intRo: Data visualisation with R

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# intRo: Data visualisation with R
## 05 — Research Data Management
### Stefano Coretta

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# RStudio

.center[![:scale 85%](img/rstudio.png)]

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# RStudio options

.center[![:scale 60%](img/general-options.png)]

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# RStudio projects

RStudio **projects** are self-contained environments in which you keep code and data.

.center[![:scale 70%](img/new-project.png)]

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# RStudio projects

.pull-left[
.f2[Advantages]

- You can open and work on **multiple projects** at a time.

- The files of each individual projects are easily accessible by using **relative paths**, so goodby to `setwd()` (for example `./data/results.csv` if your project has a file `results.csv` in the `data/` folder).

- You can **isolate** package **dependencies** with `renv`.

- It simplifies the **distribution** of your research (for example, as an R package).
]

.pull-right[
.f2[Disadvantages]

- **None**!
]

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# Save code in scripts

- R scripts are files with the extension `.R`.

- Be sure to write standalone code (= code that runs from start to finish without errors).

- Comment your code, for your future self and for others.

- Even better... use Rmarkdown files!

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# R Markdown

**Dynamic report** writing in R with R Markdown.

* <http://rmarkdown.rstudio.com>

* Text and code in a single document (`.Rmd`).

* Several output formats (`.html`, `.pdf`, `.docx`, ...).

* R Markdown templates for journal submissions: <https://github.com/rstudio/rticles>.

* You can also write books, presentations, websites and blogs.

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# Organising folders and files

From the [Open Science Framework](http://help.osf.io/m/bestpractices/l/611391-organizing-files).

* Separate data from code/text.

* Separate raw data from derived data.

* Treat raw data as read-only.

* Use a versioning system (like `git` with GitHub).

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# Summary

* Use **RStudio**.

* **Don't save `.Rdata`** and do not load it at start up.

* Separate **code** from **data** (*raw* and *derived*).

* Write **dynamic reports** with R Markdown (and avoid copy-paste).

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background-image: url(../img/nick-fewings-2qXNT7LMfpY-unsplash.jpg)
background-size: cover

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Photo by <a href="https://unsplash.com/@jannerboy62?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Nick Fewings</a> on <a href="https://unsplash.com/s/photos/mouse?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Unsplash</a>

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# Extra: Research compendia with R packages

* <https://github.com/ropensci/rrrpkg>

* <https://www.r-bloggers.com/how-to-develop-good-r-packages-for-open-science/>

* <http://r-pkgs.had.co.nz>