[CHNOSZ-commits] r126 - in pkg/CHNOSZ: . R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Feb 4 03:51:28 CET 2017
Author: jedick
Date: 2017-02-04 03:51:27 +0100 (Sat, 04 Feb 2017)
New Revision: 126
Added:
pkg/CHNOSZ/vignettes/elementa.csl
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/basis.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/EOSregress.Rmd
pkg/CHNOSZ/vignettes/anintro.Rnw
pkg/CHNOSZ/vignettes/anintro.lyx
pkg/CHNOSZ/vignettes/newintro.Rmd
pkg/CHNOSZ/vignettes/vig.bib
pkg/CHNOSZ/vignettes/wjd.Rnw
pkg/CHNOSZ/vignettes/wjd.lyx
Log:
work on newintro.Rmd; add elementa.csl
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-04 02:51:27 UTC (rev 126)
@@ -1,6 +1,6 @@
-Date: 2017-02-02
+Date: 2017-02-04
Package: CHNOSZ
-Version: 1.0.8-15
+Version: 1.0.8-16
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/R/basis.R 2017-02-04 02:51:27 UTC (rev 126)
@@ -27,7 +27,7 @@
if( nrow(comp) < ncol(comp) ) stop("underdetermined system; square stoichiometric matrix needed")
# the second test: matrix is invertible
if(class(try(solve(comp), silent=TRUE))=='try-error')
- stop("singular stoichiometric matrix; invertible one needed")
+ stop("singular stoichiometric matrix")
# store the basis definition in thermo$basis, including
# both numeric and character data, so we need to use a data frame
comp <- cbind(as.data.frame(comp), ispecies, logact, state, stringsAsFactors=FALSE)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-04 02:51:27 UTC (rev 126)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-15 (2017-02-02)
+CHANGES IN CHNOSZ 1.0.8-16 (2017-02-04)
---------------------------------------
- Add "AA" as a keyword for preset species in basis() (cysteine,
Modified: pkg/CHNOSZ/vignettes/EOSregress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-02-04 02:51:27 UTC (rev 126)
@@ -19,6 +19,7 @@
\usepackage[utf8]{inputenc}
bibliography: vig.bib
link-citations: yes
+csl: elementa.csl
---
```{r setup, include=FALSE}
Modified: pkg/CHNOSZ/vignettes/anintro.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rnw 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/vignettes/anintro.Rnw 2017-02-04 02:51:27 UTC (rev 126)
@@ -1,8 +1,9 @@
-%% LyX 2.1.3 created this file. For more info, see http://www.lyx.org/.
+%% LyX 2.2.2 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[english,noae,round]{article}
\usepackage{mathpazo}
\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
\usepackage[letterpaper]{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\usepackage{color}
@@ -48,7 +49,6 @@
\title{An introduction to CHNOSZ}
-
\author{Jeffrey M. Dick}
\maketitle
@@ -81,13 +81,12 @@
species using very similar commands. Examples below are intended to
demonstrate basic usage to new users.
-
\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
is an updated version of the flowchart from \citet{Dic08} (boxes
--- functions; ellipses -- datasets; bold text -- major user functions).
+– functions; ellipses – datasets; bold text – major user functions).
\includegraphics[bb=0bp 440bp 612bp 792bp,clip,width=0.75\columnwidth]{flowchart}
@@ -119,7 +118,6 @@
results. The results can then be reproduced on demand by yourself
or others with whom you might share your scripts.
-
\subsection{Installing and loading CHNOSZ}
If you have just installed R, and you are online, installing the CHNOSZ
@@ -150,7 +148,6 @@
The rest of this document assumes that the CHNOSZ package and data
are loaded.
-
\section{Thermodynamic database}
@@ -168,7 +165,7 @@
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
+\ref{subsec: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
@@ -219,7 +216,7 @@
@
-\subsection{\texttt{\label{sub:thermo_refs}thermo\$refs}}
+\subsection{\texttt{\label{subsec: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
@@ -329,7 +326,6 @@
the first call to\texttt{ info()} just above had a side effect of
adding the computed properties and parameters to \texttt{thermo\$obigt}.
-
\section{Reaction properties}
@@ -362,7 +358,6 @@
package uses a Fortran subroutine taken from SUPCRT for these calculations.
See \texttt{help(water)} for more information.
-
\subsection{A reaction}
To calculate the properties of a reaction, enter the stoichiometric
@@ -404,7 +399,6 @@
an unbalanced reaction). In the next section we'll see how to use
another feature of CHNOSZ to automatically balance reactions.
-
\section{Basis species}
@@ -425,6 +419,7 @@
<<basis_not,eval=FALSE>>=
basis(c("CO2","H2O","NH3","H2S","H+"))
@
+
\begin{lyxcode}
Error~in~put.basis(basis,~mystates)~:~
@@ -450,7 +445,6 @@
name. These represent the elements in the commonly-occurring amino
acids, together with charge, denoted by ``Z''.
-
\subsection{Auto-balancing a reaction}
Now that the basis species are defined, try the unbalanced reaction
@@ -503,7 +497,6 @@
coming up with a useful basis definition is in relating the species
to observable quantities.
-
\subsection{It works for proteins too!}
Let's set the basis definition again, this time using a keyword that
@@ -588,7 +581,6 @@
directory where CHNOSZ is installed) to change the calculation from
calcite to $\mathrm{CO_{2}}$.
-
\subsection{Stability diagram for proteins}
Suppose that we are asked to calculate the relative stabilities of
@@ -622,8 +614,8 @@
formation reactions. The chemical affinity is the negative of the
Gibbs energy change of a reaction per unit of reaction progress; it
is calculated in CHNOSZ using $\boldsymbol{A}=2.303RT\log(K/Q)$ ($R$
--- gas constant, $T$ -- temperature, $K$ -- equilibrium constant,
-$Q$ -- activity product).
+– gas constant, $T$ – temperature, $K$ – equilibrium constant, $Q$
+– activity product).
\texttt{affinity()} can accept arguments describing the range of chemical
conditions we're interested in. The names of the arguments can refer
@@ -654,7 +646,6 @@
Notably, the protein from the organism found at the highest temperatures
is relatively stable at more reduced conditions.
-
\subsection{More proteins, more dimensions}
Now let's add some bacterial surface-layer proteins. They are in some
@@ -720,7 +711,7 @@
\setkeys{Gin}{width=1.0\textwidth}
The 999's in the assignment of logarithms of activities of basis species
-could be any number -- these settings do not affect the outcome of
+could be any number – these settings do not affect the outcome of
the calculation. This is so because 1) $\mathrm{HCl}$, $\mathrm{CO_{2}}$
and $\mathrm{O_{2}}$ have zero stoichiometric coefficients in the
species, 2) the activities of $\mathrm{Ca}^{+2}$ and $\mathrm{Mg}^{+2}$
@@ -743,7 +734,6 @@
diagrams for organic and inorganic species. Try it for your favorite
system!
-
\section{Where to go from here}
You can explore the package documentation through R's help system;
@@ -765,7 +755,7 @@
Or you can use the following to run \emph{all} of the examples provided
in the documentation for the package. You will see a lot of text fly
by on the screen, as well as a variety of plots. The examples will
-take about 5--10 minutes to run, depending on your machine.
+take about 5–10 minutes to run, depending on your machine.
<<examples,eval=FALSE>>=
examples()
@@ -787,7 +777,6 @@
Have fun!
-
\section{More activity diagrams}
The following pages contain activity diagrams created with more complex
@@ -815,7 +804,7 @@
of difference.
Toward the end of the script, points are added for Eh-pH values from
-soils \citep{BKM60} and hot springs in Yellowstone ($+$) \citep{SWM+05}
+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 drawn to identify the lines and symbols. The \texttt{describe.property()}
@@ -851,7 +840,7 @@
\subsection{Subcellular proteins}
-Localizations and abundances of proteins from YeastGFP \citep{HFG+03,GHB+03}
+Localizations and abundances of proteins from YeastGFP \citep{HFG_03,GHB_03}
are used here to calculate an abundance-weighted average of amino
acid compositions of proteins in different subcellular compartments
of yeast. The relative stabilities of these 23 model proteins are
@@ -907,7 +896,7 @@
both $\mathrm{S_{2}}$ and $\mathrm{O_{2}}$ by pyrite-pyrrhotite-magnetite,
and the buffers have effects on equilibrium activity diagrams) while
the latter is more convenient (no need to set up the buffer in \texttt{thermo\$buffer}
--- the buffers come from the species of interest). The plot below,
+– the buffers come from the species of interest). The plot below,
based on Fig. 6 of \citet{SS95}, shows values of $\log f_{\mathrm{H_{2}}_{\left(g\right)}}$
buffered by minerals and in equilibrium with different activities
of organic species that are calculated using these two methods.
@@ -1065,7 +1054,6 @@
it remains a matter of discussion what the optimized chemical activities
of the basis species and the amino acids signify.
-
\section{Document information}
Revision history:
Modified: pkg/CHNOSZ/vignettes/anintro.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.lyx 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/vignettes/anintro.lyx 2017-02-04 02:51:27 UTC (rev 126)
@@ -1,7 +1,9 @@
-#LyX 2.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 474
+#LyX 2.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 508
\begin_document
\begin_header
+\save_transient_properties true
+\origin unavailable
\textclass article
\begin_preamble
%\VignetteIndexEntry{An introduction to CHNOSZ}
@@ -17,18 +19,18 @@
\maintain_unincluded_children false
\language english
\language_package default
-\inputencoding default
+\inputencoding utf8
\fontencoding global
-\font_roman palatino
-\font_sans default
-\font_typewriter default
-\font_math auto
+\font_roman "palatino" "default"
+\font_sans "default" "default"
+\font_typewriter "default" "default"
+\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
+\font_sf_scale 100 100
+\font_tt_scale 100 100
\graphics default
\default_output_format default
\output_sync 0
@@ -211,7 +213,7 @@
\end_inset
- (boxes -- functions; ellipses -- datasets; bold text -- major user functions).
+ (boxes – functions; ellipses – datasets; bold text – major user functions).
\end_layout
\begin_layout Standard
@@ -509,7 +511,7 @@
; see Section
\begin_inset CommandInset ref
LatexCommand ref
-reference "sub:thermo_refs"
+reference "subsec:thermo_refs"
\end_inset
@@ -738,7 +740,7 @@
\family typewriter
\begin_inset CommandInset label
LatexCommand label
-name "sub:thermo_refs"
+name "subsec:thermo_refs"
\end_inset
@@ -2196,7 +2198,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Standard
\begin_inset ERT
@@ -2501,19 +2503,19 @@
\begin_inset Formula $R$
\end_inset
- -- gas constant,
+ – gas constant,
\begin_inset Formula $T$
\end_inset
- -- temperature,
+ – temperature,
\begin_inset Formula $K$
\end_inset
- -- equilibrium constant,
+ – equilibrium constant,
\begin_inset Formula $Q$
\end_inset
- -- activity product).
+ – activity product).
\end_layout
\begin_layout Standard
@@ -2970,8 +2972,8 @@
\begin_layout Standard
The 999's in the assignment of logarithms of activities of basis species
- could be any number -- these settings do not affect the outcome of the
- calculation.
+ could be any number – these settings do not affect the outcome of the calculati
+on.
This is so because 1)
\begin_inset Formula $\mathrm{HCl}$
\end_inset
@@ -3137,7 +3139,7 @@
of the examples provided in the documentation for the package.
You will see a lot of text fly by on the screen, as well as a variety of
plots.
- The examples will take about 5--10 minutes to run, depending on your machine.
+ The examples will take about 5–10 minutes to run, depending on your machine.
\end_layout
@@ -3398,7 +3400,7 @@
)
\begin_inset CommandInset citation
LatexCommand citep
-key "SWM+05"
+key "SWM_05"
\end_inset
@@ -3617,7 +3619,7 @@
Localizations and abundances of proteins from YeastGFP
\begin_inset CommandInset citation
LatexCommand citep
-key "HFG+03,GHB+03"
+key "HFG_03,GHB_03"
\end_inset
@@ -3870,7 +3872,7 @@
\family typewriter
thermo$buffer
\family default
- -- the buffers come from the species of interest).
+ – the buffers come from the species of interest).
The plot below, based on Fig.
6 of
\begin_inset CommandInset citation
Added: pkg/CHNOSZ/vignettes/elementa.csl
===================================================================
--- pkg/CHNOSZ/vignettes/elementa.csl (rev 0)
+++ pkg/CHNOSZ/vignettes/elementa.csl 2017-02-04 02:51:27 UTC (rev 126)
@@ -0,0 +1,453 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+ <info>
+ <title>Elementa</title>
+ <title-short>Elementa</title-short>
+ <id>http://www.zotero.org/styles/elementa</id>
+ <link href="http://www.zotero.org/styles/elementa" rel="self"/>
+ <link href="http://www.zotero.org/styles/council-of-science-editors-author-date" rel="template"/>
+ <link href="http://www.zotero.org/styles/apa" rel="template"/>
+ <link href="https://home.elementascience.org/for-authors/style-guide/" rel="documentation"/>
+ <link href="http://lynn-library.libguides.com/cse" rel="documentation"/>
+ <link href="http://writing.wisc.edu/Handbook/DocCSE_CitationSystems.html" rel="documentation"/>
+ <author>
+ <name>Akos Kokai</name>
+ <email>akokai at berkeley.edu</email>
+ </author>
+ <category citation-format="author-date"/>
+ <category field="science"/>
+ <eissn>2325-1026</eissn>
+ <summary>Based on The Council of Science Editors style, Name-Year system: author-date in text, sorted in alphabetical order by author.</summary>
+ <updated>2016-07-26T01:00:00+00:00</updated>
+ <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+ </info>
+ <locale xml:lang="en">
+ <terms>
+ <term name="editortranslator" form="long">
+ <single>editor and translator</single>
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+ <single>editor</single>
+ <multiple>editors</multiple>
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+ <label form="long" prefix=", " strip-periods="true"/>
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+ <text macro="title"/>
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+ <macro name="year-date">
+ <choose>
+ <if variable="issued">
+ <group delimiter=" ">
+ <date variable="issued" delimiter=" ">
+ <date-part name="year"/>
+ </date>
+ <choose>
+ <if type="patent article-newspaper webpage" match="any">
+ <date variable="issued" delimiter=" ">
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </if>
+ <else-if type="article-journal article-magazine" match="any">
+ <choose>
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+ <date variable="issued" delimiter=" ">
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+ <text variable="title" font-style="italic" text-case="title"/>
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+ <text variable="title"/>
+ </else>
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+ <choose>
+ <if type="thesis dataset speech interview broadcast" match="any">
+ <text variable="genre" form="long" prefix="[" suffix="]"/>
+ </if>
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+ <!-- Book reviews -->
+ <if variable="reviewed-author">
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+ <group delimiter=" ">
+ <text variable="title"/>
+ <group delimiter=", " prefix="[" suffix="]">
+ <text variable="reviewed-title" font-style="italic" prefix="Review of "/>
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+ <text term="in" text-case="capitalize-first" suffix=": "/>
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+ <if type="bill legal_case legislation" match="none">
+ <group delimiter=". ">
+ <text macro="container-contributors"/>
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+ </if>
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+ </group>
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+ <macro name="edition">
+ <choose>
+ <if is-numeric="edition">
+ <group delimiter=" ">
+ <number variable="edition" form="ordinal"/>
+ <label variable="edition" form="short"/>
+ </group>
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+ <else>
+ <text variable="edition"/>
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+ </choose>
+ </macro>
+ <macro name="pages">
+ <choose>
+ <if type="chapter entry-dictionary entry-encyclopedia" match="any">
+ <group delimiter="; ">
+ <group>
+ <label variable="page" form="short" suffix=" " plural="never"/>
+ <text variable="page"/>
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+ <group>
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+ </if>
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+ <macro name="journal-locators">
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+ <choose>
+ <if variable="volume issue page" match="none">
+ <choose>
+ <if type="article-journal review review-book">
+ <text term="in press" prefix=", "/>
+ </if>
+ </choose>
+ </if>
+ <else>
+ <group>
+ <text variable="volume" prefix=" " font-weight="bold"/>
+ <text variable="issue" prefix="(" suffix=")"/>
+ <text variable="page" prefix=": "/>
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+ </else>
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+ </macro>
+ <macro name="locators">
+ <choose>
+ <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+ <text macro="journal-locators"/>
+ </if>
+ <else-if type="paper-conference">
+ <choose>
+ <if variable="container-title">
+ <text macro="journal-locators"/>
+ </if>
+ <else>
+ <date variable="issued" delimiter=" " suffix=".">
+ <date-part name="year"/>
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </else>
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+ </else-if>
+ <else-if type="bill legal_case legislation" match="none">
+ <text macro="edition" suffix="."/>
+ </else-if>
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+ <macro name="legal-cites">
+ <!-- Bluebook style; adapted from apa.csl -->
+ <choose>
+ <if type="bill legal_case legislation" match="any">
+ <group delimiter=" ">
+ <choose>
+ <if variable="container-title">
+ <text variable="volume"/>
+ <text variable="container-title"/>
+ <group delimiter=" ">
+ <!--change to label variable="section" as that becomes available -->
+ <text term="section" form="symbol"/>
+ <text variable="section"/>
+ </group>
+ <text variable="section"/>
+ <text variable="page"/>
+ </if>
+ <else>
+ <choose>
+ <if type="legal_case">
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+ </if>
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+ <!--change to label variable="section" as that becomes available -->
+ <text term="section" form="symbol"/>
+ <text variable="section"/>
+ </group>
+ <text variable="section"/>
+ </else>
+ </choose>
+ </else>
+ </choose>
+ </group>
+ </if>
+ </choose>
+ </macro>
+ <macro name="event">
+ <choose>
+ <if variable="event">
+ <choose>
+ <if variable="container-title" match="none">
+ <!-- Don't give event info if part of a publication
+ (e.g., conference proceedings) -->
+ <choose>
+ <if type="paper-conference" match="none">
+ <group delimiter=" ">
+ <text variable="genre" text-case="capitalize-first"/>
+ <text term="presented at" text-case="capitalize-first"/>
+ </group>
+ </if>
+ </choose>
+ <group prefix=" " suffix="." delimiter="; ">
+ <text variable="event"/>
+ <text variable="event-place"/>
+ </group>
+ </if>
+ </choose>
+ </if>
+ </choose>
+ </macro>
+ <macro name="publisher">
+ <group delimiter=": ">
+ <choose>
+ <if type="thesis">
+ <text variable="publisher-place" prefix="[" suffix="]"/>
+ </if>
+ <else-if variable="event" match="none">
+ <text variable="publisher-place"/>
+ </else-if>
+ </choose>
+ <text variable="publisher"/>
+ </group>
+ </macro>
+ <macro name="collection">
+ <!-- This is to appear at the end of the citation:
+ after publisher, before access. -->
+ <choose>
+ <if type="report">
+ <group prefix=" " suffix="." delimiter=" ">
+ <text variable="collection-title"/>
+ <text variable="number" prefix="Report No.: "/>
+ </group>
+ </if>
+ <else-if type="book">
+ <group prefix=" (" suffix=")." delimiter=" ">
+ <names variable="collection-editor" suffix=". ">
+ <name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+ <label prefix="; "/>
+ </names>
+ <group delimiter="; ">
+ <text variable="collection-title"/>
+ <choose>
+ <if variable="collection-number">
+ <group>
+ <text term="volume" form="short" text-case="capitalize-first" suffix=". "/>
+ <text variable="collection-number"/>
+ </group>
+ </if>
+ <else>
+ <group>
+ <label variable="volume" form="short" text-case="capitalize-first" suffix=". "/>
+ <text variable="volume"/>
+ </group>
+ </else>
+ </choose>
+ </group>
+ </group>
+ </else-if>
+ <!-- Add other types that need collection info after publisher. -->
+ </choose>
+ </macro>
+ <macro name="access">
+ <choose>
+ <if variable="DOI">
+ <text variable="DOI" prefix="doi: "/>
+ </if>
+ <else-if variable="URL">
+ <group suffix=". " delimiter=" ">
+ <text term="available at" text-case="capitalize-first"/>
+ <text variable="URL"/>
+ </group>
+ <group suffix=". " delimiter=" ">
+ <text term="accessed" text-case="capitalize-first"/>
+ <date variable="accessed" delimiter=" ">
+ <date-part name="year"/>
+ <date-part name="month" form="short" strip-periods="true"/>
+ <date-part name="day"/>
+ </date>
+ </group>
+ </else-if>
+ </choose>
+ </macro>
+ <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true">
+ <sort>
+ <key macro="year-date"/>
+ <key macro="author-short"/>
+ </sort>
+ <layout prefix="(" suffix=")" delimiter="; ">
+ <group delimiter=", ">
+ <text macro="author-short"/>
+ <text macro="year"/>
+ </group>
+ <text variable="locator" prefix=": "/>
+ </layout>
+ </citation>
+ <bibliography hanging-indent="true" et-al-min="11" et-al-use-first="10">
+ <sort>
+ <key macro="author"/>
+ <key macro="year-date"/>
+ </sort>
+ <layout>
+ <group delimiter=". " suffix=".">
+ <text macro="author"/>
+ <text macro="year-date"/>
+ <text macro="title"/>
+ <group delimiter="">
+ <text macro="container"/>
+ <text macro="locators"/>
+ </group>
+ <text macro="legal-cites"/>
+ <text macro="event"/>
+ <text macro="publisher"/>
+ <text macro="pages"/>
+ <text macro="collection"/>
+ </group>
+ <text prefix=" " macro="access"/>
+ </layout>
+ </bibliography>
+</style>
Modified: pkg/CHNOSZ/vignettes/newintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/newintro.Rmd 2017-02-02 17:17:22 UTC (rev 125)
+++ pkg/CHNOSZ/vignettes/newintro.Rmd 2017-02-04 02:51:27 UTC (rev 126)
@@ -19,6 +19,7 @@
\usepackage[utf8]{inputenc}
bibliography: vig.bib
link-citations: yes
+csl: elementa.csl
---
```{r options, include=FALSE}
@@ -31,8 +32,11 @@
knitr::opts_chunk$set(tidy = FALSE, cache.extra = packageVersion('tufte'))
options(htmltools.dir.version = FALSE)
knitr::knit_hooks$set(small.mar = function(before, options, envir) {
- if (before) par(mar = c(4, 4, .1, .1)) # smaller margin on top and right
+ if (before) par(mar = c(4.2, 4.2, .1, .1)) # smaller margin on top and right
})
+knitr::knit_hooks$set(tiny.mar = function(before, options, envir) {
+ if (before) par(mar = c(.1, .1, .1, .1)) # tiny margin all around
+})
```
# About
@@ -47,7 +51,7 @@
## Installing and loading CHNOSZ
-If you have just installed R for the first time, and you have an internet connection, installing CHNOSZ should be as simple as selecting the "Install packages from CRAN" or similar menu item in the R GUI or using the following command to start the package installation process:^[Or, install the package from a local package file, which you can download from [CRAN](http://cran.r-project.org) or from the [CHNOSZ website](http://chnosz.net).
+If you have just installed R for the first time, and you have an Internet connection, installing CHNOSZ should be as simple as selecting the "Install packages from CRAN" or similar menu item in the R GUI or using the following command to start the package installation process:^[Or, install the package from a local package file, which you can download from [CRAN](http://cran.r-project.org) or from the [CHNOSZ website](http://chnosz.net).
][]()
```{r install_CHNOSZ, eval=FALSE}
install.packages("CHNOSZ")
@@ -239,7 +243,7 @@
```
<p> <!--- needed to make the citation appear correction 20170202 -->
-In order to make a plot like that shown by Manning et al. [- at MSS13, Figure 18], let's run more calculations and store the results.
+In order to make a plot like Figure 18 of @MSS13, let's run more calculations and store the results.
In addition to the reaction definition, we specify a greater number of temperature points than the default:
```{r dissolution, echo=FALSE, message=FALSE}
T <- seq(0, 350, 10)
@@ -262,15 +266,149 @@
## Unbalanced reactions
+A balanced chemical reaction conserves mass.
+`subcrt()` won't stop you from running an unbalanced reaction, but it will give you a warning:
+```{r subcrt_unbalanced, results="hide"}
+subcrt(c("CO2", "CH4"), c(-1, 1))
+```
+
+In other words, to balance the reaction, we should add exactly 4 H to the left and 2 O to the right.
+That could be done manually be redefining the reaction with the appropriate species.
+There is another option: balancing the reaction automatically using basis species.
+
## Setting the basis species
+_Basis species_ are a minimal number of chemical species that represent the compositional variation in a system.
+The basis species are similar to thermodynamic components, but can include charged species.
+You might want to use basis species to automatically balance reactions.
+A basis setting is also required for making chemical activity diagrams.
+
+Let's start with an example that **doesn't** work:
+```{r basis_singular, error=TRUE}
+basis(c("CO2", "H2", "H2CO2"))
+```
+
+That set of species has a singular (non-invertible) stoichiometric matrix.
+An error would also result from either an underdetermined or overdetermined system.
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 126
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