MEB Advanced R group

Table of Contents

Meetings & presentations

TODO Reading: Advanced R - Non-standard evaluation   All Alex

<2017-11-09 tor 10:30>–<2017-11-09 tor 11:30>

DONE Reading: Advanced R - Functionals and Non-standard evaluation   All Alex

<2017-10-12 tor 10:30>–<2017-10-12 tor 11:30>

DONE Reading: Advanced R - Functional programming   All Mark Peter

<2017-09-28 tor 10:30>–<2017-09-28 tor 11:30>

DONE Reading: Advanced R - Debugging, condition handling, and defensive programming   All Johan

<2017-06-08 tor 10:30>–<2017-06-08 tor 11:30>

DONE Reading: Advanced R - Environments   All Alex

<2017-04-27 tor 10:30>–<2017-04-27 tor 11:30>

DONE Reading: Advanced R - OO field guide   All

<2017-03-30 tor 10:30>–<2017-03-30 tor 11:30>

  • Read & do the exercises in the OO field guide chapter before the meeting.
  • The material is available here:
  • Also, Alex will briefly go through something that came up during the previous meeting.
  • Location: Wargentin

DONE Reading: Advanced R - vocabulary, style and functions   All Andreas

<2017-02-23 tor 10:30>–<2017-02-23 tor 11:30>

DONE Reading: Advanced R - subsetting   All

<2016-06-21 tis 13:00>–<2016-06-21 tis 14:00>

DONE Reading: Advanced R - data structures   All

<2016-05-31 tis 09:00>–<2016-05-31 tis 11:00>

DONE R environments   Johan

<2016-05-12 tor 10:30>–<2016-05-12 tor 11:30>

DONE Robust variance   Arvid

<2016-04-21 tor 10:30>–<2016-04-21 tor 11:30>

  • Location: Tomtebodavägen 18A, Room: Marie

DONE Meetings <2016-03-31 tor>

Attendees

Xingrong, Elisabeth, Andreas, Nathalie, Henric, Arvid, Peter, Mark and Alex

Decisions

  • The meeting will take place every three weeks.
  • The meeting format will be casual with one person presenting (inspired by the applied biostat group).
  • There were also discussions regarding a reading group with particular interest in the Advanced R book http://adv-r.had.co.nz/.

Purpose of the meetings

There is a lot of knowledge and advanced usage of R within MEB. It would be nice to be able to share some of that knowledge. Preferably this could be done without creating too much extra work.

Potential topics pool

The assigned names here are only preliminary.

Making R-packages

Documentation

  • Roxygen
  • Rmarkdown

Testing

  • testthat
  • assertthat
  • r-travis

Debugging   Henric

  • traceback
  • debug
  • browser
  • trace
  • recover

http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf

Rcpp

  • Valgrind

Profiling   Henric

  • Rprof
  • lineprof
  • microbenchmark

Permutation test   Henric

  • coin package

Data analysis   Alex

  • Hmisc, multcomp, car
  • non-linear contrasts, car??

Work flow   Alex

  • literate programming

Splines   Xingrong

  • Xingrong

Extending R

Rcpp   Mark

  • Rcpp
  • Armadillo

JS   Andreas Tobba

rCharts, plotly, ggvis & htmlwidgets

Speeding up R

Multi-core   Henric

  • parallel, foreach, snow
  • openmp?

Multi-node

  • Rmpi, RHadoop

Compiled R code   Henric

Compiling R code using LLVM by Duncan Temple Lang: http://projecteuclid.org/download/pdfview_1/euclid.ss/1408368570

Plotting

ggplot2   Robert

More advanced version of Roberts student seminar

Data Management   Andreas

  • dplyr, data.table, sqldf and base
  • DB queries from R

General coding schemes

The distinction between functional OOP, as in S3 and S4, and Java/C++-style encapsulated OOP, as in Reference Classes and R6. Here’s a link to nice paper by John Chambers http://projecteuclid.org/download/pdfview_1/euclid.ss/1408368569 discussing these issues. For more on this, the paper has now grown into a book that’ll be published later this year: https://www.crcpress.com/Extending-R/Chambers/9781498775717

R classes and object oriented coding in R   Alex Henric

Hosting R processes   Andreas

  • shiny
  • opencpu

Server misc

  • rocker
  • Rstudio-server

Simulation

Bootstrapping

Reporting simulation results

  • Graph and table designs

Predictive modelling   Peter

Misc

  • GAMS
  • Imputation
  • R and version control

Read & discuss

Other activities

  • Introduce R to new users within MEB
  • Offer courses in R
  • Host Stockholm R useR (SRUG) group meetup at MEB
  • Reuse some study-group material for SRUG presentation

Author: Andreas Karlsson

Created: 2017-11-01 ons 10:19

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