This repo is the basis for the bookdown reader of the "Exploratory Data Analysis & Data Mining" Course of the Master of Informatics at HU University of Applied Sciences, Utrecht, The Netherlands.
The materials in this repo are under CC BY-NC 4.0 licence. Meaning you can use and adapt these materials for non-commercial ends as long as you provide proper credits and attribution to the copyright holder and the referenced sources (Marc A.T. Teunis, HU - 2021).
The material in this repo is a bookdown project. When you clone the repo to your local computer and you have R and RStudio installed, run the commands below to get a local html version of the book in the root of the cloned github repo. Open the project as an RStudio Project:
install.packages("bookdown")
bookdown::render_book()The repo was developed to work with R version above or equal to version 4.0. If you want to learn which R packages are used as dependencies, you can take a look at the DESCRIPTION file in this repo. We advise developing and working with R in RStudio. You can download R and RStudio from these links:
To run the code in this repository we recommend a system with at least 8 cores and 16 Gb of RAM. Building of the reader could consume even more resources and was preformed on a UBUNTU Virtual Machine running R Version: 4.1.1 (2021-08-10) -- "Kick Things" and RStudio Version: Version 1.4.1717 . This machine had
To work with Docker you need to have a Docker Deamon installed. See the Docker homepage for more details
To work with Git and to be able to clone repositories you need Git installed. See the Git homepage for details.
{devtools}In order to install the edamoi as a package, you need to have the R packages {devtools} and {rmarkdown} available from your R environment. Run install.packages(c("devtools", "rmarkdown)) from the R Console to install it. Please be aware that for Linux based OS you will probably need underlying system dependencies to install {devtools}. Refere to the Public RStudio Package Manager page for {devtools}, to find the system requirements for your OS.
This repo is basically an R package and a bookdown site. To provide a reproducible way to deploy the content on your preferred device/online, a Dockerfile is also included. The Dockerfile defines a Docker image that can be used to run and further develop the materials in RStudio and to build the bookdown site. If you are familiar with Docker, I advise you to look at section Docker. Below a step-wise instruction on how to get the materials and how to build the book. These steps assume you have all prerequisites listed above.
A1. Clone the edamoi repo by running git clone https://github.com/uashogeschoolutrecht/redamoi. Pay attention that you are in a location where you want the folder 'redamoi' to land. For example 'Users/myname/myRprojects/'
A2. Go to RStudio and initiate a new RStudio project from the redamoi folder you created in step 1
A3. From the R Console (the R command line) in your 'redamoi' RStudio Project, run devtools::install("."). This installs all neccessary requirements (R package dependencies) for the bookdown project. This will enable you to build the reader for the course locally and run all the code.
A4. When all dependencies are installed, you will see a notification on the R Console that should look something like this:
Running /usr/local/lib/R/bin/R CMD INSTALL /tmp/RtmpYatPJy/edamoi_0.2.tar.gz \
--install-tests installing to library '/home/rstudio/R/aarch64-unknown-linux-gnu-library/4.0'
installing source package 'edamoi' ... using staged installation R data inst byte-compile and prepare package for lazy loading help * installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path
DONE (edamoi)
If you experience any problems with this step, create an issue in this repo explaining what happended and we will try to reach out to solve it.A5. You are now ready to build the bookdown site locally. Run bookdown::render_book(".") in the R Console. This will genererate a stand alone html site version of the reader in a folder called '_book'. You can view the bookdown site by opening the '_book' folder and opening the 'index.html' file in a browser.
For users that want to create a Docker container running RStudio with a compatible version of R and all the dependencies as well as a pre-build version of the bookdown reader already available in the container:
docker build . -t redamoiThis will build the required Docker image locally. Once finished you will be able to run the container with the next command.
B4. To run the Docker container with the contents of the repo mounted inside the container run:
docker run -d -p 8787:8787 -v <full_path_to_local_redamoi_cloned_dir>:/home/rstudio -e PASSWORD=abcd redamoi
Change the password if you like. You will now be able to login into the running Docker container by pointing your webbrowser to local address: http://localhost:8787/. Login with username rstudio and password <your_password_of_choice>.
There are many more options to the docker run command. See the Rocker project or Rocker on Docker Hub for more use cases.
The base image for the Docker image used here was derived from this repo: https://github.com/elbamos/rstudio-m1. It is optimized for users on Mac with M1 Apple Silicon Chipset. I have not tested this Docker image on other OS or Mac Intel. Please file an issue if you are experiencing any problems.