Course Introduction

Prerequisites

Participants must be able to use a laptop/computer capable of running recent RStudio. See the Installation section below for more details.

Teachers

Szymon M. Kiełbasa, (smkielbasa@lumc.nl)
Ramin Monajemi, (rmonajemi@lumc.nl)
Mo Arkani (m.arkani@lumc.nl)

Goals

R is an open-source, free environment/language for statistical computing and graphics. It provides a large repository of statistical analysis methods.

The goal of the course is to teach students how the R language, extended by tidyverse package, can be used to build a report with a simple statistical analysis of data provided in a table. NOTE: This is not a statistics course! The course assumes no prior programming knowledge. Elementary statistics knowledge is necessary to understand examples.

After the course you will be able to:

Use R language expressions.
Use R to create simple data objects (vectors, lists) and change their content.
Apply R descriptive statistics functions to data in vectors.
Use R to read tables (tibbles), filter their rows, select/rename/add columns (with tidyverse/dplyr and tidyverse/tidyr).
Apply R descriptive statistics functions to summarize data from grouped table rows.
Use R to create scatter plots (with tidyverse/ggplot2).
Locate other methods for data manipulation or plotting.
Locate and install packages extending base R functionality (e.g. advanced statistical methods).
Explain R factors.
Use R Markdown to create a reproducible data analysis leading to a report (HTML, PDF, DOC).
Recognize and explain simple tidyverse-based R code written by others.

Course structure

The course is divided in 4 half-day interactive lectures followed by a 2 hour exam.

The slots

The topics are split in a number of small sections (a few per a half-day slot) and each section will have:

A short online introduction/demonstration.
A self/group-study practice session (with primary exercises end extra exercises).
Questions and Answers discussed in an online (live) chat channel.

The students are asked to type the commands being presented and observe their effects (avoid copy-paste; own typing is important in order to learn how R responds to mistakes).

The exam

There will be an exam. Please check the date and the location on the LUMC Onderwijsrooster/Studenten/Biomedische Wetenschappen/B1R.

During the exam you will need to prepare an R Markdown document reporting an analysis on a dataset. You will carry out the following steps:

Create an RStudio project and an R Markdown document.
Write R code to read a provided table.
Write R code to perform simple manipulations/analyses of the table or its columns.
Write R code to produce some plots of the table data.

During the exam it is allowed to use the course (or other) materials but it is strictly forbidden to communicate with other persons.

The extra exercises will not be part of the exam. They are elective and may contain more advanced topics.

Installation

Before the course prepare your computer.
NOTE: Resolving installation problems during the course may be impossible, therefore please follow the steps below a week before the start of the course. In case of failure, please inform the teachers. In some situations intervention of the administrator of your computer might be necessary.

Install R: Go to the R Project for Statistical Computing (https://www.r-project.org/) and follow the download and installation instructions.
Install RStudio: Go to the RStudio download page (https://www.rstudio.com/products/rstudio/download/#download), select a version of RStudio appropriate for your laptop, download it and then install. Please check whether you can start RStudio.

Some additional packages are needed for the course. During the course the participants will learn how to install packages but this process occasionally fails (because e.g.: additional steps are needed in a particular operating system, or there is lack of permissions to access some system directories, or other software is too old, …).

Install Rtools (Windows only!): During installation of some packages you may encounter the following error Rtools is required to build R packages but is not currently installed. If that is the case, follow the Rtools installation (https://cran.rstudio.com/bin/windows/Rtools/).
Install tidyverse package: Start RStudio. Go to menu Tools/Install Packages... In the field Packages select tidyverse. Press Install. (Now, a lot of messages will be shown in the Console window - wait till it finishes). In the Console window type library( tidyverse ) and press Enter. Some messages might be displayed but when there is no error the installation is completed.
Install packages needed for R Markdown: Start RStudio. Go to menu File/New File/R markdown.... A New R Markdown window is displayed. Press OK. Now, in case of missing R Markdown packages, you will be asked to install them. Finally, you will see an editor window with Untitled1 header. Put the cursor in that window, then click Knit. Some messages might be displayed but when later a window with some text and a plot is shown the installation is completed.

During the course applications in multiple windows will be used. For better experience we advice a setup with two monitors (e.g. laptop and an external monitor).

R Introduction →