• Start date:
  • 8 June 2021
  • Duration:
  • 4 days
  • Working as:
  • PhD

Prerequisites

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

Moreover, Zoom Client needs to be installed (please do not join in a browser window; we observe problems then).

Teachers

What we teach

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. The course assumes no prior programming knowledge. This is not a statistics course! Elementary statistics knowledge is necessary to understand examples.

After the course you will be able to:

  • Understand and write (tidyverse-based) R code.
  • Use R to perform statistical analyses of your own data tables.
  • Generate reproducible reports from your own data in HTML, PDF or DOC formats.

We will cover the following topics:

  • R expressions.
  • R data objects: vectors, data frames (tibbles), lists.
  • R Markdown for building reproducible reports.
  • Data manipulation: filtering, sorting, summarising of a table; joining/merging multiple tables (with tidyverse/dplyr and tidyverse/tidyr).
  • Visualisation: scatter plots, histograms, boxplots (with tidyverse/ggplot2).
  • R packages: installation and usage.

Course structure

The course is divided in 8 half-day slots (23-26.11.2020: morning slot 9:00-12:30 and afternoon slot 13:30-17:00).
The teachers are available for chatting online during all teaching slots.

The slots #1-#7: practicing

Each half-day slot is organised as follows:

  • the first 3h: online plenary room with a few small topics cycling as follows:
    • a short online (live video) lecture for introduction/demonstration,
    • a self-study practice session (with primary exercises end extra exercises) with chat interactions,
    • (when needed) a short chat question and live video answers session.
  • the last 30min: group breakout rooms; solving remaining exercises and chat/video interactions between all (participants and teachers).

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 slot #8: self study assignment

self study assignment (SSA) will be offered during the last (#8) slot. A set of tasks will be provided to be solved within 2 hours. After there will be a chat question and live video answers session.

The overall SSA goal will be to prepare an R Markdown document reporting an analysis of a dataset. You will carry out the following steps:

  • Create a RStudio project, knit a R Markdown document.
  • Read a table which will be provided.
  • Show some filtered/summarized content of the table.
  • Produce some plots of the data.

Installation

Before the course prepare your computer:

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, …). Resolving installation problems during the course may be impossible, therefore please try to follow the steps below. In case of failure, please inform the teachers during the first day of the course.

  • install package tidyverse: 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.
  CONCEPT PROGRAM
  Tuesday 8 June 2021
08:30 Online registration
09:00 Lectures
12:30 Break
13:30 Lectures
17:00 End of day 1

 

  Wednesday 9 June 2021
08:30 Online registration
09:00 Lectures
12:30 Break
13:30 Lectures
17:00 End of day 2
  Thursday 10 June 2021
08:30 Online registration
09:00 Lectures
12:30 Break
13:30 Lectures
17:00 End of day 3

 

  Friday 11 June 2021
08:30 Online registration
09:00 Lectures
12:30 Break
13:30 Lectures
17:00 End of day 4
dr. S.M. Kielbasa
Leids Universitair Medisch Centrum (LUMC)
R. Monajemi
(Wetenschappelijk) onderzoeker Leids Universitair Medisch Centrum (LUMC)
Online
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Participation is free of charge* for students of the Leiden University or VU University:

  • If you have filled in your student number and use your student email address to subcribe 
  • If you are present every day of the course
  • Please note that we have limited access for students and a fee will be charged to students who do not attend courses or who are too late cancelling their participation of the course.
Course fee € 450,-
Employees LUMC / VUmc / Prinses Maxima Hospital € 150,-
Students of the Leiden University or VU University Free of charge*