Publications by csgillespie
Shiny benchmarks
A couple of months ago, the first version of benchmarkme was released. Around 140 machines have now been benchmarked. From the fastest (an Apple i7) which ran the tests in around 10 seconds, to the slowest (an Atom(TM) CPU N450 @ 1.66GHz) which took 420 seconds! Other interesting statistics: Around 6% of people ran BLAS optimised versions of R; ...
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RANDU: The case of the bad RNG
The German Federal Office for Information Security (BSI) has established criteria for quality random number generator (rng): A sequence of random numbers has a high probability of containing no identical consecutive elements. A sequence of numbers which is indistinguishable from true random’ numbers (tested using statistical tests. It should b...
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RStudio addins manager
RStudio addins let you execute a bit of R code or a Shiny app through the RStudio IDE, either via the Addins dropdown menu or with a keyboard shortcut. This package is an RStudio addin for managing other addins. To run these addins, you need the latest version of RStudio. Installation The package can be installed via devtools ## Need the latest ...
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R Courses at Newcastle
Over the next two months I’m running a number of R courses at Newcastle University. May 2016 May 10th, 11th: Predictive Analytics May 16th – 20th: Bioconductor May 23rd, 24th: Advanced programming June 2016 June 8th: R for Big Data June 9th: Interactive graphics with Shiny Since these courses are on advanced topics, numbers are limite...
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R Courses at London, Leeds and Newcastle
Over the next few months we’re running a number of R courses at London, Leeds and Newcastle. September 2016 (Newcastle) Sept 12th: Introduction to R Sept 13th: Statistical modelling Sept 14th: Programming with R Sept 15th: Efficient R: speeding up your code Sept 16th: Advanced graphics October 2016 (London) Oct 3rd: Introduction to R Oct 4...
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List of R conferences and useR groups
Recently Steph Locke asked on twitter if there was a list of R conferences. After some googling, all that I came up was a list of useR groups maintained by Microsoft. While the list was lengthy, it was missing a few groups (and twitter handles). So the other night I created a github repository listing conferences/groups. If you spot any missing g...
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benchmarkme Update
When discussing how to speed up slow R code, my first question is what is your computer spec? It always surprises me when complex biological experiments, costing a significant amount of money, are analysed using a six year old laptop. A new desktop machine costs around £1000 and that money would be saved within a month in user time. Typically th...
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Input/output benchmarks
To quantify the impact of the CPU on an analysis, I created the package benchmarkme. The idea is simple. If everyone runs the same R script, we can easily compare machines. One of the benchmarks in the package is for comparing read/write speeds; we write a large CSV file (using write.csv) and read it back in using read.csv The package is on CRAN...
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Training courses: R, Stan and Scala
Over the next few months we’re running a number of R, Stan and Scala courses around the UK. Feburary Mon 13 – Introduction to R (London) Tue 14 – Programming with R (London) Wed 15 – Advanced Graphics with R (London) Thur 16 (2-day course) – Predictive Analysis (London) March Tue Mar 21 – R for Big Data (Edinburgh) Mon Mar 27 – ...
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Security: the dangers of copying and pasting R code
Most of the time when we stumble across a code snippet online, we often blindly copy and paste it into the R console. I suspect almost everyone does this. After all, what’s the harm? Consider this simple piece of R code that performs simple linear regression # Generate data x = rnorm(10) y = rnorm(10) message(“All your base are belong to ...
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