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AUGUST - Reproducible Research using R & other tools (with Rich FitzJohn)

  • Aug 26, 2014 · 6:00 PM
  • This location is shown only to members

This month we co-host with "The Statistical Society of Australia, NSW Branch". 

Arrive from  6pm for drinks, 6.30pm for talk & 7:30pm for finger food & networking. (The room is in use prior to 6pm.) 

Talk Outline: Reproducibility in research is increasingly called for, but carrying it out remains a challenge.  I will give a tour through the tools used in a recent real-life research project where we attempted to make the project reproducible from data acquisition to generating the manuscript.  These tools include the R packages "knitr" (for generating reports directly from R output) and "packrat" (for dependency management), as well as tools outside of R: make for pipeline management, git for version control, and travis for continuous testing of the research.  Our experience shows both the potential benefits of reproducible research, but also the challenges remaining in implementing it.

About the speaker: Rich FitzJohn is a computational biologist, currently based at Macquarie University.  His research interests are about reconstructing trait evolution and diversification over millions of years.  He has been using R in a research context for 10 years, and is the author of a number of packages for evolutionary analysis.  He also teaches R skills through Software Carpentry.

Co-host organisation: NSW branch of SSAI.

 

 

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  • Daniel F.

    During the meeting, someone asked Rich: "how do you find out about these tools, what journals do you read?" to which Rich answered "twitter". As several people seemed surprised by that answer, I thought I would enlarge on this: * Slides were posted on twitter after the talk (https://twitter.com/phylorich/status/504238092606128129)
    * Rich himself has over 500 followers on twitter, but in addition the tweet about his slides was retweeted 26 times. So in all the tweet was read over 4000 times (in the last week).
    * The slides themselves were then downloaded by more than 100 twitter users from around the world.

    September 1, 2014

  • Louise L.

    Thank you everyone for attending, and braving the rainy weather. Rich - thank you for presenting! We now have a better understanding of available tools to use with R with productionising our work.

    The presentation has also been uploaded to the member directory.

    1 · August 27, 2014

  • Vino

    Excellent

    August 27, 2014

  • A former member
    A former member

    August 26, 2014

  • Louise L.

    Hi everyone,
    Thank you for your interest. Space is limited for this presentation (65 members only). We now have 10 people on the waiting list (who have a very good chance of being able to attend) .

    I am closing the event to new RSVPs.
    Should you be sad to have missed out, we suggest you come back again 1-2 days prior to event. It might reopen to new RSVPs then.

    1 · August 13, 2014

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