rticles/inst/rmarkdown/templates/acs_article/skeleton/skeleton.Rmd

---
journal: jacsat
type: article
author:
  - name: Andrew N. Other
    altaff: A shared footnote
  - name: Fred T. Secondauthor
    altaff: "Current address: Some other place, Germany"
  - name: I. Ken Groupleader
    altaff: A shared footnote
    email: \email{[email protected]}
    phone: +123 (0)123 4445556
    fax: +123 (0)123 4445557
    aff: Department of Chemistry, Unknown University, Unknown Town
    alsoaff: Department of Chemistry, Second University, Nearby Town
  - name: Susanne K. Laborator
    email: \email{[email protected]}
    aff: Lead Discovery, BigPharma, Big Town, USA
  - name: Kay T. Finally
    aff: Department of Chemistry, Unknown University, Unknown Town
    alsoaff: Department of Chemistry, Second University, Nearby Town
title:
  formatted: A demonstration of the \textsf{achemso} \LaTeX\
   class\footnote{A footnote for the title}
  short: An \textsf{achemso} demo
abbr: IR,NMR,UV
keywords: American Chemical Society, \LaTeX
abstract: |
  This is an example document for the \textsf{achemso} documentclass, intended for submissions to the American Chemical Society for publication. The class is based on the standard \LaTeXe\ \textsf{report} file, and does not seek to reproduce the appearanceof a published paper.

  This is an abstract for the \textsf{achemso} document class demonstration document.  An abstract is only allowed for certain manuscript types.  The selection of \texttt{journal} and \texttt{manuscript} will determine if an abstract is valid.  If not, the class will issue an appropriate error.This is the abstract.

bibliography: acstest.bib
output: rticles::acs_article
---

\begin{tocentry}
Some journals require a graphical entry for the Table of Contents.
This should be laid out ``print ready'' so that the sizing of the
text is correct.

Inside the \texttt{tocentry} environment, the font used is Helvetica
8\,pt, as required by \emph{Journal of the American Chemical
Society}.

The surrounding frame is 9\,cm by 3.5\,cm, which is the maximum
permitted for  \emph{Journal of the American Chemical Society}
graphical table of content entries. The box will not resize if the
content is too big: instead it will overflow the edge of the box.

This box and the associated title will always be printed on a
separate page at the end of the document.
\end{tocentry}

# Introduction
This is a paragraph of text to fill the introduction of the
demonstration file.  The demonstration file attempts to show the
modifications of the standard \LaTeX\ macros that are implemented by
the \textsf{achemso} class.  These are mainly concerned with content,
as opposed to appearance.

# Results and discussion

## Outline

The document layout should follow the style of the journal concerned.
Where appropriate, sections and subsections should be added in the
normal way. If the class options are set correctly, warnings will be
given if these should not be present.

## References

The class makes various changes to the way that references are
handled.  The class loads \textsf{natbib}, and also the
appropriate bibliography style.  References can be made using
the normal method; the citation should be placed before any
punctuation, as the class will move it if using a superscript
citation style [@Garnier2007].
The use of \textsf{natbib} allows the use of the various citation
commands of that package have shown
something.  Long lists of authors will be
automatically truncated in most article formats, but not in
supplementary information or reviews. If you
encounter problems with the citation macros, please check that
your copy of \textsf{natbib} is up to date. The demonstration
database file \texttt{achemso-demo.bib} shows how to complete
entries correctly. Notice that ``\latin{et al.}'' is auto-formatted
using the \texttt{\textbackslash latin} command.

Multiple citations to be combined into a list can be given as
a single citation.  This uses the \textsf{mciteplus} package.
Citations other than the first of the list should be indicated
with a star.

The class also handles notes to be added to the bibliography.  These
should be given in place in the document.  As with
citations, the text should be placed before punctuation.  A note is
also generated if a citation has an optional note.  This assumes that
the whole work has already been cited: odd numbering will result if
this is not the case .

## Floats

New float types are automatically set up by the class file.  The
means graphics are included as follows (Scheme \ref{sch:example}).  As
illustrated, the float is ``here'' if possible.
\begin{scheme}
  Your scheme graphic would go here: \texttt{.eps} format\\
  for \LaTeX\, or \texttt{.pdf} (or \texttt{.png}) for pdf\LaTeX\\
  \textsc{ChemDraw} files are best saved as \texttt{.eps} files:\\
  these can be scaled without loss of quality, and can be\\
  converted to \texttt{.pdf} files easily using \texttt{eps2pdf}.\\
  %\includegraphics{graphic}
  \caption{An example scheme}
  \label{sch:example}
\end{scheme}

```{r,echo=FALSE,fig.cap='test'}
plot(1:10)
```

\begin{figure}
  As well as the standard float types \texttt{table}\\
  and \texttt{figure}, the class also recognises\\
  \texttt{scheme}, \texttt{chart} and \texttt{graph}.
  \caption{An example figure}
  \label{fgr:example}
\end{figure}

Charts, figures and schemes do not necessarily have to be labelled or
captioned.  However, tables should always have a title. It is
possible to include a number and label for a graphic without any
title, using an empty argument to the \texttt{\textbackslash caption}
macro.

The use of the different floating environments is not required, but
it is intended to make document preparation easier for authors. In
general, you should place your graphics where they make logical
sense; the production process will move them if needed.

## Math(s)

The \textsf{achemso} class does not load any particular additional
support for mathematics.  If packages such as \textsf{amsmath} are
required, they should be loaded in the preamble.  However,
the basic \LaTeX\ math(s) input should work correctly without
this.  Some inline material $y = mx + c$ or $1 + 1 = 2$
followed by some display. $$ A = \pi r^2 $$

It is possible to label equations in the usual way (Eq. \ref{eqn:example}).
\begin{equation}
  \frac{\mathrm{d}}{\mathrm{d}x} \, r^2 = 2r \label{eqn:example}
\end{equation}
This can also be used to have equations containing graphical
content. To align the equation number with the middle of the graphic,
rather than the bottom, a minipage may be used.
\begin{equation}
  \begin{minipage}[c]{0.80\linewidth}
    \centering
    As illustrated here, the width of \\
    the minipage needs to allow some  \\
    space for the number to fit in to.
    %\includegraphics{graphic}
  \end{minipage}
  \label{eqn:graphic}
\end{equation}

# Experimental

The usual experimental details should appear here.  This could
include a table, which can be referenced as Table \ref{tbl:example}.
Notice that the caption is positioned at the top of the table.
\begin{table}
  \caption{An example table}
  \label{tbl:example}
  \begin{tabular}{ll}
    \hline
    Header one  & Header two  \\
    \hline
    Entry one   & Entry two   \\
    Entry three & Entry four  \\
    Entry five  & Entry five  \\
    Entry seven & Entry eight \\
    \hline
  \end{tabular}
\end{table}

Adding notes to tables can be complicated.  Perhaps the easiest
method is to generate these using the basic
\texttt{\textbackslash textsuperscript} and
\texttt{\textbackslash emph} macros, as illustrated (Table \ref{tbl:notes}).
\begin{table}
  \caption{A table with notes}
  \label{tbl:notes}
  \begin{tabular}{ll}
    \hline
    Header one                            & Header two \\
    \hline
    Entry one\textsuperscript{\emph{a}}   & Entry two  \\
    Entry three\textsuperscript{\emph{b}} & Entry four \\
    \hline
  \end{tabular}

  \textsuperscript{\emph{a}} Some text;
  \textsuperscript{\emph{b}} Some more text.
\end{table}

The example file also loads the optional \textsf{mhchem} package, so
that formulas are easy to input: \texttt{\textbackslash ce\{H2SO4\}}
gives \ce{H2SO4}.  See the use in the bibliography file (when using
titles in the references section).

The use of new commands should be limited to simple things which will
not interfere with the production process.  For example,
\texttt{\textbackslash mycommand} has been defined in this example,
to give italic, mono-spaced text: \mycommand{some text}.

# Extra information when writing JACS Communications

When producing communications for \emph{J.~Am.\ Chem.\ Soc.}, the
class will automatically lay the text out in the style of the
journal. This gives a guide to the length of text that can be
accommodated in such a publication. There are some points to bear in
mind when preparing a JACS Communication in this way.  The layout
produced here is a \emph{model} for the published result, and the
outcome should be taken as a \emph{guide} to the final length. The
spacing and sizing of graphical content is an area where there is
some flexibility in the process.  You should not worry about the
space before and after graphics, which is set to give a guide to the
published size. This is very dependant on the final published layout.

You should be able to use the same source to produce a JACS
Communication and a normal article.  For example, this demonstration
file will work with both \texttt{type=article} and
\texttt{type=communication}. Sections and any abstract are
automatically ignored, although you will get warnings to this effect.

\begin{acknowledgement}

Please use ``The authors thank \ldots'' rather than ``The
authors would like to thank \ldots''.

The author thanks Mats Dahlgren for version one of \textsf{achemso},
and Donald Arseneau for the code taken from \textsf{cite} to move
citations after punctuation. Many users have provided feedback on the
class, which is reflected in all of the different demonstrations
shown in this document.

\end{acknowledgement}

\begin{suppinfo}

This will usually read something like: ``Experimental procedures and
characterization data for all new compounds. The class will
automatically add a sentence pointing to the information on-line:

\end{suppinfo}
## References