@@ -1003,7 +1020,6 @@
\begin{small}
\setkeys{Gin}{width=0.4\textwidth}
-\selectlanguage{english}%
<<findit, fig=T, results=hide, width=4, height=4>>=
basis("CHNOS")
species(c("isoleucine", "tyrosine", "glutamic acid", "methionine", "aspartic acid"))
@@ -1022,7 +1038,6 @@
\begin{small}
\setkeys{Gin}{width=0.6\textwidth}
-\selectlanguage{english}%
<<findit_alpha, fig=T, results=hide, width=6, height=4>>=
a <- affinity()
par(mfrow=c(1, 2))
@@ -1057,6 +1072,8 @@
\item 2011-08-15 Add \texttt{browse.refs()}; modifying database hint changed
to \texttt{help(thermo)}
\item 2012-06-16 Add ``More activity diagrams''
+\item 2015-05-14 Add warning about internal consistency of thermodynamic
+data
\end{itemize}
R session information:
Modified: pkg/CHNOSZ/vignettes/anintro.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.lyx 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/vignettes/anintro.lyx 2015-05-14 09:07:47 UTC (rev 81)
@@ -193,7 +193,7 @@
\end_layout
-\begin_layout Section
+\begin_layout Subsection
Outline of workflow
\end_layout
@@ -328,7 +328,7 @@
\end_layout
-\begin_layout Section
+\begin_layout Subsection
Installing and loading CHNOSZ
\end_layout
@@ -480,8 +480,66 @@
status open
\begin_layout Subsection
+Warning about internal consistency of thermodynamic data
+\end_layout
+\begin_layout Standard
+All thermodynamic data and examples are provided on an as-is basis.
+ It is up to you to check not only the accuracy of the data, but also
+\emph on
+the suitability of the data AND computational techniques
+\emph default
+ for your problem.
+ By combining data taken from different sources, it is possible to build
+ an inconsistent and/or nonsensical calculation.
+ An attempt has been made to provide a primary database (OBIGT.csv) that
+ is internally consistent, but no guarantee can be made.
+ Where possible, data with known or suspected inconsistencies have been
+ placed into a secondary database (OBIGT-2.csv) that should be regarded as
+ experimental.
+ If there is any doubt about the accuracy or suitability of data for a particula
+r problem, please
+\emph on
+consult the primary sources
+\emph default
+ (which can be located using
\family typewriter
+browse.refs()
+\family default
+; see Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sub:thermo_refs"
+
+\end_inset
+
+).
+ Do not assume that by adding any species to your calculation (or to any
+ of the examples), you will necessarily obtain a reasonable answer.
+ Do not assume that the examples are correct, or that they can be applied
+ to your problem.
+ As with the data, please
+\emph on
+compare the construction and output of the examples to the primary sources
+\emph default
+, cited in the reference list in each help page.
+ Examples without a reference (and some with references) demonstrate experimenta
+l features of CHNOSZ.
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Branch stuff
+status open
+
+\begin_layout Subsection
+
+\family typewriter
info()
\family default
part I
@@ -678,6 +736,12 @@
\begin_layout Subsection
\family typewriter
+\begin_inset CommandInset label
+LatexCommand label
+name "sub:thermo_refs"
+
+\end_inset
+
thermo$refs
\end_layout
@@ -2245,7 +2309,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status collapsed
@@ -2520,7 +2583,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status collapsed
@@ -2631,7 +2693,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -2816,7 +2877,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -3360,7 +3420,7 @@
\end_inset
.
- Finally legends are draws to identify the lines and symbols.
+ Finally legends are drawn to identify the lines and symbols.
The
\family typewriter
describe.property()
@@ -3378,7 +3438,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -3592,7 +3651,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -4227,7 +4285,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -4406,7 +4463,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -4516,7 +4572,6 @@
status open
\begin_layout Standard
-
\begin_inset ERT
status open
@@ -4692,6 +4747,10 @@
\end_layout
+\begin_layout Itemize
+2015-05-14 Add warning about internal consistency of thermodynamic data
+\end_layout
+
\begin_layout Standard
R session information:
\end_layout
Modified: pkg/CHNOSZ/vignettes/hotspring.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.Rnw 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/vignettes/hotspring.Rnw 2015-05-14 09:07:47 UTC (rev 81)
@@ -36,8 +36,10 @@
library(knitr)
## set global chunk options
opts_chunk$set(fig.path='figure/hotspring-', cache.path='cache/hotspring-', fig.align='center', fig.show='hold', par=TRUE)
-## set code/output width to be 60
-options(width=80)
+## set code/output width
+options(width=85)
+## set number of digits
+options(digits=5)
## tune details of base graphics (http://yihui.name/knitr/hooks)
knit_hooks$set(par=function(before, options, envir){
if (before && options$fig.show!='none') par(mar=c(4,4,1,1),cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)
@@ -47,6 +49,9 @@
\title{Hot-spring proteins in CHNOSZ}
+
+\author{Jeffrey M. Dick and Everett L. Shock}
+
\maketitle
\section{Introduction}
@@ -68,8 +73,8 @@
In order to keep the code here as short and efficient as possible,
some aspects of the published figures including manual labeling and
higher resolution are not all reproduced; these changes are noted
-where possible. Also, some tricks (e.g. using \texttt{xtabs()} to
-create the BLAST frequency table, and \texttt{revisit()} to calculate
+where possible. Also, some shortcuts (e.g. using \texttt{xtabs()}
+to create the BLAST frequency table, and \texttt{revisit()} to calculate
the $\Delta G_{tr}$) have been introduced here in order to streamline
the code.
@@ -115,7 +120,7 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0022782.g005}{DOI link}
-to original figure (panels A and B). The length of \texttt{xpoints}
+to published figure (panels A and B). The length of \texttt{xpoints}
here, 128, is the resolution used for the figures in the 2011 paper
(defined in the \texttt{mkargs()} function of the Supporting Information).
@@ -153,7 +158,7 @@
modifications):
<<names>>=
-# the names of the phyla in alphabetical order (Deinococcus-Thermus at end)
+# the names of the phyla in alphabetical order (except Deinococcus-Thermus at end)
phyla.abc <- sort(unique(aa.phyla$organism))[c(1:7,9:11,8)]
# an abbreviation for Dein.-Thermus
phyla.abbrv <- phyla.abc
@@ -299,7 +304,7 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0022782.t005}{DOI link}
-to original table.
+to published table.
The affinities are expressed as dimensionless values, i.e. $\boldsymbol{A}/2.303RT$
where $\boldsymbol{A}$, $R$ and $T$ stand for chemical affinity,
@@ -322,9 +327,9 @@
apply(a.res, 2, which.max)
@
-This 1-2-4 progression of stabilities is visualized below, and for
-some groups of proteins, an update to the thermodynamic properties
-of the methionine sidechain causes site 3 also to become stable.
+This 1-2-4 progression of stabilities is visualized below; for some
+groups of proteins, an update to the thermodynamic properties of the
+methionine sidechain causes site 3 also to become stable.
\subsection{Relative stabilities along a chemical gradient}
@@ -370,7 +375,7 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0022782.g005}{DOI link}
-to original figure (panels B and F).
+to published figure (panels B and F).
\clearpage
@@ -401,18 +406,19 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0022782.g007}{DOI link}
-to original figure.
+to published figure.
\clearpage
\section{Comparing old and new methionine sidechain parameters}
-Make some $T-\log a_{\mathrm{H_{2}}}$ protein metastable equilibrium
-predominance diagrams using old and new methionine sidechain {[}Met{]}
-parameters. When this is run, the old {[}Met{]} is in the database
-(since \texttt{add.obigt()} was called above), so in the second row
-(j=2), we reset the database to use the new {[}Met{]}.
+Make some $T-\log a_{\mathrm{H_{2}}}$ metastable equilibrium predominance
+diagrams using different values for the thermodynamic properties of
+the methionine sidechain group {[}Met{]}. The first row shows the
+results using the old values (since \texttt{add.obigt()} was called
+above); for the second row (j=2), we reset the database to use the
+current (revised) parameters.
<<methionine, fig.width=6, fig.height=4, message=FALSE, results='hide', cache=TRUE>>=
par(mfrow=c(2, 3))
@@ -437,9 +443,9 @@
}
@
-\href{http://10.1371/journal.pone.0072395.g002}{DOI link} to original
-figure. The original was made with higher resolution (256) and some
-labels were manually placed.
+\href{http://dx.doi.org/10.1371/journal.pone.0072395.g002}{DOI link}
+to published figure, which was made with higher resolution (256) and
+manual placement of some labels.
\section{Relative abundance calculations}
@@ -453,7 +459,7 @@
# put it in correct order, then turn counts into fractions
out <- out[c(1,5:2), c(1:7,9:11,8)]
out <- out/rowSums(out)
- return(as.data.frame(out))
+ return(out)
}
@
@@ -655,7 +661,7 @@
text(66, -9, "optimal parameterization\nfor observed\nphylum abundances", adj=0)
@
-DOI links to original versions: \href{http://dx.doi.org/10.1371/journal.pone.0022782.g009}{plot 1},
+DOI links to published versions: \href{http://dx.doi.org/10.1371/journal.pone.0022782.g009}{plot 1},
\href{http://dx.doi.org/10.1371/journal.pone.0072395.g004}{plot 2}.
@@ -663,7 +669,8 @@
Let's make some plots comparing the relative abundances calculated
above (stored in \texttt{equil.results}) with the abundances from
-BLAST counts. We'll also store the optimal models in \texttt{equil.opt}.
+BLAST counts. We'll also store the results of the optimized models
+in \texttt{equil.opt}.
<<alphaplot5, fig.width=9, fig.height=6, out.width='.88\\textwidth', cache=TRUE>>=
layout(matrix(c(1, 2, 3, 4, 5, 6), nrow=2, byrow=TRUE), widths=c(2, 2, 2))
@@ -694,7 +701,7 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0072395.g005}{DOI link}
-to original figure.
+to published figure.
\clearpage
@@ -722,7 +729,7 @@
@
\href{http://dx.doi.org/10.1371/journal.pone.0072395.g006}{DOI link}
-to original figure.
+to published figure.
\section{Document history}
@@ -730,8 +737,8 @@
\item 2011-08-23 Initial version (CHNOSZ\_0.9-7)
\item 2012-01-07 Use \texttt{add.obigt()} for superseded properties of methionine
sidechain group.
-\item 2014-02-01 Include results from 2013 paper and use knitr instead of
-Sweave.
+\item 2014-02-01 Include results from 2013 paper and change VignetteEngine
+to knitr.
\end{itemize}
\bibliographystyle{unsrtnat}
\bibliography{vig}
Modified: pkg/CHNOSZ/vignettes/hotspring.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.lyx 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/vignettes/hotspring.lyx 2015-05-14 09:07:47 UTC (rev 81)
@@ -95,7 +95,7 @@
\begin_layout Standard
\begin_inset ERT
-status collapsed
+status open
\begin_layout Plain Layout
@@ -120,16 +120,26 @@
\begin_layout Plain Layout
-## set code/output width to be 60
+## set code/output width
\end_layout
\begin_layout Plain Layout
-options(width=80)
+options(width=85)
\end_layout
\begin_layout Plain Layout
+## set number of digits
+\end_layout
+
+\begin_layout Plain Layout
+
+options(digits=5)
+\end_layout
+
+\begin_layout Plain Layout
+
## tune details of base graphics (http://yihui.name/knitr/hooks)
\end_layout
@@ -163,6 +173,12 @@
Hot-spring proteins in CHNOSZ
\end_layout
+\begin_layout Author
+Jeffrey M.
+ Dick and Everett L.
+ Shock
+\end_layout
+
\begin_layout Section
Introduction
\end_layout
@@ -202,7 +218,7 @@
In order to keep the code here as short and efficient as possible, some
aspects of the published figures including manual labeling and higher resolutio
n are not all reproduced; these changes are noted where possible.
- Also, some tricks (e.g.
+ Also, some shortcuts (e.g.
using
\family typewriter
xtabs()
@@ -417,7 +433,7 @@
\end_inset
- to original figure (panels A and B).
+ to published figure (panels A and B).
The length of
\family typewriter
xpoints
@@ -574,7 +590,8 @@
\begin_layout Plain Layout
-# the names of the phyla in alphabetical order (Deinococcus-Thermus at end)
+# the names of the phyla in alphabetical order (except Deinococcus-Thermus
+ at end)
\end_layout
\begin_layout Plain Layout
@@ -1244,7 +1261,7 @@
\end_inset
- to original table.
+ to published table.
\end_layout
\begin_layout Standard
@@ -1341,8 +1358,8 @@
\end_layout
\begin_layout Standard
-This 1-2-4 progression of stabilities is visualized below, and for some
- groups of proteins, an update to the thermodynamic properties of the methionine
+This 1-2-4 progression of stabilities is visualized below; for some groups
+ of proteins, an update to the thermodynamic properties of the methionine
sidechain causes site 3 also to become stable.
\end_layout
@@ -1541,7 +1558,7 @@
\end_inset
- to original figure (panels B and F).
+ to published figure (panels B and F).
\end_layout
\begin_layout Standard
@@ -1683,7 +1700,7 @@
\end_inset
- to original figure.
+ to published figure.
\end_layout
\begin_layout Standard
@@ -1711,14 +1728,14 @@
\begin_inset Formula $T-\log a_{\mathrm{H_{2}}}$
\end_inset
- protein metastable equilibrium predominance diagrams using old and new
- methionine sidechain [Met] parameters.
- When this is run, the old [Met] is in the database (since
+ metastable equilibrium predominance diagrams using different values for
+ the thermodynamic properties of the methionine sidechain group [Met].
+ The first row shows the results using the old values (since
\family typewriter
add.obigt()
\family default
- was called above), so in the second row (j=2), we reset the database to
- use the new [Met].
+ was called above); for the second row (j=2), we reset the database to use
+ the current (revised) parameters.
\end_layout
\begin_layout Standard
@@ -1845,13 +1862,12 @@
\begin_inset CommandInset href
LatexCommand href
name "DOI link"
-target "10.1371/journal.pone.0072395.g002"
+target "http://dx.doi.org/10.1371/journal.pone.0072395.g002"
\end_inset
- to original figure.
- The original was made with higher resolution (256) and some labels were
- manually placed.
+ to published figure, which was made with higher resolution (256) and manual
+ placement of some labels.
\end_layout
\begin_layout Section
@@ -1873,7 +1889,7 @@
\begin_layout Standard
\begin_inset ERT
-status collapsed
+status open
\begin_layout Plain Layout
@@ -1907,7 +1923,7 @@
\begin_layout Plain Layout
- return(as.data.frame(out))
+ return(out)
\end_layout
\begin_layout Plain Layout
@@ -1942,7 +1958,7 @@
\begin_layout Standard
\begin_inset ERT
-status collapsed
+status open
\begin_layout Plain Layout
@@ -2082,7 +2098,7 @@
\begin_layout Standard
\begin_inset ERT
-status collapsed
+status open
\begin_layout Plain Layout
@@ -2753,7 +2769,7 @@
\end_layout
\begin_layout Standard
-DOI links to original versions:
+DOI links to published versions:
\begin_inset CommandInset href
LatexCommand href
name "plot 1"
@@ -2783,7 +2799,7 @@
equil.results
\family default
) with the abundances from BLAST counts.
- We'll also store the optimal models in
+ We'll also store the results of the optimized models in
\family typewriter
equil.opt
\family default
@@ -2947,7 +2963,7 @@
\end_inset
- to original figure.
+ to published figure.
\end_layout
\begin_layout Standard
@@ -3092,7 +3108,7 @@
\end_inset
- to original figure.
+ to published figure.
\end_layout
\begin_layout Section
@@ -3112,7 +3128,8 @@
\end_layout
\begin_layout Itemize
-2014-02-01 Include results from 2013 paper and use knitr instead of Sweave.
+2014-02-01 Include results from 2013 paper and change VignetteEngine to
+ knitr.
\end_layout
\begin_layout Standard
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2015-03-10 16:00:18 UTC (rev 80)
+++ pkg/CHNOSZ/vignettes/vig.bib 2015-05-14 09:07:47 UTC (rev 81)
@@ -1,1311 +1,615 @@
-% This file was created with JabRef 2.9.2.
+% This file was created with JabRef 2.10.
% Encoding: ISO8859_1
- at ARTICLE{AH97a,
- author = {Amend, Jan P. and Helgeson, Harold C.},
- title = {{G}roup additivity equations of state for calculating the standard
- molal thermodynamic properties of aqueous organic species at elevated
- temperatures and pressures},
- journal = {Geochimica et Cosmochimica Acta},
- year = {1997},
- volume = {61},
- pages = {11 -- 46},
- abstract = {Group additivity equations of state for aqueous organic molecules
- have been generated by combining the revised Helgeson-Kirkham-Flowers
- (HKF) equations of state (Shock and Helgeson, 1988, 1990; Tanger
- and Helgeson, 1988; Shock et al., 1989, 1992) with experimental values
- of the standard molal properties of aqueous alkanes, alkanols, alkylbenzenes,
- carboxylic acids, amides, and amines. Equations of state parameters
- for the groups represented by -cn2 , -CH3, -CHCH3-, -C6H5, -CH2OH,
- -COOH, -CONH2, and -CH2NH2 were determined by regression of the experimental
- data. This procedure permits calculation of the standard molal thermodynamic
- properties of these groups at elevated tempera-tures and pressures.
- Although curves representing the apparent standard molal Gibbs free
- energies ( A G °) and enthalpies ( A H °) of formation, and the standard
- molal entropies (S °) of the groups as a function of temperature
- and pressure are respectively similar for each of them, the temperature
- dependence of the standard molal heat capacities (C~) and volumes
- (V°) of a number of the groups are quite different from one another.
- For example, the standard molal heat capacities of the hydrocarbon
- groups minimize with increasing temperature, but those of -CHEOH
- and -CH2NH2 maximize. Computed values of AG °, A H °, S °, C~, V
- °, and the equations of state parameters for the various groups were
- used together with group additivity relations to generate corresponding
- values of these properties for aqueous n-alkanes, 2-methylalkanes,
- n-alkylbenzenes, n-alkanols, n-carboxylic acids, n-amides, and n-amines
- at temperatures -< 250°C and pressures - 1 kbar. The validity and
- generality of the equations of state are supported by the fact that
- predicted equilibrium constants for liquid n-alkane solubility reactions
- in water compare favorably with experimental values reported in the
- literature for temperatures as high as 200°C. Furthermore, equilibrium
- constants for aqueous ethane coexisting with ethene at 325 and 350°C
- at 350 bars predicted from the equations of state are in close agreement
- with independently determined experimental values reported by Seewald
- (1994). The standard molal thermodynamic properties and equations
- of state parameters reported below provide the means to characterize
- the thermodynamic behavior of a wide variety of aqueous organic species
- involved in hydrothermal reactions at elevated temperatures and pressures.},
- doi = {10.1016/S0016-7037(96)00306-7},
+
+ at Article{AH97a,
+ Title = {{G}roup additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures},
+ Author = {Amend, Jan P. and Helgeson, Harold C.},
+ Journal = {Geochimica et Cosmochimica Acta},
+ Year = {1997},
+ Pages = {11 -- 46},
+ Volume = {61},
+
[TRUNCATED]
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svnlook diff /svnroot/chnosz -r 81
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