[CHNOSZ-commits] r85 - in pkg/CHNOSZ: . inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun May 17 11:20:42 CEST 2015
Author: jedick
Date: 2015-05-17 11:20:41 +0200 (Sun, 17 May 2015)
New Revision: 85
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/sideeffects.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/util.expression.Rd
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
Log:
clean up documentation formatting
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/DESCRIPTION 2015-05-17 09:20:41 UTC (rev 85)
@@ -1,6 +1,6 @@
Date: 2015-05-17
Package: CHNOSZ
-Version: 1.0.3-22
+Version: 1.0.3-23
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 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/inst/CHECKLIST 2015-05-17 09:20:41 UTC (rev 85)
@@ -2,26 +2,38 @@
release checklist for CHNOSZ
****************************
-- remove all "<<-" from sources (leftover from debugging)
-
-- update list of documentation topics in examples() with any new ones
-
- run examples() to make sure that all examples can be run
(that includes \donttest ones that aren't run by R CMD check)
- run demos() to run all demos
+- check output of demo("sources") to make sure all data sources are cited
+
+- check output of R CMD Rd2pdf: fix lines truncated by page margins
+
+- run R CMD check using R compiled without long doubles (as in Solaris checks on CRAN)
+ (CFLAGS=-ffloat-store ./configure --disable-long-double)
+
+- build the package on the source directory;
+ try both qpdf and ghostscript to compact vignettes:
+ R CMD build --compact-vignettes=both chnosz/
+
+OTHER THINGS TO CHECK:
+
+- remove all "<<-" from sources (leftover from debugging)
+
+- update list of documentation topics in examples() with any new ones
+
- run test_package("CHNOSZ") to run all tests
-- check output of demo("sources") to make sure all data sources are cited
-
- recreate extdata/thermo/obigt_check.csv after all data updates:
co <- check.obigt()
write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
- especially on Windows:
- data files are uncompressed on installation? (from BuildResaveData: no)
- anim.*() produce pngs / movies (ImageMagick dependency)?
+ - data files are uncompressed on installation? (from BuildResaveData: no)
+ (so that users can copy and modify the thermodynamic database)
+ - anim.*() produce pngs / movies (ImageMagick dependency)?
- check that uniprot.aa() works with current UniProt web pages
@@ -33,10 +45,3 @@
- update .Rinstignore with any new/deleted files
-- run R CMD check using R compiled without long doubles (as in Solaris checks on CRAN)
- (CFLAGS=-ffloat-store ./configure --disable-long-double)
-
-- build the package on the source directory:
- R CMD build --compact-vignettes chnosz/
- don't use --no-vignettes, that keeps the Rnw files from being copied to inst/doc,
- causing vignettes to disappear from CRAN webpage
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/inst/NEWS 2015-05-17 09:20:41 UTC (rev 85)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-22 (2015-05-17)
+CHANGES IN CHNOSZ 1.0.3-23 (2015-05-17)
---------------------------------------
NEW FEATURES:
@@ -9,7 +9,8 @@
- 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.
+- Add 'solubility.R' demo, and add calcite solubility plot to
+ anintro.Rnw.
DATA CONSISTENCY:
@@ -21,8 +22,8 @@
OTHER CHANGES:
- 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
+ useRaster=TRUE. This speeds up plotting, eliminates artifacts (i.e.
+ blank lines) at some resolutions, and greatly reduces the size
of PDF files.
- diagram() returns 'lx', 'ly' and 'is' for calculated positions of
@@ -39,8 +40,8 @@
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).
+ Pool hot spring 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.
@@ -57,7 +58,7 @@
- In test-diagram.R, test that same diagrams are produced using
'as.residue' in equilibrate() or diagram().
-- Add 'tplot' argument to diagram() (set to FALSE to use R's default
+- Add 'tplot' argument to diagram() (change to FALSE to use R's default
plot set-up).
CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -12,10 +12,10 @@
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 consult the primary sources (see \code{\link{browse.refs}}).
+If there is any doubt about the accuracy or suitability of data for a particular problem, please \emph{consult the primary sources} (see \code{\link{browse.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 compare the construction and output of the examples to the primary sources, cited in the reference list in each help page.
+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.
}
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -134,7 +134,8 @@
var <- c("invTTTheta3", "invTX")
EOSregress(d, var)
# give them a "label" attribute for use in the legend
-attr(invTTTheta3, "label") <- quote(phantom()\%*\%2*italic(T)/(italic(T)-italic(T)*Theta)^3)
+attr(invTTTheta3, "label") <-
+ quote(phantom()\%*\%2*italic(T)/(italic(T)-italic(T)*Theta)^3)
attr(invTX, "label") <- quote(phantom()/italic(T*X))
# uncomment the following to make the plot
#EOSplot(d, var)
Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/data.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -51,9 +51,9 @@
\code{state} \tab character \tab The default physical state for searching species (\samp{aq} by default)\cr
\code{water} \tab character \tab Computational option for properties of water (\samp{SUPCRT} (default) or \samp{IAPWS})\cr
\code{online} \tab logical \tab Allow online searches of protein composition? Default (\code{NA}) is to ask the user.\cr
- \code{G.tol} \tab numeric \tab Absolute difference between tabulated and calculated value of G above which \code{\link{checkGHS}} produces a message (cal mol\eqn{^{-1}}{^-1}).\cr
- \code{Cp.tol} \tab numeric \tab Absolute difference between tabulated and calculated value of Cp above which \code{\link{checkEOS}} produces a message (cal K\eqn{^{-1}}{-1} mol\eqn{^{-1}}{^-1}).\cr
- \code{V.tol} \tab numeric \tab Absolute difference between tabulated and calculated value of V above which \code{\link{checkEOS}} produces a message (cm\eqn{^{3}}{3} mol\eqn{^{-1}}{^-1}).\cr
+ \code{G.tol} \tab numeric \tab Difference in value of G above which \code{\link{checkGHS}} produces a message (cal mol\eqn{^{-1}}{^-1}).\cr
+ \code{Cp.tol} \tab numeric \tab Difference in value of Cp above which \code{\link{checkEOS}} produces a message (cal K\eqn{^{-1}}{-1} mol\eqn{^{-1}}{^-1}).\cr
+ \code{V.tol} \tab numeric \tab Difference in value of V above which \code{\link{checkEOS}} produces a message (cm\eqn{^{3}}{3} mol\eqn{^{-1}}{^-1}).\cr
\code{varP} \tab logical \tab Use variable-pressure standard state for gases (default \code{FALSE})? See \code{\link{subcrt}}.\cr
}
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/examples.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -37,11 +37,11 @@
\code{nucleobase} \tab relative stabilities of nucleobases and some amino acids \cr
\code{orp} \tab oxidation-reduction potential of redox standards as a function of temperature \cr
\code{findit} \tab detailed example of usage of \code{\link{findit}} using log-normal distribution as an objective \cr
- \code{CO2Ac} \tab activity of CO2 buffered by acetic acid; comparing \code{\link{affinity}(return.buffer=TRUE)} with \code{\link{diagram}(what="CO2")} \cr
+ \code{CO2Ac} \tab activity of CO2 buffered by acetic acid; comparing \code{\link{affinity}} with \code{\link{diagram}} \cr
\code{nonideal} \tab activity coefficient of charged species (Alberty, 2003), using the \code{IS} argument of \code{subcrt} \cr
\code{TPX} \tab metastablilities of selected ionized bacterial thiol peroxidases as a chemical activity buffer \cr
- \code{mosaic} \tab Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species (Garrels and Christ, 1965) \cr
- \code{solubility} \tab solubility of calcite (cf. Manning et al., 2013 Fig. 4A) or CO2(gas) (cf. Stumm and Morgan, 1996 Fig 4.5) as a function of pH \cr
+ \code{mosaic} \tab Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
+ \code{solubility} \tab solubility of calcite (cf. Manning et al., 2013) or CO2(gas) (cf. Stumm and Morgan, 1996) \cr
}
}
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/extdata.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -21,7 +21,7 @@
Files in \code{bison} contain BLAST results and taxonomic information for a metagenome:
\itemize{
- \item \code{bisonN_vs_refseq57.blast.xz}, \code{bisonS_vs_refseq57.blast.xz}, \code{bisonR_vs_refseq57.blast.xz}, \code{bisonQ_vs_refseq57.blast.xz}, \code{bisonP_vs_refseq57.blast.xz} are partial tabular BLAST results for proteins in the Bison Pool Environmental Genome. Protein sequences predicted in the metagenome were downloaded from the Joint Genome Institute's IMG/M system on 2009-05-13. The target database for the searches was constructed from microbial protein sequences in National Center for Biotechnology Information (NCBI) RefSeq database version 57, representing 7415 microbial genomes. The \sQuote{blastall} command was used with the default setting for E value cuttoff (10.0) and options to make a tabular output file consisting of the top 20 hits for each query sequence. The function \code{\link{read.blast}} was used to extract only those hits with E values less than or equal to 1e-5 and with sequence similarity (percent identity) at least 30 percent, and to keep only the first hit for each query sequence. The function \code{\link{write.blast}} was used to save partial BLAST files (only selected columns). The files provided with CHNOSZ contain the first 5,000 hits for each sampling site at Bison Pool, representing between about 7 to 15 percent of the first BLAST hits after similarity and E value filtering.
+ \item \code{bisonN_vs_refseq57.blast.xz}, \code{bisonS...}, \code{bisonR...}, \code{bisonQ...}, \code{bisonP...} are partial tabular BLAST results for proteins in the Bison Pool Environmental Genome. Protein sequences predicted in the metagenome were downloaded from the Joint Genome Institute's IMG/M system on 2009-05-13. The target database for the searches was constructed from microbial protein sequences in National Center for Biotechnology Information (NCBI) RefSeq database version 57, representing 7415 microbial genomes. The \sQuote{blastall} command was used with the default setting for E value cuttoff (10.0) and options to make a tabular output file consisting of the top 20 hits for each query sequence. The function \code{\link{read.blast}} was used to extract only those hits with E values less than or equal to 1e-5 and with sequence similarity (percent identity) at least 30 percent, and to keep only the first hit for each query sequence. The function \code{\link{write.blast}} was used to save partial BLAST files (only selected columns). The files provided with CHNOSZ contain the first 5,000 hits for each sampling site at Bison Pool, representing between about 7 to 15 percent of the first BLAST hits after similarity and E value filtering.
\item \code{gi.taxid.txt.xz} is a table that lists the sequence identifiers (gi numbers) that appear in the example BLAST files (see above), together with the corresponding taxon ids used in the NCBI databases. This file is \emph{not} a subset of the complete \sQuote{gi_taxid_prot.dmp.gz} available at \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/} but instead is a subset of \sQuote{gi.taxid.txt} generated from the RefSeq release catalog using \sQuote{gencat.sh} in the \code{refseq} directory. See \code{\link{id.blast}} for an example that uses this file and the BLAST files described above.
}
Modified: pkg/CHNOSZ/man/sideeffects.Rd
===================================================================
--- pkg/CHNOSZ/man/sideeffects.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/sideeffects.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -10,7 +10,7 @@
When the package is loaded, \code{\link{.onAttach}} creates a \code{\link{list}} object named \code{\link{thermo}} that is placed in an \code{\link{environment}} named \samp{CHNOSZ}.
Some functions in CHNOSZ have side effects that modify the contents of \code{thermo}; all such changes can be reverted, and the object restored to its original state, by calling \code{\link{data}(thermo)}.
-The \samp{CHNOSZ} environment is \emph{not} (as of CHNOSZ 1.0.0) \code{\link{attach}ed}, rather the \code{thermo} object is accessed in functions using \code{\link{get}} (as in \code{get("thermo")}), \code{\link{assign}} (\code{assign("thermo", thermo, "CHNOSZ")}) and occasionally \code{\link{with}} (\code{with(as.environment("CHNOSZ"), ...)}).
+The \samp{CHNOSZ} environment is \emph{not} (as of CHNOSZ 1.0.0) \code{\link{attach}ed}, rather the \code{thermo} object is accessed in functions by e.g. \code{\link{get}("thermo")}, \code{\link{assign}("thermo", thermo, "CHNOSZ")} and occasionally \code{\link{with}(as.environment("CHNOSZ"), ...)}.
In the functions in the package, the greatest number of accessions are to the thermodynamic database (\code{thermo$obigt}), followed by the basis and species definitions (\code{thermo$basis} and \code{thermo$species}).
For example, \code{\link{info}} can be used to look up thermodynamic data in \code{thermo$obigt} by the name or chemical formula of a species.
Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/subcrt.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -253,7 +253,8 @@
# start plot with extra room on right
par(mar=c(5, 4, 4, 4))
# plot G
-plot(sb$water$T, sb$water$G, ylim=c(-63000, -56000), xlab=axis.label("T"), ylab=axis.label("DG0"))
+plot(sb$water$T, sb$water$G, ylim=c(-63000, -56000), xlab=axis.label("T"),
+ ylab=axis.label("DG0"))
points(sb$`Na+`$T, sb$`Na+`$G, pch=2)
# add Cp
# change y-axis
Modified: pkg/CHNOSZ/man/util.expression.Rd
===================================================================
--- pkg/CHNOSZ/man/util.expression.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/util.expression.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -15,9 +15,10 @@
expr.property(property)
expr.units(property, prefix = "", per = "mol")
axis.label(label, units = NULL, basis = get("thermo")$basis, prefix = "")
- describe.basis(basis = get("thermo")$basis, ibasis = 1:nrow(basis), digits = 1,
- oneline = FALSE)
- describe.property(property, value, digits = 1, oneline = FALSE, ret.val = FALSE)
+ describe.basis(basis = get("thermo")$basis, ibasis = 1:nrow(basis),
+ digits = 1, oneline = FALSE)
+ describe.property(property, value, digits = 1, oneline = FALSE,
+ ret.val = FALSE)
describe.reaction(reaction, iname = numeric(), states = NULL)
}
Modified: pkg/CHNOSZ/man/wjd.Rd
===================================================================
--- pkg/CHNOSZ/man/wjd.Rd 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/man/wjd.Rd 2015-05-17 09:20:41 UTC (rev 85)
@@ -38,8 +38,9 @@
dimnames=list(NULL,c("H","N","O"))),
B = c(2,1,1), method="stoich", minX = 0.001, iguess = 1, ic = NULL
)
- run.wjd(ispecies, B = NULL, method = "stoich", Y = run.guess(ispecies, B, method),
- P=1, T=25, nlambda=101, imax = 10, Gfrac = 1e-7, tol = 0.01)
+ run.wjd(ispecies, B = NULL, method = "stoich",
+ Y = run.guess(ispecies, B, method), P=1, T=25, nlambda=101, imax = 10,
+ Gfrac = 1e-7, tol = 0.01)
run.guess(ispecies, B = NULL, method = "stoich", iguess = NULL)
equil.potentials(w, tol=0.01, T=25)
}
Modified: pkg/CHNOSZ/vignettes/hotspring.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.Rnw 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/vignettes/hotspring.Rnw 2015-05-17 09:20:41 UTC (rev 85)
@@ -56,15 +56,15 @@
\section{Introduction}
-The intention of this document is to demonstrate the calculations
-described in two recent papers \citep{DS11,DS13} dealing with the
-distribution and abundances of proteins in ``Bison Pool'', a hot
-spring in Yellowstone National Park. The calculations use metastable
-equilibrium to interrelate the compositions of proteins (from metagenomic
-data) with environmental conditions, particularly pH, temperature,
-and redox chemistry. This document is focused on the details of the
-calculations and has little in the way of introduction of concepts
-or interpretation and discussion; please see the papers for more details.
+This document is intended to demonstrate the calculations described
+in two recent papers \citep{DS11,DS13} dealing with the distribution
+and abundances of proteins in ``Bison Pool'', a hot spring in Yellowstone
+National Park. The calculations use metastable equilibrium to interrelate
+the compositions of proteins (from metagenomic data) with environmental
+conditions, particularly pH, temperature, and redox chemistry. This
+document is focused on the details of the calculations and has little
+in the way of introduction of concepts or interpretation and discussion;
+please see the papers for more details.
There is no hidden code in this document; all code used to make the
figures is shown in the blocks, but much of the text output (particularly
@@ -187,7 +187,8 @@
<<ZCplot, fig.width=5, fig.height=5, out.width='.49\\textwidth'>>=
# 2011 plot
-plot(0, 0, xlim=c(-0.5, 5), ylim=c(-0.27, -0.11), xlab="location", xaxt="n", ylab=expression(bar(italic(Z))[C]))
+ylab <- expression(bar(italic(Z))[C])
+plot(0, 0, xlim=c(-0.5, 5), ylim=c(-0.27, -0.11), xlab="location", xaxt="n", ylab=ylab)
axis(1, at=1:5)
col <- c("green", rep("black", 20))
lwd <- c(3, rep(1, 20))
@@ -204,7 +205,7 @@
pf.phyla <- protein.formula(aa.phyla)
ZC.phyla <- ZC(pf.phyla)
# set up plot
-plot(0, 0, xlim=c(1, 5), ylim=c(-0.27, -0.11), xlab="location", ylab=as.expression(quote(bar(italic(Z))[C])))
+plot(0, 0, xlim=c(1, 5), ylim=c(-0.27, -0.11), xlab="location", ylab=ylab)
for(i in 1:length(phyla.abc)) {
# which of the model proteins correspond to this phylum
iphy <- which(aa.phyla$organism==phyla.abc[i])
@@ -641,8 +642,10 @@
<<logaH2plot, fig.width=4, fig.height=4, out.width='.45\\textwidth', cache=TRUE>>=
# 2011 plot
+xlab <- axis.label("T")
+ylab <- axis.label("H2")
plot(Tlim, get.logaH2(Tlim), xlim=Tlim, ylim=c(-45,0),
- xlab=axis.label("T"), ylab=axis.label("H2"), type="l", lty=3)
+ xlab=xlab, ylab=ylab, type="l", lty=3)
points(T.ORP, logaH2.ORP, pch=15)
lines(T.ORP, logaH2.ORP, lty=2)
points(bison.T, logaH2.O, pch=16)
@@ -654,7 +657,7 @@
# 2013 plot
plot(Tlim, get.logaH2(Tlim), xlim=Tlim, ylim=c(-11,-2),
- xlab=axis.label("T"), ylab=axis.label("H2"), type="l", lty=3)
+ xlab=xlab, ylab=ylab, type="l", lty=3)
lines(bison.T, sapply(equil.results, "[", "logaH2.opt"), lty=2)
points(bison.T, sapply(equil.results, "[", "logaH2.opt"), pch=21, bg="white")
text(90, -5.3, "Equation 2")
Modified: pkg/CHNOSZ/vignettes/hotspring.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.lyx 2015-05-17 04:44:02 UTC (rev 84)
+++ pkg/CHNOSZ/vignettes/hotspring.lyx 2015-05-17 09:20:41 UTC (rev 85)
@@ -184,8 +184,8 @@
\end_layout
\begin_layout Standard
-The intention of this document is to demonstrate the calculations described
- in two recent papers
+This document is intended to demonstrate the calculations described in two
+ recent papers
\begin_inset CommandInset citation
LatexCommand citep
key "DS11,DS13"
@@ -736,8 +736,13 @@
\begin_layout Plain Layout
+ylab <- expression(bar(italic(Z))[C])
+\end_layout
+
+\begin_layout Plain Layout
+
plot(0, 0, xlim=c(-0.5, 5), ylim=c(-0.27, -0.11), xlab="location", xaxt="n",
- ylab=expression(bar(italic(Z))[C]))
+ ylab=ylab)
\end_layout
\begin_layout Plain Layout
@@ -822,8 +827,7 @@
\begin_layout Plain Layout
-plot(0, 0, xlim=c(1, 5), ylim=c(-0.27, -0.11), xlab="location", ylab=as.expression(
-quote(bar(italic(Z))[C])))
+plot(0, 0, xlim=c(1, 5), ylim=c(-0.27, -0.11), xlab="location", ylab=ylab)
\end_layout
\begin_layout Plain Layout
@@ -2667,12 +2671,22 @@
\begin_layout Plain Layout
+xlab <- axis.label("T")
+\end_layout
+
+\begin_layout Plain Layout
+
+ylab <- axis.label("H2")
+\end_layout
+
+\begin_layout Plain Layout
+
plot(Tlim, get.logaH2(Tlim), xlim=Tlim, ylim=c(-45,0),
\end_layout
\begin_layout Plain Layout
- xlab=axis.label("T"), ylab=axis.label("H2"), type="l", lty=3)
+ xlab=xlab, ylab=ylab, type="l", lty=3)
\end_layout
\begin_layout Plain Layout
@@ -2731,7 +2745,7 @@
\begin_layout Plain Layout
- xlab=axis.label("T"), ylab=axis.label("H2"), type="l", lty=3)
+ xlab=xlab, ylab=ylab, type="l", lty=3)
\end_layout
\begin_layout Plain Layout
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