---
title: "PLOS template"
format:
  plos-pdf:
    number-sections: false
    journal:
      # This is an identifier for the target journal: 
      # from https://plos.org/resources/writing-center/ following submission guidelines link, the identifier is the part of the URL after https://journals.plos.org/<id>/s/submission-guidelines
      id: plosone
    include-in-header:
      text: |
        % Remove comment for double spacing
        % \usepackage{setspace} 
        % \doublespacing
author:
  - name: Name1 Surname
    equal-contributor: true
    affiliations:
      - ref: aff1
      - ref: aff2
  - name: Name2 Surname
    equal-contributor: true
    affiliations:
      - ref: aff2
  - name: Name3 Surname
    affiliations:
      - ref: aff2
      - ref: aff3
    notes: |
      "Current Address: Dept/Program/Center, Institution Name, City, State, Country"
  - name: Name4 Surname
    affiliations:
      - ref: aff2
  - name: Name5 Surname
    affiliations:
      - ref: aff2
    deceased: true
  - name: Name6 Surname
    affiliations:
      - ref: aff2
  - name: Name7 Surname
    affiliations:
      - ref: aff1
      - ref: aff2
      - ref: aff3
    corresponding: true
    email: correspondingauthor@institute.edu
  - name: with the Lorem Ipsum Consortium
    group: true
author-notes:
  equal-contributor: These authors contributed equally to this work.
  deceased: Deceased
  group: Membership list can be found in the Acknowledgments sections
affiliations:
  - id: aff1
    name: Affiliation Dept, Institution Name
    city: City
    state: State
    country: Country
  - id: aff2
    name: Affiliation Center, Institution Name
    city: City
    state: State
    country: Country
  - id: aff3
    name: Affiliation Program, Institution Name
    city: City
    state: State
    country: Country
abstract: |
  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur eget porta erat. Morbi consectetur est vel gravida pretium. Suspendisse ut dui eu ante cursus gravida non sed sem. Nullam sapien tellus, commodo id velit id, eleifend volutpat quam. Phasellus mauris velit, dapibus finibus elementum vel, pulvinar non tellus. Nunc pellentesque pretium diam, quis maximus dolor faucibus id. Nunc convallis sodales ante, ut ullamcorper est egestas vitae. Nam sit amet enim ultrices, ultrices elit pulvinar, volutpat risus.
author-summary: |
  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur eget porta erat. Morbi consectetur est vel gravida pretium. Suspendisse ut dui eu ante cursus gravida non sed sem. Nullam sapien tellus, commodo id velit id, eleifend volutpat quam. Phasellus mauris velit, dapibus finibus elementum vel, pulvinar non tellus. Nunc pellentesque pretium diam, quis maximus dolor faucibus id. Nunc convallis sodales ante, ut ullamcorper est egestas vitae. Nam sit amet enim ultrices, ultrices elit pulvinar, volutpat risus.
bibliography: bibliography.bib 
---

# General guidelines for this Quarto template

This template shows how to use PLOS template from <https://plos.org/resources/writing-center/>. Each journal has a submission guideline page; please refer to it. 

 - [PLOS Biology](https://journals.plos.org/plosbiology/s/submission-guidelines) 
 - [PLOS Climate](https://journals.plos.org/climate/s/submission-guidelines)
 - [PLOS Digital Health](https://journals.plos.org/digitalhealth/s/submission-guidelines)
 - [PLOS Computational Biology](https://journals.plos.org/ploscompbiol/s/submission-guidelines)
 - [PLOS Genetics](https://journals.plos.org/plosgenetics/s/submission-guidelines)
 - [PLOS Global Public Health](https://journals.plos.org/globalpublichealth/s/submission-guidelines)
 - [PLOS Medicine](https://journals.plos.org/plosmedicine/s/submission-guidelines)
 - [PLOS Neglected Tropical Diseases](https://journals.plos.org/plosntds/s/submission-guidelines)
 - [PLOS ONE](https://journals.plos.org/plosone/s/submission-guidelines)
 - [PLOS Pathogens](https://journals.plos.org/plospathogens/s/submission-guidelines)
 - [PLOS Sustainability and Transformation](https://journals.plos.org/sustainabilitytransformation/s/submission-guidelines)
 - [PLOS Water](https://journals.plos.org/water/s/submission-guidelines)

This template file contains some guidelines and recommandation initially given in `plos_latex_template.tex` that can be found in <https://github.com/quarto-journals/plos/blob/main/style-guide/plos_latex_template.tex>

## Metadata

### About journal id field

This is an identifier for the target journal. It can be derived from https://plos.org/resources/writing-center/ following submission guidelines link, the identifier is the part of the URL after `https://journals.plos.org/<id>/s/submission-guidelines`

| Journal                               | id                          |
|:--------------------------------------|:----------------------------|
|PLOS Biology                           |plosbiology                  |
|PLOS Climate                           |climate                      |
|PLOS Digital Health                    |digitalhealth                |
|PLOS Computational Biology             |ploscompbiol                 |
|PLOS Genetics                          |plosgenetics                 |
|PLOS Global Public Health              |globalpublichealth           |
|PLOS Medicine                          |plosmedicine                 |
|PLOS Neglected Tropical Diseases       |plosntds                     |
|PLOS ONE                               |plosone                      |
|PLOS Pathogens                         |plospathogens                |
|PLOS Sustainability and Transformation |sustainabilitytransformation |
|PLOS Water                             |water                        |

Example :

```yaml
format:
  plos-pdf:
    journal:
      id: water
```

## Once your paper is accepted for publication, 

Do not include track change in LaTeX file and leave only the final text of your manuscript. 
PLOS recommends the use of latexdiff to track changes during review, as this will help to maintain a clean tex file.
Visit <https://www.ctan.org/pkg/latexdiff?lang=en> for info or contact us at <latex@plos.org>.

_This should not be a problem using Quarto but still a recommandation from the journal_

There are no restrictions on package use within the LaTeX files except that no packages listed in the template may be deleted.  

Please do not include colors or graphics in the text. Color can be used to apply background shading to table cells only.

The manuscript LaTeX source should be contained within a single file (do not use` \input`, `\externaldocument`, or similar commands).

Please contact <latex@plos.org> with any questions submission guidelines. For anything Quarto related, please open an issue in <https://github.com/quarto-journals/plos>. If this is related to the LaTeX template, this could also be a good idea to contact PLOS directly.

## Figures and Tables

Please include tables/figure captions directly after the paragraph where they are first cited in the text.

### Figures

However, do not include graphics in your manuscript

- Figures should be uploaded separately from your manuscript file. 
- Figures generated using LaTeX should be extracted and removed from the PDF before submission. 
- Figures containing multiple panels/subfigures must be combined into one image file before submission.

**This means that, depending on how you create your figure, a manual post processing will be required.**

For figure citations, please use "Fig" instead of "Figure". This has been made the default in this Quarto format:

```yaml
crossref:
  fig-title: Fig 
```

Also, place figure captions after the first paragraph in which they are cited.

See PLOS figure guidelines at <https://journals.plos.org/plosone/s/figures> and in your specific journal guideline.

### Tables

Tables should be cell-based and may not contain:

- spacing/line breaks within cells to alter layout or alignment
- do not nest tabular environments (no tabular environments within tabular environments)
- no graphics or colored text (cell background color/shading OK)

See PLOS table guidelines at <http://journals.plos.org/plosone/s/tables> and in your specific journal guideline. 

For tables that exceed the width of the text column, use the adjustwidth environment as illustrated in the example table in text below. If you are in this case, you'll either need to manually post process the `.tex` file and recreate the PDF, or you need to include LaTeX tables directly. 

Also, place tables after the first paragraph in which they are cited.

## Equations, math symbols, subscripts, and superscripts

Below are a few tips to help format your equations and other special characters according to our specifications. For more tips to help reduce the possibility of formatting errors during conversion, please see our LaTeX guidelines at http://journals.plos.org/plosone/s/latex

*  For inline equations, please be sure to include all portions of an equation in the math environment. For example, `x$^2$` is incorrect; this should be formatted as $x^2$ (or $\mathrm{x}^2$ if the romanized font is desired).

* Do not include text that is not math in the math environment. For example, `CO2` should be written as `CO\textsubscript{2}` giving CO\textsubscript{2} instead of `CO$_2$`.
* Please add line breaks to long display equations when possible in order to fit size of the column. 
* For inline equations, please do not include punctuation (commas, etc) within the math environment unless this is part of the equation.
* When adding superscript or subscripts outside of brackets/braces, please group using `{}`.  For example, change `"[U(D,E,\gamma)]^2"` to `"{[U(D,E,\gamma)]}^2"`.  
* Do not use `\cal` for caligraphic font. Instead, use `\mathcal{}`

## Title and headings

Please use "sentence case" for title and headings (capitalize only the first word in a title (or heading), the first word in a subtitle (or subheading), and any proper nouns).

PLOS does not support heading levels beyond the 3rd, meaning no 4th level headings. Header 4 levels `####` is used for the  _Supporting information_ section

## Abstract and author summary

Abstract must be kept below 300 words. 

Author Summary must be kept between 150 and 200 words and first person must be used. 

For PLOS ONE, author summary won't be included as it is not valid for submission.

## Supplementary information syntax

Use this markdown syntax to create the supplementary information block with a custom block of class `.supp`
```markdown
::: {.supp}
## SI TYPE {#id}

First paragraph is a title sentence that will be bold. (required)

Optionnaly, add descriptive text after the title of the
item. No third paragraph is allowed
:::
```

They need to be referenced in text using `nameref` by using this syntax `[id](.nameref)` where `ìd` will be the id used on the header.

## References

Within Quarto, `natbib` will be used with `plos2015.bst`, which expect numeric style citation. Use brackets for references, e.g `[@ref]`. 

## Quarto features limitation

Some features are not working with this format in PDF:

* Callouts
* Code highlighting customization (border left, background color)

----

> **Following content of this document is from the LaTeX template content to demo journal style.**

----

# Introduction

Lorem ipsum dolor sit [@bib1] amet, consectetur adipiscing elit.
Curabitur eget porta erat. Morbi consectetur est vel gravida pretium.
Suspendisse ut dui eu ante cursus gravida non sed sem. Nullam
@eq-schemeP sapien tellus, commodo id velit id, eleifend
volutpat quam. Phasellus mauris velit, dapibus finibus elementum vel,
pulvinar non tellus. Nunc pellentesque pretium diam, quis maximus dolor
faucibus id. [@bib2] Nunc convallis sodales ante, ut ullamcorper est
egestas vitae. Nam sit amet enim ultrices, ultrices elit pulvinar,
volutpat risus.

$$
\begin{aligned}
\mathrm{P_Y} = \underbrace{H(Y_n) - H(Y_n|\mathbf{V}^{Y}_{n})}_{S_Y} + \underbrace{H(Y_n|\mathbf{V}^{Y}_{n})- H(Y_n|\mathbf{V}^{X,Y}_{n})}_{T_{X\rightarrow Y}}
\end{aligned}
$$ {#eq-schemeP}

# Materials and methods 

## Etiam eget sapien nibh

Nulla mi mi, `Fig~\ref{fig1}`{=latex} venenatis sed ipsum varius, volutpat euismod diam.
Proin rutrum vel massa non gravida. Quisque tempor sem et dignissim
rutrum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi
at justo vitae nulla elementum commodo eu id massa. In vitae diam ac
augue semper tincidunt eu ut eros. Fusce fringilla erat porttitor lectus
cursus, vel sagittis arcu lobortis. Aliquam in enim semper, aliquam
massa id, cursus neque. Praesent faucibus semper libero.

```{=tex}
% Place figure captions after the first paragraph in which they are cited.
\begin{figure}[!h]
\caption{{\bf Bold the figure title.}
Figure caption text here, please use this space for the figure panel descriptions instead of using subfigure commands. A: Lorem ipsum dolor sit amet. B: Consectetur adipiscing elit.}
\label{fig1}
\end{figure}
```

# Results

Results and Discussion can be combined.

Nulla mi mi, venenatis sed ipsum varius, `Table~\ref{table1}`{=latex} volutpat euismod diam. 
Proin rutrum vel massa non gravida. Quisque
tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur
adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id
massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce
fringilla erat porttitor lectus cursus, [s1-video]{.nameref} vel sagittis arcu lobortis.
Aliquam in enim semper, aliquam massa id, cursus neque. Praesent
faucibus semper libero.

```{=tex}
% Place tables after the first paragraph in which they are cited.
\begin{table}[!ht]
\begin{adjustwidth}{-2.25in}{0in} % Comment out/remove adjustwidth environment if table fits in text column.
\centering
\caption{
{\bf Table caption Nulla mi mi, venenatis sed ipsum varius, volutpat euismod diam.}}
\begin{tabular}{|l+l|l|l|l|l|l|l|}
\hline
\multicolumn{4}{|l|}{\bf Heading1} & \multicolumn{4}{|l|}{\bf Heading2}\\ \thickhline
$cell1 row1$ & cell2 row 1 & cell3 row 1 & cell4 row 1 & cell5 row 1 & cell6 row 1 & cell7 row 1 & cell8 row 1\\ \hline
$cell1 row2$ & cell2 row 2 & cell3 row 2 & cell4 row 2 & cell5 row 2 & cell6 row 2 & cell7 row 2 & cell8 row 2\\ \hline
$cell1 row3$ & cell2 row 3 & cell3 row 3 & cell4 row 3 & cell5 row 3 & cell6 row 3 & cell7 row 3 & cell8 row 3\\ \hline
\end{tabular}
\begin{flushleft} Table notes Phasellus venenatis, tortor nec vestibulum mattis, massa tortor interdum felis, nec pellentesque metus tortor nec nisl. Ut ornare mauris tellus, vel dapibus arcu suscipit sed.
\end{flushleft}
\label{table1}
\end{adjustwidth}
\end{table}
````

## **LOREM** and **IPSUM** nunc blandit a tortor

### 3rd level heading

Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget
sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod
ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
Quisque augue sem, tincidunt sit amet feugiat eget, ullamcorper sed
velit. Sed non aliquet felis. Lorem ipsum dolor sit amet, consectetur
adipiscing elit. Mauris commodo justo ac dui pretium imperdiet. Sed
suscipit iaculis mi at feugiat.

1.  react

2.  diffuse free particles

3.  increment time by dt and go to 1

## Sed ac quam id nisi malesuada congue

Nulla mi mi, venenatis sed ipsum varius, volutpat euismod diam. Proin
rutrum vel massa non gravida. Quisque tempor sem et dignissim rutrum.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi at justo
vitae nulla elementum commodo eu id massa. In vitae diam ac augue semper
tincidunt eu ut eros. Fusce fringilla erat porttitor lectus cursus, vel
sagittis arcu lobortis. Aliquam in enim semper, aliquam massa id, cursus
neque. Praesent faucibus semper libero.

-   First bulleted item.

-   Second bulleted item.

-   Third bulleted item.

# Discussion

Nulla mi mi, venenatis sed ipsum varius,see `Table~\ref{table1}`{=latex}
volutpat euismod diam. Proin rutrum vel massa non gravida. Quisque
tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur
adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id
massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce
fringilla erat porttitor lectus cursus, vel sagittis arcu lobortis.
Aliquam in enim semper, aliquam massa id, cursus neque. Praesent
faucibus semper libero [@bib3].

# Conclusion

CO~2~ Maecenas convallis mauris sit amet sem ultrices gravida. Etiam
eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod
ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
Quisque augue sem, tincidunt sit amet feugiat eget, ullamcorper sed
velit.

Sed non aliquet felis. Lorem ipsum dolor sit amet, consectetur
adipiscing elit. Mauris commodo justo ac dui pretium imperdiet. Sed
suscipit iaculis mi at feugiat. Ut neque ipsum, luctus id lacus ut,
laoreet scelerisque urna. Phasellus venenatis, tortor nec vestibulum
mattis, massa tortor interdum felis, nec pellentesque metus tortor nec
nisl. Ut ornare mauris tellus, vel dapibus arcu suscipit sed. Nam
condimentum sem eget mollis euismod. Nullam dui urna, gravida venenatis
dui et, tincidunt sodales ex. Nunc est dui, sodales sed mauris nec,
auctor sagittis leo. Aliquam tincidunt, ex in facilisis elementum,
libero lectus luctus est, non vulputate nisl augue at dolor. For more
information, see [s1-appendix]{.nameref}.

# Supporting information 

::: {.supp}
## S1 Fig. {#s1-fig}

Bold the title sentence.

Add descriptive text after the title of the item (optional).
:::

::: {.supp}
## S2 Fig. {#s2-fig}

Lorem ipsum.

Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
:::


::: {.supp}
## S1 File. {#s1-file}

Lorem ipsum.

:::

::: {.supp}

## S1 Video. {#s1-video}

Lorem ipsum.

Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
:::

::: {.supp}
## S1 Appendix. {#s1-appendix}

Lorem ipsum.

Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
:::

::: {.supp}
## S1 Table. {#s1-table}

Lorem ipsum.

Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.
:::

# Acknowledgments

Cras egestas velit mauris, eu mollis turpis pellentesque sit amet.
Interdum et malesuada fames ac ante ipsum primis in faucibus. Nam id
pretium nisi. Sed ac quam id nisi malesuada congue. Sed interdum aliquet
augue, at pellentesque quam rhoncus vitae.
