+ - 0:00:00
Notes for current slide
Notes for next slide

Welcome to the R3 course!

1 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Please do these as we get ready:

  • ✅ Go to your assigned table and group (see list)

  • ✅ Introduce yourself to your group members

  • ✅ Re-install r3 remotes::install_gitlab("rostools/r3")

  • ✅ Accept the GitHub Organization invite by going to https://github.com/r-cubed-2020-06

2 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Question:

Before this course...

How many knew or have heard about reproducibility?

3 / 23

Raise your hands.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Question:

Before this course...

How many knew or have heard about open science?

4 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Question:

Before this course...

...or even open access, open data, open methods/protocols, or open source?

5 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

How many have read a method in a paper and wondered how they actually did it?

6 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

How many have read a method in a paper and wondered how they actually did it?

... you've probably realize by now, way more is done than shown in the "Methods"

6 / 23

Because you are trying to do the same or similar?

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Have you ever received confusing code? Or maybe have written your own confusing code?

7 / 23

I definitely have in my research career. We want to change the culture around code by encouraging and teaching how to share code and to write better code in general.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Code sharing: From scientific principle of "reproducibility"

... often confused with "replicability" [1]1

8 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Code sharing: From scientific principle of "reproducibility"

... often confused with "replicability" [1]1

Replicability

  • Repeating a study by independently performing another identical study
  • Difficult, usually needs funding
  • Linked to the "irreproducibility crisis"2
8 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Code sharing: From scientific principle of "reproducibility"

... often confused with "replicability" [1]1

Replicability

  • Repeating a study by independently performing another identical study
  • Difficult, usually needs funding
  • Linked to the "irreproducibility crisis"2

Reproducibility

  • Generating the exact same results when using the same data and code
  • Should be easy right? Wrong, often just as hard
  • Question: If we can't even reproduce a studies results, how can we expect to replicate it?
  1. Also from an American Statistical Association statement.
  2. Or rather "irreplicability crisis".
8 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Biomedical studies almost entirely don't publish code with the published paper

9 / 23

Very few papers provide code [2; 3]. Except maybe bioinformatics, where about 60% of studies do.

Why? Likely due to:

  • Lack of awareness and training
  • Difficulty of adoption
  • No incentive or reward
  • Little to no culture to do it
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

These issues can be fixed by creating and nurturing a culture of openness

10 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Goal of this course? Start changing the culture by providing the training

11 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Often asked: So why are we using R and why learn it?

  • Open source, free
  • Very large online community
    • Learning resources, support, help
  • Massive selection of packages
    • Latest statistical methods
    • Productivity tools
    • Report writing
    • Visualization
  • Recent push to improve teaching, usability
    • e.g. with tidyverse, RStudio
  • One of best visualization tools available
  • Powerful capabilities
    • Big Data
    • Programming
    • Reproducibility
12 / 23

Regarding it being free, that means that you can take the knowledge and skills for using R anywhere you go.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Course setup and layout

13 / 23

With the final group project, you'll be in the same group for the course, working together on it and on the final exercises. As a team, you'll help each other out with learning and overcoming any struggles, with of course our help too!

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Getting or asking for help 🙋

  • Put the sticky on your laptop to get help
    • There are lots of helpers
    • Team members, try to help out too
  • We're all learning here!
14 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Practice using stickies: Have you re-installed r3 and joined the GitHub Organization?

15 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Activity: Stand and arrange based on question

16 / 23

We're going to do a "stand and re-arrange yourself" activity based on some questions I ask.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Who has not yet used R?

17 / 23

Go into different corners for "yes" and "no".

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Those who've used R, how do you perceive your skill in R?

18 / 23

Along the wall, arrange to one side is "novice/basic" and other side is "advanced".

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Those who've used R, have you had formal training in "coding" in R or in general?

19 / 23

Raise hands.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Who has struggled with using R?

20 / 23

Raise hands.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

How do you perceive your general skill in data analysis?

21 / 23

Along the wall, arrange from "novice/basic" to "advanced".

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Get back into your groups and get to know each other a bit more

22 / 23

I've tried to organize the groups to include a range of skills and experiences, so there is a mix of novice and more experienced users.

So, as we prepare for the next session, introduce yourselves to the group and get to know each other more. You'll be relying on them for help, so find out who is the "more experienced" R user.

Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

References

[1] H. E. Plesser. "Reproducibility Vs. Replicability: A Brief History of a Confused Terminology". In: Frontiers in Neuroinformatics 11 (Jan. 2018). DOI: 10.3389/fninf.2017.00076.

[2] J. T. Leek and L. R. Jager. "Is Most Published Research Really False?" In: Annual Review of Statistics and Its Application 4.1 (Mar. 2017), pp. 109-122. DOI: 10.1146/annurev-statistics-060116-054104.

[3] E. C. Considine, G. Thomas, et al. "Critical Review of Reporting of the Data Analysis Step in Metabolomics". In: Metabolomics 14.1 (Dec. 2017). DOI: 10.1007/s11306-017-1299-3.

23 / 23
Danish Diabetes Academy Steno Diabetes Center Aarhus Aarhus University

Please do these as we get ready:

  • ✅ Go to your assigned table and group (see list)

  • ✅ Introduce yourself to your group members

  • ✅ Re-install r3 remotes::install_gitlab("rostools/r3")

  • ✅ Accept the GitHub Organization invite by going to https://github.com/r-cubed-2020-06

2 / 23
Paused

Help

Keyboard shortcuts

↑, ←, Pg Up, k Go to previous slide
↓, →, Pg Dn, Space, j Go to next slide
Home Go to first slide
End Go to last slide
Number + Return Go to specific slide
b / m / f Toggle blackout / mirrored / fullscreen mode
c Clone slideshow
p Toggle presenter mode
t Restart the presentation timer
?, h Toggle this help
Esc Back to slideshow