Here are some things I have learned 
and some things I have loved 
about it…
1/10
(Examples from a paper I co-authored sciencedirect.com/science/articl…)![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="460" height="368"><rect fill-opacity="0"/></svg>)
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Dividing the work
Each member can work on a part of the project on a separate Rmd file 
All files can be incorporated in the “main” Rmd by using the option “child” of a R chunk 
A comment in the R chunk can be used to remind the team who is assigned to what 
2/10![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="452" height="410"><rect fill-opacity="0"/></svg>)
Numeric results: no need to copy/paste!
Numeric summaries of analysis (e.g. sample size) can be computed and printed directly in the text using "inline code" 
Fewer accidents due to copy/paste 
No having to find&change numbers if data or analysis changes 
3/10![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="900" height="299"><rect fill-opacity="0"/></svg>)
Plots: no need to save and upload them anywhere!
Can generate plot from data directly in final document 
No having to re-make, re-save and re-upload all plots if data or analysis changes. The plot is automatically updated 
4/10![diagram of screenshots showing how the code of a plot in the child document "03-results.Rmd" is shown as a histogram in the pdf of the final article](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="307"><rect fill-opacity="0"/></svg>)
Can make pretty complicated tables too!
And this implies (you might have already guessed 
)
If data or analysis change, table will update automatically 
5/10![diagram of screenshot showing how the code of a table in an R chunk using "knitr::kable" results in a publication-quality table in the rendered pdf](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="359"><rect fill-opacity="0"/></svg>)
Correct templates 
for many journals 
can be set using the package rticles
github.com/rstudio/rticles
6/10![Screenshot of R Studio editor pane with a R Markdown "main.Rmd" is open and shows a YAML section where a yellow arrow points to the field "output: rticles::elsevier" surrounded by a yellow rectangle](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="593"><rect fill-opacity="0"/></svg>)
Adding packages and including bibliography is possible, and easy!
7/10![Screenshot of Editor pane in R Studio showing that the YAML of a file "main.Rmd" specifies the fields "header-includes: -\usepackage{amsmath} -\usepackage{booktabs}" and "bibliography: references.bib"](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="642" height="680"><rect fill-opacity="0"/></svg>)
Can save auxiliary files (e.g. .tex file) if you need to!
8/10![Screenshot of R Studio editor pane with a R Markdown "main.Rmd" is open and shows a YAML section where a yellow arrow points to the field "keep_tex: true" under "output: rticles::elsevier" surrounded by a yellow rectangle](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="477"><rect fill-opacity="0"/></svg>)
Supports lots of formats
All sounds cool BUT adopting a tool takes time and efforts. Why is Rmd worth it?
Can write papers (like in this ) but also prepare professional reports 
make presentations create websites...
9/10![collage of 4 R markdown yaml: for academic article (with "output: rticles::isba_article"), for a report (with "output:html_document"), for a presentation (with "output: xaringan::moon_reader") and for a website (with "site: distill::distill_website")](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="301"><rect fill-opacity="0"/></svg>)
The main project in the examples
Why do I 
it? Because it shows that..
Bayesian hierarchical models can be used if we gently explain the model and how to interpret results 
even if they suggest there is NO evidence for an effect 
sciencedirect.com/science/articl![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="679" height="507"><rect fill-opacity="0"/></svg>)
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