# Why?

## January 20, 2017

Filed under: Computing, R — Tags: , — csgillespie @ 3:31 pm

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 can be installed in the usual way

install.packages("benchmarkme")

Running

library(benchmarkme)
## If your computer is relatively slow, remove 200 from below
res = benchmark_io(runs = 3, size = c(5, 50, 200))

creates three matrices of size 5MB, 20MB and 200MB, writes the associated CSV file to the directory

Sys.getenv("TMPDIR")

and then reads the data set back into R. The object res contains the timings which can compared to other users via

plot(res)

The above graph plots the current benchmarking results for writing a 5MB file (my machine is relatively fast).

## Shiny

You can also compare your results using the Shiny interface. Simply create a results bundle

create_bundle(res, filename = "results.rds")

## Network drives

Often the dataset we wish to access is on a network drive. Unfortunately, network drives can be slow. The benchmark_io function has an argument that allows us to change the directory and estimate the network drive impact

res_net = benchmark_io(runs = 3, size = c(5, 20, 200),
tmpdir = "path_to_dir")

## January 9, 2017

### benchmarkme Update

Filed under: Computing, R — Tags: , — csgillespie @ 8:36 pm

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 the more the RAM you have, the larger the dataset you can handle. However it’s not so obvious of the benefit of upgrading the processor.

To quantify the impact of the CPU on an analysis, I created the package benchmarkme. The aim of this package is to provide a set of benchmarks routines and data from past runs. You can then compare your machine, with other CPUs.

The package is now on CRAN and can be installed in the usual way

install.packages("benchmarkme")

The benchmark_std() function assesses numerical operations such as loops and matrix operations. This benchmark comprises of three separate benchmarks: prog, matrix_fun, and matrix_cal. If you have less than 3GB of RAM (run get_ram() to find out how much is available on your system), then you should kill any memory hungry applications, e.g. firefox, and set runs = 1 as an argument.

library("benchmarkme")
res = benchmark_std(runs = 3)

You can compare your results to other users via

plot(res)

My laptop is ranked around 50 out of 300. However, relative to the fastest processor, there’s not much difference.

## You can control exactly what is uploaded. See details below.

## Shiny

You can also compare your results using the Shiny interface. Simply create a results bundle

create_bundle(res, filename = "results.rds")

1. Your benchmarks from benchmark_std or benchmark_io;
2. A summary of your system information (get_sys_details()).

The get_sys_details() returns:

Sys.info();
get_platform_info();
get_r_version();
get_ram();
get_cpu();
get_byte_compiler();
get_linear_algebra();
installed.packages();
Sys.getlocale();
– The benchmarkme version number;
– Unique ID – used to extract results;
– The current date.

The function Sys.info() does include the user and nodenames. In the public release of the data, this information will be removed. If you don’t wish to upload certain information, just set the corresponding argument, i.e.

## November 1, 2016

### List of R conferences and useR groups

Filed under: Conferences, R — Tags: , — csgillespie @ 9:05 pm

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 groups or conferences, feel free to make a pull request at the GitHub Repository.

## April 22, 2016

### R Courses at Newcastle

Filed under: Computing, R, Teaching — Tags: , — csgillespie @ 7:09 pm

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 limited (there’s only a couple of places left on Predictive Analytics). If you are interested in attending, sign up as soon as possible.

Getting to Newcastle is easy. The airport is 10 minutes from the city centre and has direct flights to the main airport hubs: Schiphol, Heathrow, and Paris.  The courses at Newcastle attract participants from around the world; at the April course, we had representatives from North America, Sweden, Germany,  Romania and Geneva.

Cost: The courses cost around £130 per day (more than half the price of certain London courses!)

Onsite courses available on request.

## April 1, 2016

Filed under: Computing, R — Tags: — csgillespie @ 12:36 am

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

devtools::install_github('rstudio/DT')

After installing the package, the Addins menu toolbar will be populated with a new addin called Addin Manager. When you launch this addin, a DT table will be launched:

In the screenshot above, the highlighted addins, shinyjs and ggThemeAssit, indicate that this addins have already installed.

When you click Done

• Highlighted addins will be installed.
• Un-highlighted addins will be removed.

Simple!

Just fork and alter the addin file which is located in the inst/extdata directory of the package. This file is a csv file with three columns:

• Brief Description
• Package. If the package is only on github, use name/repo.

The initial list of addins was obtain from daattali’s repo.

## February 16, 2016

### RANDU: The case of the bad RNG

Filed under: Computing, R — Tags: , , — csgillespie @ 12:15 pm

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 be impossible to calculate, or guess, from any given sub-sequence, any previous or future values in the sequence.
• It should be impossible, for all practical purposes, for an attacker to calculate, or guess the values used in the random number algorithm.

Points 3 and 4 are crucial for many applications. Everytime you make a
phone call, contact to a wireless point, pay using your credit card random
numbers are used.

Designing a good random number generator is hard and as a general rule you should never try to. R comes with many good quality random generators. The default generator is the Mersenne-Twister. This rng has a huge period of $2^{19937}-1$ (how many random numbers are generated before we have a repeat).

## Linear congruential generators

A linear congruential generator (lcg) is a relatively simple rng (popular in the 60’s and 70’s). It has a simple form of

$r_{i}=(ar_{i-1}+b) \textrm{ mod }m, \quad i=1, 2, \ldots, m$

where $latexr_0$ is the initial number, known as the seed, and $$a,b,m$$ are the multiplier, additive constant and modulo respectively. The parameters are all integers.

The modulo operation means that at most $m$ different numbers can be generated
before the sequence must repeat – namely the integers $0,1,2, \ldots, m-1$. The
actual number of generated numbers is $h \leq m$, called the period of
the generator.

The key to random number generators is in setting the parameters.

### RANDU

RANDU was a lcg with parameters $m=2^{31}, a=65539$ and $b=0$. Unfortunately this is a spectacularly bad choice of
parameters. On noting that $a=65,539=2^{16}+3$, then

$r_{i+1} = a r_i = 65539 \times r_i = (2^{16}+3)r_i \;.$

So

$r_{i+2} = a\;r_{i+1} = (2^{16}+3) \times r_{i+1} = (2^{16}+3)^2 r_i \;.$

On expanding the square, we get

$r_{i+2} = (2^{32}+6\times 2^{16} + 9)r_i = [6 (2^{16}+3)-9]r_i = 6 r_{i+1} - 9 r_i \;.$

Note: all these calculations should be to the mod $2^{31}$. So there is a large
correlation between the three points!

If compare randu to a standard rng (code in a gist)

It’s obvious that randu doesn’t produce good random numbers. Plotting  $x_i$, $x_{i-1}$ and $x_{i-2}$ in 3d

### Generating the graphics

The code is all in a gist and can be run via

devtools::source_gist("https://gist.github.com/csgillespie/0ba4bbd8da0d1264b124")

You can then get the 3d plot via

scatterplot3d::scatterplot3d(randu[,1], randu[,2], randu[,3],
angle=154)
## Interactive version
threejs::scatterplot3js(randu[,1], randu[,2], randu[,3])

## February 15, 2016

### Shiny benchmarks

Filed under: Computing, R — Tags: , — csgillespie @ 5:49 pm

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;
• No-one (except for machines that I used) ran a byte compiled version of the package.

I intend to write to a blog post or two on BLAS and byte compiling, but for the meantime you can investigate the results via the new shiny interface. The package is still only available on github and can be installed via:

## Update the package
install.packages(c("drat", "httr", "Matrix", "shiny"))
install.packages("benchmarkme", type="source")

You then load the package in the usual way

library("benchmarkme")
## View past results
plot_past()
## shine() # Needs shiny
## get_datatable_past() # Needs DT

## This will take somewhere between 0.5 and 5 minutes
## Increase runs if you have a higher spec machine
res = benchmark_std(runs=3)

You can then compare your results other users

plot(res)
## shine(res)
## get_datatable(res)

## You can control exactly what is uploaded. See details below.

This function returns a unique identifier that will allow you to identify your results from the public data sets.

## December 1, 2015

### Crowd sourced benchmarks

Filed under: Computing, R — Tags: , — csgillespie @ 10:25 am

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 the more the RAM you have, the larger the dataset you can handle. However it’s not so obvious of the benefit of upgrading the processor.

To quantify the impact of the CPU on an analysis, I’ve create a simple benchmarking package. The aim of this package is to provide a set of benchmarks routines and data from past runs. You can then compare your machine, with other CPUs. The package currently isn’t on CRAN, but you can install it via my drat repository

install.packages(c("drat", "httr", "Matrix"))
install.packages("benchmarkme", type="source")

You can load the package in the usual way, and view past results via

library("benchmarkme")
plot_past()

to get

Currently around forty machines have been benchmarked. To benchmark and compare your own system just run

## On slower machines, reduce runs.
res = benchmark_std(runs=3)
plot(res)

gives

## You can control exactly what is uploaded. See the help page

The current record is held by a Intel(R) Core(TM) i7-4712MQ CPU.

## July 1, 2015

### useR 2015: Romain Francois: My R adventures

Filed under: R, useR 2015 — Tags: , — csgillespie @ 8:05 am

Using R since 2002 and has been working on Rcpp, Rcpp11, Rcpp14 and dplyr
internals. Worked on a number of big projects.

• 2005 he set up the R Graph Gallery
• 2009 worked on rJava
• 2010 Rcpp
• 2013 dplyr

Key themes are Performance and usabililty

## rJava 0.7-*

Creating objects was messy

d <-jnew("java/lang/Double", 42
.jcal(d, "D", "doubleValue)

### rJava 0.8-*

d <- new(J("java/lang/Double"), 42)
d\$doubleview

Also much easier to import java packages.

## Rcpp

Suppose you have

double add(double a, double b){ return a+b;}

and you want to use it in R. This used to be a lot of work. Before Rcpp, you
used the R/C Api, i.e. use SEXP. A lot of work and boilerplate. With Rcpp the
number of characters needed to translate the simple function above went from 250
to 50. Around 66% of CRAN packages depend (on some way) on Rcpp.

## RcppParallel (tbb: thread building blocks)

The package makes it much easier to run things in parallel. Amazingly, a simple
parallel version of sqrt is faster than sqrt

## dplyr (everyone knows what it does)

Uses hybrid evaluation. Looking to bring RcppParallel in the (near?) future.

Please note that the notes/talks section of this post is merely my notes on the
presentation. I may have made mistakes: these notes are not guaranteed to be
correct. Unless explicitly stated, they represent neither my opinions nor the
opinions of my employers. Any errors you can assume to be mine and not the
speaker’s. I’m happy to correct any errors you may spot – just let me know!

## July 13, 2012

### Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

Filed under: latex, Microarray, Publications, R — Tags: , , — csgillespie @ 2:32 pm

A few years ago I was involved in analysing some time-course microarray data. Our biological collaborators were interested in how we analysed their data, so this lead to a creation of tutorial, which in turn lead to a paper. When we submitted the paper, one the referees “suggested” that we write the paper using Sweave; I had never used Sweave. At the time this was a massive pain and I regularly cursed the name of the anonymous referee.  A few years later, I’ve just updated code (due to a change in Bioconductor) and it was a breeze. A belated thanks to the referee.

In this latest update to the paper I’ve

• moved the paper to github;
• changed from Sweave to knitr;
• used RStudio instead of emacs.

You can find details full details about analysis on the associated github page.

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