Epidemiology with R

NovoNordisk Epidemiology, Tuesday 11 & Friday 14 August 2015

• Venue & time: Vandtaarnsvej, Tue 11: VTBK02; Fri 14: VTBK03
  09:00 - 16:30
• Topics covered:
  
  • R:
    • Data objects (vectors, data frames, ...)
    • Packages
    • Reading and writing data
    • Language
    • Functions
    • Graphics
  • Rates, survival function, etc.:
    Connection between all basic concepts from a probability point of view.
  • Estimating and showing smooth rates and RRs.
  • Lexis diagrams and representation of follow-up data
  • Splitting the follow-up.
  • Cox-modelling of rates.
  • Poisson modelling of rates.
  • Reporting rates and probabilities from models (demo).
• Lectures and computer practicals:
  
  • Bendix Carstensen, Senior Statistician, Steno Diabetes Center & Department of Biostatistics, University of Copenhagen, Denmark.
  • Dorte Vistisen, Senior Statistician, Steno Diabetes Center
• Course program. Also included in Computer practicals.
• Course material:
  
  • Slides in pdf-format and as 3-ups, 8-ups or 10-ups.
  • Overview of basic concepts in survival analysis. A compressed overview of essential quantities and their interrelations. Also included in Computer practicals.
  • Computer practicals Should be version 2.1.
  • Datasets.
  • R-programs.
• R topics:
  • Installing R on your computer:
    Go to http://mirrors.dotsrc.org/cran/bin/windows/base/ and download the latest version of R (3.2.1) and install it.
    
  • Getting the Epi package:
    Once you have installed / updated R install the Epi package using the menu button Packages and then Install packages or Update packages.
    
  • Finally, from inside R type:
    > library(Epi)
    > sessionInfo()
    - and you should be informed that you have version 3.2.1 of R and version 1.1.68 of the Epi package.
  • If you are not familiar with R, you can use "A work-book introduction to basic R" by Micheal Hills:
    First go here and click on the link "readme.fst" and follow the instructions.
  • A slightly more advanced text is A short introduction to R for epidemiology.
  • Mailing list: A mailing list for users of R in epidemiology has been set up.
    Join the list and use it for getting help with your R-problems: Join here.
• Papers of relevance in pdf-format:
  • Whitehead: Fitting Cox's regression model to survival data using GLIM.
  • Demography and epidemiology: Practical use of the Lexis diagram in the computer age or: Who needs the Cox-model anyway?
  • Lexis: An R Class for Epidemiological Studies with Long-term Follow-up.
  • Using Lexis Objects for Multi-state Models in R.
  • Rates and (competing) risks: Example calculations using Danish cause of death data.
  • Andersen et al.: Competing risks as a multi-state model.
  • Andersen et al.: Competing risks in epidemiology: possibilities and pitfalls.
  • Andersen & Keiding: Interpretability and importance of functionals in competing risks and multistate models.
• Other courses of similar content are here.