This github project hosts the sources of the RECON learn platform, live at: https://reconlearn.netlify.com/.

This RECON learn website uses blogdown, which generates static content for a website through the compilation of a series of Rmarkdown (.Rmd) documents.

You will need to install blogdown and its dependencies (especially Hugo):

install.packages("blogdown") # install blogdown
blogdown::install_hugo() # install hugo

See detailed installation guidelines for more information.

You will also need to git clone this project, which using git command lines would look like:

git clone https://github.com/reconhub/learn
cd learn

Once this is done, start R and type:

blogdown::serve_site()

This will open up the website at 127.0.0.1:4321. This website is updated in real time based on the content of learn/.

The general workflow would include the following steps:

1. Fork the project from the github RECON learn project:

This will create a copy of the project in your own github account. You will need to clone this archive, and make the modifications there. You git clone would look like:

git clone https://github.com/johnsnow/learn

If your github user name is johnsnow.

2. Add new content, typically in the form of a new .Rmd file and associated media (most often images). Regular posts such as practicals, tutorials, and case studies are stored in content/post/. Other content which is not rendered as typical html reports such as lecture slides can be stored in static.

3. Test new content and revise until satisfying by visualising the local website using blogdown::serve_site(), where the current working directory is set to the project folder (learn/ by default).

4. git commit and git push all changes; don't forget to add new images as well (run git status to see which files haven't been added).

5. Make a pull request against the main project (master branch), from the github RECON learn project:

Make sure you use reconhub/learn, branch master as base fork:

Practicals, tuorials, case studies are contributed as Rmarkdown (.Rmd) documents. They are stored in content/post. The best way to create a new document is copy-paste an existing one and rename it. Naming conventions are as follows:

• start with practical for practicals, study for case studies
• use lower case, no special characters
• be hypen-separated ("-")

For instance, for a practical using a SEIR model for influenza data:

• practical-seir-influenza is good
• SEIR-flu is bad as lacking 'practical' (it could be a lecture), and has capitalised letters
• practical-new is bad, as it is non-informative

The YAML header is the beginning of the Rmd document, within the ---. For instance:

---
title: Phylogenetic tree reconstruction
author: Thibaut Jombart
categories: ["practicals"]
tags: ["genetics"]
date: 2017-11-01
image: img/highres/trees.jpg
showonlyimage: true
bibliography: practical-phylogenetics.bib
---

Fields are mostly self-explanatory, and can be adapted to your needs. The date should respect the format provided.

The image will be the image associated with the document on the website. We try using natural, high-resolution, evocative images having a link, if only figurative, with the topic covered. These images are stored in static/img/highres/. Do not forget to add and push this file as well, as it will be required for your post to be successfully integrated. The path to the file provided in the header assumes static/ as root folder (see example above), so that the right path will look like: img/highres/your-image.jpg.

The bibliography is optional. If provided, it should contain references cited in the document as a bibtex file (.bib). Do not forget to add and push this file as well, as it will be required for your post to be successfully integrated.

Slides cannot be rendered as usual html reports using blogdown. Instead, material for slides is stored in static/slides. Currently, two files are needed for a lecture:

1. a .Rmd post in content/post (see above) to introduce the lecture and link to the slides; for an example, look at content/post/lecture-reproducibility.Rmd.

2. the slides themselves, stored in static/slides.

For the slides, we recommended using .Rmd there again, as such slides will be automatically compiled and updated in real time when running blogdown::serve_site(). If your slides use images, store them in static/img/slides. You will be able to refer to them using ../../img/slides/your-image.jpg. For an example of rmarkdown+ioslides slides, look at static/slides/intro_reproducibility_Rmd/intro_reproducibility.Rmd.