R In Physics

“reflecting on a decade of using R for data & science”

I’ve been using R for about 12 years for data analysis, numerical simulations, reporting, documentation, scripting, graphics, and random hobbies. Before that I dabbled in Matlab, Octave, etc.. I am increasingly looking at julia for my computational projects, but R is likely to remain my go-to language for the foreseeable future.

This post is basically a chaotic summary of my learning curve, contributions, frustrations, and thoughts. I’ll keep editing it as new thoughts/memories come to me. Below is a partial list of my interactions with the R ecosystem, which I’ve found instructive to reflect upon recently.

r packages

physics-related

cda

Coupled-dipole simulations for electromagnetic scattering of light by sub-wavelength particles in arbitrary 3-dimensional configurations.

This package uses RcppArmadillo to speed up linear algebra calculations on complex matrices.

Currently removed from CRAN, following an ever-recurring Lapack issue between R and Armadillo that I could not address at the time.

planar

Solves the electromagnetic problem of reflection and transmission of electromagnetic waves at a planar multilayer interface.

This package uses RcppArmadillo to speed up linear algebra calculations on complex matrices.

RcppFaddeeva

Access to a family of Gauss error functions for arbitrary complex arguments is provided via the ‘Faddeeva’ package by Steven G. Johnson

This package wraps the original library with Rcpp.

dielectric

Physical constants of use in optics.

mie

Numerical implementation of Mie scattering theory for light scattering by spherical particles.

raman

Custom utility functions to work with experimental data in the lab.

graphics-related

gridExtra

Provides a number of user-level functions to work with “grid” graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

egg

Misc. extensions for ggplot2.

ggExtra

(ca. 2009, now defunct) Misc. extensions for ggplot2 (first ggplot2 extension package)

proof-of-concept and private projects

caption

Extract legend items and weave them with the text of a figure caption.

ggflags

Implements a custom geom to map a country identifier to a raster flag image. Later generalised as egg::geom_custom.

flickr

Query flick api and generate static html pages for my photography website.

rip

[work in abandon] “R in physics” — book draft, expanding this post into different chapters.

tolstoy

[work in abandon] “toy tutorials on light scattering” — book draft, about electromagnetic scattering.

community

My interaction with the R community has always been virtual — I have tried going to / or even organising R meet-ups, but it’s always fallen through lamentably. And R is generally considered too weird in my physics circles.

misc uses

I’ve used R in various personal projects: to generate my websites, to automate Gandalf’s CV, or a recent poster creation, to produce interactive maps, lecture slides, assignments, etc.

Shiny apps

I’ve recently taken to producing interactive explorables with Shiny, to provide online calculators for various projects. Examples: SPR, Mie, port, etc.

talks and presentations

I have given several presentations about graphics, in which I occasionally included a few concepts from the Grammar of Graphics, illustrated with a bit of R code (or pseudo R code). The core message, however, was not about using the language.

review

I’ve reviewed a couple of articles about R graphics for the R Journal, mostly about grid if memory serves. I’ve also provided feedback on a couple of ggplot-related books.

misc. initiatives

I was briefly moderator and contributor to the short-lived ggplot2 blog.

I contributed a substantial portion of the content on the ggplot2 wiki, as well as unofficial documentation for gtable.

mailing lists & forums

R-help, R-devel (2009—2012)

Nabble lists 537 items under my name (Qs and As), which sounds about right. I left those lists years ago but they provided very useful information before SO and other platforms existed.

ggplot2 google group (2009—2014)

I left the group in 2014 but remain in the top 4 posters, with 383 contributions according to the site.

StackOverflow (2009—2017)

55,473 rep, mostly in R tag

923 answers

65 questions

I grew tired of some frustrating and unproductive interactions last year and am currently taking an indefinite break.

github (2008—)

89 repositories

4500 contributions since I joined

(870 + 1340 + 1212 + 684 + 76 + 200 + 182 + 14 + 2 + 1)

notable ideas, bug reports, and suggestions

R core

• (cannot remember anything noteworthy)

grid & graphics

• bug report: duplicate labels
• bug report: unit.list
• absolute.size, absolute.units
• subassignment methods for unit objects

Rcpp

• Xptr question
• modules use
• unit test, use of complex numbers

RcppArmadillo

• recurring discussion re support of complex numbers on various platforms

ggplot2

• many bug reports and suggestions through various channels
• first extension package in 2009 (ggExtra)
• grid.arrange
• dotplot grob
• top-aligned legend (I’ve lost my actual answer)
• defaults in themes
• guides as plots
• rasterise layers
• custom grobs in themes
• annotation_custom
• clipping
• align panels
• ggplotGrob

gtable

• docs
• tableGrob
• children grob
• bugs, issues

knitr

• chunk headers, more like R’s lazy formals?: triggered a new approach to handle chunk options
• first use as GH wiki
• reverse sync idea
• knit as a pandoc filter

thoughts for the future

• julia: more dots
• MKL
• complex numbers
• community
• pandoc
• d3, vega, gadfly

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