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

---
title: Template for preparing your manuscript submission to Copernicus journals using RMarkdown
journal: "`r rticles::copernicus_journal_abbreviations(journal_name = 'communication')`"
author:
  - given_name: Daniel
    surname: Nüst
    affiliation: 1
    email: [email protected]
    corresponding: true
  - given_name: Josiah
    surname: Carberry
    affiliation: 2
    email: [email protected]
  - given_name: Markus
    surname: Konkol
    affiliation: 1
affiliation:
  - code: 1
    address: Institute for Geoinformatics, University of Münster, 48149 Münster, Germany
  - code: 2
    address: Psychoceramics, Wesleyan University, Middletown, CT, United State
abstract: |
  The abstract goes here.
  It can also be on _multiple lines_.
bibliography: sample.bib
running:
  title: RMarkdown Template for Copernicus
  author: Nüst et al.
# This section is mandatory even if you declare that no competing interests are present.
competinginterests: |
  The authors declare no competing interests.
# OPTIONAL:
algorithms: true
# See https://publications.copernicus.org/for_authors/licence_and_copyright.html, normally used for transferring the copyright, if needed.
copyrightstatement: |
  The author's copyright for this publication is transferred to institution/company.
### The following commands are for the statements about the availability of data sets and/or software code corresponding to the manuscript.
### It is strongly recommended to make use of these sections in case data sets and/or software code have been part of your research the article is based on.
availability:
  #code: |
  #  use this to add a statement when having only software code available
  #data: |
  #  use this to add a statement when having only data sets available
  codedata: |
    use this to add a statement when having data sets and software code available
authorcontribution: |
  Daniel wrote the package. Josiah thought about poterry. Markus filled in for a second author.
disclaimer: |
  We like Copernicus.
acknowledgements: |
  Thanks to the rticles contributors!
appendix: |
  \section{Figures and tables in appendices}
  Regarding figures and tables in appendices, the following two options are possible depending on your general handling of figures and tables in the manuscript environment:
  \subsection{Option 1}
  If you sorted all figures and tables into the sections of the text, please also sort the appendix figures and appendix tables into the respective appendix sections.
  They will be correctly named automatically.
  \subsection{Option 2}
  If you put all figures after the reference list, please insert appendix tables and figures after the normal tables and figures.
  
  To rename them correctly to A1, A2, etc., please add the following commands in front of them:
  `\appendixfigures` needs to be added in front of appendix figures
  `\appendixtables` needs to be added in front of appendix tables
  
  Please add `\clearpage` between each table and/or figure. Further guidelines on figures and tables can be found below.
output:
  rticles::copernicus_article:
    base_format: rmarkdown::pdf_document
---

\introduction

Introduction text goes here.
You can change the name of the section if neccessary using `\introduction[modified heading]`.

The following settings can or must be configured in the header of this file and are bespoke for Copernicus manuscripts:

- The `journal` you are submitting to using the official abbreviation. You can use the function `rticles::copernicus_journal_abbreviations(name = '...')` to search the existing journals.

- Specific sections of the manuscript:

  - `running` with `title` and `author`

  - `competinginterests`

  - `copyrightstatement` (optional)

  - `availability` (strongly recommended if any used), one of `code`, `data`, or `codedata`

  - `authorcontribution`

  - `disclaimer`

  - `acknowledgements`

See the defaults and examples from the skeleton and the official Copernicus documentation for details.

**Important**: Always double-check with the official manuscript preparation guidelines at [https://publications.copernicus.org/for_authors/manuscript_preparation.html](https://publications.copernicus.org/for_authors/manuscript_preparation.html), especially the sections "Technical instructions for LaTeX" and "Manuscript composition".
Please contact Daniel Nüst, `[email protected]`, with any problems.

# Content section one

## Subsection Heading Here

Subsection text here. 

### Subsubsection Heading Here

Subsubsection text here. 

# Content section with citations

See the [R Markdown docs for bibliographies and citations](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html).

Copernicus supports biblatex and a sample bibliography is in file `sample.bib`.
Read [@Feynman1963118], and [see @Dirac1953888].

# Content section with R code chunks

```{r, echo = FALSE}
sum <- 1 + 41
```

You should always use `echo = FALSE` on R Markdown code blocks as they add formatting and styling not desired by Copernicus.
The hidden workflow results in `r sum`.

You can add verbatim code snippets without extra styles by using ` ``` ` without additional instructions.

```
sum <- 1 + 41
```

# Content section with list

If you want to insert a list, you must

- leave

- empty lines

- between each list item

because the `\tightlist` format used by R Markdown is not supported in the Copernicus template. Example:

```
- leave

- empty lines

- between each list item
```

# Examples from the official template

## FIGURES

When figures and tables are placed at the end of the MS (article in one-column style), please add \clearpage between bibliography and first table and/or figure as well as between each table and/or figure.

### ONE-COLUMN FIGURES

Include a 12cm width figure of Nikolaus Copernicus from [Wikipedia](https://en.wikipedia.org/wiki/File:Nikolaus_Kopernikus.jpg) with caption using R Markdown.

```{r, out.width = "8.3cm", echo = FALSE, fig.cap = "one column figure"}
knitr::include_graphics("Nikolaus_Kopernikus.jpg")
```

### TWO-COLUMN FIGURES

You can also include a larger figure.

```{r, out.width = "12cm", echo = FALSE, fig.cap = "two column figure"}
knitr::include_graphics("Nikolaus_Kopernikus.jpg")
```

## TABLES

You can ad \LaTeX table in an R Markdown document to meet the template requirements.

### ONE-COLUMN TABLE

\begin{table}[t]
\caption{TEXT}
\begin{tabular}{l c r}
\tophline

a & b & c \\
\middlehline
1 & 2 & 3 \\

\bottomhline
\end{tabular}
\belowtable{Table Footnotes}
\end{table}

### TWO-COLUMN TABLE

\begin{table*}[t]
\caption{TEXT}
\begin{tabular}{l c r}
\tophline

a & b & c \\
\middlehline
1 & 2 & 3 \\

\bottomhline
\end{tabular}
\belowtable{Table footnotes}
\end{table*}

## MATHEMATICAL EXPRESSIONS

All papers typeset by Copernicus Publications follow the math typesetting regulations given by the IUPAC Green Book (IUPAC: Quantities, Units and Symbols in Physical Chemistry, 2nd Edn., Blackwell Science, available at: http://old.iupac.org/publications/books/gbook/green_book_2ed.pdf, 1993).

Physical quantities/variables are typeset in italic font (t for time, T for Temperature)

Indices which are not defined are typeset in italic font (x, y, z, a, b, c)

Items/objects which are defined are typeset in roman font (Car A, Car B)

Descriptions/specifications which are defined by itself are typeset in roman font (abs, rel, ref, tot, net, ice)

Abbreviations from 2 letters are typeset in roman font (RH, LAI)

Vectors are identified in bold italic font using \vec{x}

Matrices are identified in bold roman font

Multiplication signs are typeset using the LaTeX commands `\times` (for vector products, grids, and exponential notations) or `\cdot`

The character * should not be applied as mutliplication sign

## EQUATIONS

### Single-row equation

Unnumbered equations (i.e. using `$$` and getting inline preview in RStudio) are not supported by Copernicus.

\begin{equation}
1 \times 1 \cdot 1 = 42
\end{equation}

\begin{equation}
A = \pi r^2
\end{equation}

\begin{equation}
x=\frac{2b\pm\sqrt{b^{2}-4ac}}{2c}.  
\end{equation}

### Multiline equation

\begin{align}
& 3 + 5 = 8\\
& 3 + 5 = 8\\
& 3 + 5 = 8
\end{align}

## MATRICES

$$
\begin{matrix}
x & y & z\\
x & y & z\\
x & y & z\\
\end{matrix}
$$

## ALGORITHM

If you want to use algorithms, you can either enable the required packages in the header (the default, see `algorithms: true`), or make sure yourself that the \LaTeX packages `algorithms` and `algorithmicx` are installed so that `algorithm.sty` respectively `algorithmic.sty` can be loaded by the Copernicus template.
Copernicus staff will remove all undesirable packages from your LaTeX source code, so please stick to using the header option, which only adds the two acceptable packages.

\begin{algorithm}
\caption{Algorithm Caption}
\label{a1}
\begin{algorithmic}
\STATE $i\gets 10$
\IF {$i\geq 5$} 
        \STATE $i\gets i-1$
\ELSE
        \IF {$i\leq 3$}
                \STATE $i\gets i+2$
        \ENDIF
\ENDIF
\end{algorithmic}
\end{algorithm}

## CHEMICAL FORMULAS AND REACTIONS

For formulas embedded in the text, please use `\chem{}`, e.g. \chem{A \rightarrow B}.

The reaction environment creates labels including the letter R, i.e. (R1), (R2), etc.

- `\rightarrow` should be used for normal (one-way) chemical reactions

- `\rightleftharpoons` should be used for equilibria

- `\leftrightarrow` should be used for resonance structures

\begin{reaction}
A \rightarrow B \\
\end{reaction}
\begin{reaction}
Coper \rightleftharpoons nicus \\
\end{reaction}
\begin{reaction}
Publi \leftrightarrow cations
\end{reaction}

## PHYSICAL UNITS

Please use `\unit{}` (allows to save the math/`$` environment) and apply the exponential notation, for example \( 3.14\,\unit{km\,h^{-1}} \) (using LaTeX mode: `\( 3.14\,\unit{...} \)`) or \unit{0.872\,m\,s^{-1}} (using only `\unit{0.872\,m\,s^{-1}}`).

\conclusions

The conclusion goes here.
You can modify the section name with  `\conclusions[modified heading if necessary]`.