--- 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: daniel.nuest@uni-muenster.de corresponding: true - given_name: Josiah surname: Carberry affiliation: 2 email: j.carberry@orcid.org - 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, `daniel.nuest@uni-muenster.de`, 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]`.