R learning group in THL

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R learning group in THL is a self-organised group of researchers who need and want to learn R software. Most people work at the Department of Health protections in THL in Kuopio, Finland.

Topics of interest

These are topics of interest for some or most participants (in no particular order).

  • Next generation sequencing (NGS): how to manage the data, make analyses, and visualise results? Some ideas for solutions:
    • Vegan package (developed in Oulu) for diversity studies
    • Diversity index page in Opasnet for calculating alpha and beta diversity with different q values.
    • Chime, SAS: What are the functionalities, and what are respective solutions in R?
  • Exposure assessment and big data: how to manage exposure data (e.g. PM2.5 concentration fields) with millions of rows?
    • There are packages for huge array calculations. Five ways to handle big data in r
    • UEF Bioinformatics use R to handle big data, and they have developed packages for that. We should find out about this.
  • Health impact assessment is needed for environmental exposures: how to combine different data sources and make assessments coherent?
    • OpasnetUtils package has ovariable functionalities for this. The actual objects are defined on page Health impact assessment. There is a need for update, which will be done early 2017.
  • General additive models GAM: how to perform these?
    • Package gam [1]
    • Function gam in package mgcv [2]
    • Vaccination people use these things on routine basis, so we should ask them.

Shared practices

  • We use instant communcation in Slack
  • We document our projects and R code on relevant Opasnet pages.
  • We gather together more or less regurlarly. These are the topics for meetings:
    • 2.11.2016 10-11 (Kielo): get together and how to organise
    • 16.11.2016 8.30-10 (Kielo): basics of R (objects and how to use them; typical procedures). Speaker: Jouni

Current activities

Add your own activities
  • Create new pages in Opasnet as necessary

See also