Biostatistics - Introduction to biostatistics (1st level)

Biostatistics: Introduction to biostatistics (1st level)

This course is part of the Plateforme Biostatistique de Toulouse training session: “Initiation à LA statistique, niveau 1”. The first session is scheduled for April 13-14th, 2016. More information (in French) can be found on this page.

The content of this course is basic statistics, illustrated with the software R through its graphical interface R Commander). The course covers the following topics:

  • probability and random variables

  • statistical inference

  • exploratory statistics in one and two dimensions, including plots

  • statistical tests

The course is taught by Sébastien Déjean (IMT, Université Paul Sabatier) and myself. This page gathers information about it and material to download.

Install R and R Commander

For this course, the installation of R and R Commander on your personal computer is required prior the beginning of the course. The installation steps are described below. In case of difficulty, please, contact me (emails preferred). This practical session has been prepared with R version 3.2.4 Revised (2016-03-16 r70336) – “Very Secure Dishes” and with R Commander version 2.2-3.

Install R

R can be downloaded for free on the official repository website. Choose the version depending of your OS (Windows, Linux or Mac). Mac users should also probably install tcltk which is available in the section called tools. Some linux users might also found R in their distribution repositories (this is the case for Ubuntu and Debian users; further details are provided at the beginning of this page).

Install R Commander

R Commander is better installed from within R:
  • start R (double clicking on its icon if you are a Windows or Mac user and type R in a terminal if you are a Linux user);
  • run the command line:
    install.packages("Rcmdr")
    (be careful that R is case sensitive) and choose a repository close to your location.

Additional installation for Linux users

Linux users need to install the Tcl package 'Tktable' (if it is not already installed). For Ubuntu and Debian users, this is done with:
sudo apt-get install tk-table
I don't know if a corresponding installation is required for other users...

Check your installation

At this step, all you need for the class should be installed. To check this, run the following command line in R
library("Rcmdr")
Your should see the window below (left) first (the package list can vary depending on which packages are already installed on your computer) for which you should answer "yes" (and additional packages are then installed, which can take a while). Then R Commander starts and the windows below (right) appears. You're done!

Materiel for the class

During the class, we will be using the dataset “nutrimouse” which is part of the R package mixOmics. Before the class, please, download the following files on your computer:

This reminder In French summarizes the main menus and R functions used during the practical session. A printed version will be provided at the beginning of the class.

Slides are available at this link.

Solutions…

The two following files are the results of our work:

  • a clean R script (updated March 3rd, 2017);
  • a full RData file with all data in R format (updated March 3rd, 2017);
  • the output file of R Commander (text format) (updated March 3rd, 2017).