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Continuité module 2 et création fichier template RMarkdown

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---
title: "Article Title"
runtitle: "Short Title"
documentclass: frontiersSCNS # or frontiersHLTH, or frontiersFPHY
author:
- name: First Author
affiliation: '1'
etal: LASTNAME # First author's last name.
- name: Co-Author
affiliation: '2'
- name: Co-Author
affiliation: '1,3'
email: email@uni.edu # Indicates corresponding Author
institution: Laboratory X, Institute X, Department X, Organization X
street: Street X
city: City X
state: State XX # only USA, Australia, Canada
zip: Zip Code X
country: Country X
affiliation:
- id: '1'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
- id: '2'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
- id: '3'
department: Department X
institution: Institution X
city: City X
state: State XX # only USA, Australia, Canada
country: Country X
output: rticles::frontiers_article
csl: frontiers.csl
bibliography: test.bib
---
\begin{abstract}
Abstract length and content varies depending on article type. Refer to
\url{http://www.frontiersin.org/about/AuthorGuidelines} for abstract requirement
and length according to article type.
%All article types: you may provide up to 8 keywords; at least 5 are mandatory.
\tiny
\keyFont{ \section{Keywords:} Text Text Text Text Text Text Text Text }
\end{abstract}
# Introduction {-}
Cite fancy references [@Neuro2013]. As demonstrated in @Gene2012, citations can
also be automatically reference. Multiple references are separated by semicolons
[@Neuro2013; @Neurobot2013].
# Results {-}
<!-- Comments should be HTML-style comments -->
## Subsection 1 {-}
You can use `R` chunks directly to plot graphs.
```{r graph, echo = TRUE, message=FALSE, fig.show = "hide"}
x <- 0:100
set.seed(999)
y <- 2 * (x + rnorm(length(x), sd = 3) + 3)
plot(x, y)
```
## Subsection 2 {-}
Frontiers requires figures to be submitted individually, in the same order as
they are referred to in the manuscript. Figures will then be automatically
embedded at the bottom of the submitted manuscript. Kindly ensure that each
table and figure is mentioned in the text and in numerical order. Permission
must be obtained for use of copyrighted material from other sources (including
the web). Please note that it is compulsory to follow figure instructions.
Figures which are not according to the guidelines will cause substantial delay
during the production process.
# Discussion
# Disclosure/Conflict-of-Interest Statement {-}
<!--
Frontiers follows the recommendations by the International Committee of Medical
Journal Editors (http://www.icmje.org/ethical_4conflicts.html) which require
that all financial, commercial or other relationships that might be perceived by
the academic community as representing a potential conflict of interest must be
disclosed. If no such relationship exists, authors will be asked to declare that
the research was conducted in the absence of any commercial or financial
relationships that could be construed as a potential conflict of interest. When
disclosing the potential conflict of interest, the authors need to address the
following points:
- Did you or your institution at any time receive payment or services from a
third party for any aspect of the submitted work?
- Please declare financial relationships with entities that could be perceived
to influence, or that give the appearance of potentially influencing, what
you wrote in the submitted work.
- Please declare patents and copyrights, whether pending, issued, licensed
and/or receiving royalties relevant to the work.
- Please state other relationships or activities that readers could perceive to
have influenced, or that give the appearance of potentially influencing, what
you wrote in the submitted work.
-->
The authors declare that the research was conducted in the absence of any
commercial or financial relationships that could be construed as a potential
conflict of interest.
# Author Contributions {-}
<!--
When determining authorship the following criteria should be observed:
- Substantial contributions to the conception or design of the work; or the
acquisition, analysis, or interpretation of data for the work; AND
- Drafting the work or revising it critically for important intellectual
content; AND
- Final approval of the version to be published ; AND
- Agreement to be accountable for all aspects of the work in ensuring that
questions related to the accuracy or integrity of any part of the work are
appropriately investigated and resolved.
Contributors who meet fewer than all 4 of the above criteria for authorship
should not be listed as authors, but they should be acknowledged.
(http://www.icmje.org/roles_a.html)
-->
The statement about the authors and contributors can be up to several sentences
long, describing the tasks of individual authors referred to by their initials
and should be included at the end of the manuscript before the References
section.
# Acknowledgments {-}
Funding:
# Supplemental Data
Supplementary Material should be uploaded separately on submission, if there are
Supplementary Figures, please include the caption in the same file as the
figure. LaTeX Supplementary Material templates can be found in the Frontiers
LaTeX folder
# References
A reference list should be automatically created here. However it won't. Pandoc
will place the list of references at the end of the document instead. There are
no convenient solution for now to force Pandoc to do otherwise. The easiest way
to get around this problem is to edit the LaTeX file created by Pandoc before
compiling it again using the traditional LaTeX commands.
# Figures {-}
```{r, Figure-1, ref.label = "graph", results = "hide", echo = FALSE, message = FALSE, fig.height=4, fig.width=4, fig.align='center', fig.cap='Figure caption', out.width = "85mm", out.height = "85mm"}
# You can also refer to code chunks from above to place figures at the bottom.
```
Test templates articles frontiers/frontiers.csl 0 → 100644
View file @ 39986221
<?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>Frontiers journals</title>
<id>http://www.zotero.org/styles/frontiers</id>
<link href="http://www.zotero.org/styles/frontiers" rel="self"/>
<link href="http://www.frontiersin.org/about/AuthorGuidelines" rel="documentation"/>
<author>
<name>Sebastian Karcher</name>
</author>
<contributor>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</contributor>
<category citation-format="author-date"/>
<category field="generic-base"/>
<summary>Style for the Open Access Frontiers in ... Journals</summary>
<updated>2012-09-27T22:06:38+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>
<macro name="editor">
<names variable="editor" delimiter=", ">
<label form="short" prefix=", "/>
<name and="text" initialize-with=". " delimiter=", " prefix=" "/>
</names>
</macro>
<macro name="author">
<names variable="author">
<name name-as-sort-order="all" and="text" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
<label form="short" prefix=" "/>
<substitute>
<names variable="editor"/>
<text variable="title"/>
</substitute>
</names>
</macro>
<macro name="author-short">
<names variable="author">
<name form="short" and="text" delimiter=", " initialize-with=". "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
<text variable="title"/>
</substitute>
</names>
</macro>
<macro name="access">
<choose>
<if variable="DOI">
<text variable="DOI" prefix="doi:"/>
</if>
<else-if variable="URL">
<text value="Available at:" suffix=" "/>
<text variable="URL"/>
<group prefix=" [" suffix="]">
<text term="accessed" text-case="capitalize-first" suffix=" "/>
<date variable="accessed">
<date-part name="month" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</group>
</else-if>
</choose>
</macro>
<macro name="title">
<choose>
<if type="book">
<text variable="title" font-style="italic" suffix="."/>
</if>
<else-if type="chapter">
<text variable="title" quotes="true" suffix=","/>
</else-if>
<else>
<text variable="title" suffix="."/>
</else>
</choose>
</macro>
<macro name="publisher">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</macro>
<macro name="year-date">
<date variable="issued">
<date-part name="year"/>
</date>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year">
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<text macro="author-short"/>
<text macro="year-date"/>
<text variable="locator"/>
</group>
</layout>
</citation>
<bibliography hanging-indent="true" et-al-min="11" et-al-use-first="10">
<sort>
<key macro="author"/>
<key variable="title"/>
</sort>
<layout suffix=".">
<text macro="author"/>
<date variable="issued" prefix=" (" suffix=").">
<date-part name="year"/>
</date>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=" " prefix=" ">
<text macro="title"/>
<text macro="edition"/>
<text macro="editor"/>
<text macro="publisher"/>
</group>
</if>
<else-if type="chapter paper-conference" match="any">
<group delimiter=" " prefix=" ">
<text macro="title"/>
<text term="in"/>
<text variable="container-title" font-style="italic"/>
<text variable="collection-title" suffix="."/>
</group>
<text macro="editor"/>
<group suffix=".">
<text macro="publisher" prefix=" (" suffix=")"/>
<group prefix=", ">
<text variable="page"/>
</group>
</group>
</else-if>
<else>
<text macro="title" prefix=" " suffix="."/>
<group delimiter=", " prefix=" " suffix=".">
<group delimiter=" ">
<text variable="container-title" form="short" font-style="italic"/>
<text variable="volume"/>
</group>
<text variable="page"/>
</group>
</else>
</choose>
<text prefix=" " macro="access"/>
</layout>
</bibliography>
</style>
Test templates articles frontiers/frontiersFPHY.cls 0 → 100644
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Test templates articles frontiers/frontiersHLTH.cls 0 → 100644
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Test templates articles frontiers/frontiersSCNS.cls 0 → 100644
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Test templates articles frontiers/test.bib 0 → 100644
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@Article{ Neuro2013,
author = "Author1 LastName1 and Author2 LastName2 and Author3 LastName2",
title = "Article Title",
volume = "30",
number = "30",
pages = "10127--10134",
year = "2013",
doi = "10.3389/fnins.2013.12345",
URL = "http://www.frontiersin.org/Neuroscience/10.3389/fnins.2013.12345/abstract",
journal = "Frontiers in Neuroscience"
}
@Article{ Gene2012,
author = "Name OtherAuthor and Name S. Coauthor",
title = "Article Title",
volume = "30",
number = "49",
pages = "16417--16418",
year = "2012",
doi = "10.3389/fgene.2012.54321",
URL = "http://www.frontiersin.org/Genetics/10.3389/fgene.2012.54321/abstract",
journal = "Frontiers in Genetics"
}
@Article{ Neurobot2013,
author = "Name4 Author4 and Name5 Author5",
title = "Title of the Article",
volume = "7",
number = "25",
year = "2013",
doi = "10.3389/fnbot.2013.56789",
URL = "http://www.frontiersin.org/Neurorobotics/10.3389/fnbot.2013.56789/abstract",
journal = "Frontiers in Neurorobotics"
}
journal/Journal-de-bord_MOOC-RR_Marc-Oudart_2.Rmd
View file @ 39986221
......@@ -162,6 +162,36 @@ Egalement pour un cahier de laboratoire avec classement par thèmes et étiquett
Enfin, pour un article reproductible.
- RStudio : possibilité de faire article et facile d'accès. Navigation limitée.
## Rendre compte de son activité
1. Le reporting
Compte rendu d'activité pour décrire à peu près tout ce qu'on fait pour que le tuteur puisse suivre et aider, pour faire un rapport ou article, pour que les travaux continus, pour la science ouverte.
2. Logistique
Avoir un dépot en ligne (Github/Gitlab).
Rendu public.
Faire les reporting tant que les infos sont fraiches.
3. Organisation du CRA
Structure :
- Résultats : ref biblio mais PAS ToDo list.
- Développement :
- Journal : Reporting.
- Travail effectué
- Points bloquants et questions. C'est cette partie auquelle le référant peut apporter sa contribution.
- Travaux prévus
- Conclusion : A la fin du stage. Quoi faire ensuite ? Comment j'ai tenu ce journal ? Comment continuer mon travail ?
Comme un cahier de labo, il ne faut pas éditer ce qu'on a déjà écrit ou alors il faut le préciser avec une petite marque __edit__.
### Templates RMarkdown pour articles scientifiques
```{r}
install.packages("rticles")
```
Ensuite _File_ --> _New file_ --> _RMarkdown_ --> _From template_
<!-- ## R Markdown
......
Markdown is supported
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