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Computing in R

This course is part of the PhD course program of the AMC Graduate School.

  • Location: Academic Medical Center, Amsterdam.
  • Course material: All course material is provided during the course, no need to print anything yourself
  • ECTS: 0.4
  • Teachers: Perry Moerland (coordinator), Aldo Jongejan and Michel Hof

Goal

R is a simple programming language for statistical computing. Due to its flexibility and the large variety of statistical functions available in R, it is a popular alternative for programs like SPSS. However, for a beginner mastering R can be rather difficult. This course helps the student to become familiar with the basics of R. After the course the student will be able to write short programs in R for basic (data) analyses and for plotting figures.

Schedule and course material

Location Day Time Topic Lectures Exercises Answers
L0-227 October 1, 2018 09.30-12.30   Handout Slides, Example code (R), Example code (Rmd), Example code (html) pdf pdf, R code
  October 1, 2018 12.30-13.30 Lunch break      
L0-227 October 1, 2018 13.30-16.30        
L0-227 October 4, 2018 9.30-12.30        
  October 4, 2018 12.30-13.30 Lunch break      
L0-227 October 4, 2018 13.30-16.30        

Datasets for the exercises

Information on R

  • R homepage
  • R and its packages can be downloaded from CRAN
  • Introductory material
    • Learn R interactively using swirl. Use their 'R Programming' course to refresh what you learnt in our course. There is also a web-based interface to swirl.
    • A basic introduction to R, somewhat in line with this course
    • Another short introduction to R with a nice list of common error messages (and how to maybe solve them) on the last page
    • This page shows the commands to be used for many aspects of a statistical analysis, and has been created especially for experienced users of some other statistical packages
    • Cookbook for R offers many great examples
    • Several on-line courses at the beginner and intermediate level with lots of exercises
    • Documentation for R packages organized by topical domains
    • Other sites to get you started are Impatient R and Statistics with R.
    • There is a book called "R for SAS and SPSS users''. The corresponding web site also has a freely downloadable early version of the book. It also has a comparison table that lists the corresponding R packages for many SAS and SPSS procedures.
  • Manuals (basic)
    • An introduction to R (pdf,html): R in 100 pages
    • R reference card: R in 6 pages
    • Other useful cheat sheets (for example, for ggplot2 and importing and transforming data via tidyr and dplyr) provided by the people at RStudio
  • Manuals (advanced)
    • R Data Import/Export (pdf,html)
    • R Language Definition (pdf,html)
    • Writing R Extensions (pdf,html)
    • R Installation and Administration (pdf,html)
  • Manuals (graphics)

Pointers

Information on Bioconductor

Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data in R. Much of data analysis in bioinformatics is done within the R/Bioconductor statistical environment. For example, many statistical methods for the analysis of microarray and other high-throughput data are available from Bioconductor.

Topic revision: r47 - 28 Sep 2018, PerryMoerland
 

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