Articles by Will

Configuring Azure and RStudio for text analysis

July 1, 2018 | Will

I just finished teaching Computer-Assisted Content Analysis at the IQMR summer school at Syracuse. With three lecture and three labs the problem every year is getting the right R packages onto people’s machines. In particular, anything that involves compilation – and when you’re using quanteda, readtext, and stm, that’... [Read more...]

Packaging the TheyWorkForYou API

June 4, 2017 | Will

TheyWorkForYou is a great website for keeping up with British politics and one of the many fine things mySociety does to make democracy in the UK more transparent. There’s also an API, accessible via http and wrapped up for a few languages. However, R is not amongst them, so ... [Read more...]

Identifying the OS from R

June 10, 2015 | Will

Sometimes a bit of R code needs to know what operating system it’s running on. Here’s a short account of where you can find this information and a little function to wrap the answer up neatly. Operating systems are a platform issue, so let’s start with the ... [Read more...]

Getting R and Java 1.8 to work together on OSX

December 29, 2014 | Will

Hey Mac OSX users with Java 1.8 installed. Did R just request a Java 1.6 installation and then promptly crash your session?  If so, read on… The Problem A few days ago I was attempting to use the mallet package for topic models and I found that typing __ library(mallet) caused two ... [Read more...]

There is no Such Thing as Biomedical "Big Data"

February 11, 2014 | Will

At the moment, the world is obsessed with “Big Data” yet it sometimes seems that people who use this phrase don’t have a good grasp of its meaning.  Like most good buzz-words, “Big Data” sparks the idea of something grand and complicated, while sounding ordinary enough that listeners feel ... [Read more...]

More SOTU Scaling

January 30, 2014 | Will

A couple of days ago the Monkey Cage featured Ben Lauderdale’s one-dimensional scaling model of US State of the Union addresses. In this post, I replicate the analysis with a closely related model, ask what the scaled dimension actually means, and consider what things would look like if we ... [Read more...]

A Mitochondrial Manhattan Plot

November 6, 2013 | Will

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see significant results in the rough context of their genomic position.  Manhattan plots are typically shown on a l... [Read more...]

Call them what you will

October 28, 2013 | Will

I’ve been playing around with the R package texreg for creating combined regression tables for multiple models. It’s not the only package to do that – see here for a review – but it’s often handy to be able to generate both ascii art, latex, and html versions of ... [Read more...]

R to Latex packages: Coverage

March 12, 2013 | Will

There are now quite a few R packages to turn cross-tables and fitted models into nicely formatted latex. In a previous post I showed how to use one of them to display regression tables on the fly. In this post I summarise what types of R object each of the ... [Read more...]

Tools for making a paper

March 1, 2013 | Will

Since it seems to be the fashion, here’s a post about how I make my academic papers. Actually, who am I trying to kid? This is also about how I make slides, letters, memos and “Back in 10 minutes” signs to pin on the door. Nevertheless it’s for making ... [Read more...]

Quantifying the international search for meaning

February 9, 2013 | Will

Inspired by Preis et al.’s article Quantifying the advantage of looking forward, recently published in Scientific Reports (one of Nature publishing group’s journals), I wondered if similar big-data web-based research methods might address a question even bigger than how much different countries wonder about next year. How about ... [Read more...]

Show me the pdf already

February 1, 2013 | Will

You’ve got a pdf file and you’d like to view it with whatever the system viewer is. As usual, that requires something special for Windows and something general for the rest of us. Here goes… openPDF [Read more...]

No more ascii-art

January 24, 2013 | Will

At least fourfive R packages will turn your regression models into pretty latex tables: texreg, xtable, apsrtable, memisc, and stargazer.  This is very nice if you happen to be a latex document or its final reader, but it’s not so great if you’re making those models to start ... [Read more...]

Formulae in R: ANOVA and other models, mixed and fixed

January 10, 2013 | Will

R’s formula interface is sweet but sometimes confusing. ANOVA is seldom sweet and almost always confusing. And random (a.k.a. mixed) versus fixed effects decisions seem to hurt peoples’ heads too. So, let’s dive into the intersection of these three. I’m aware that there are lots ... [Read more...]

Unicode in R packages (not)

January 1, 2013 | Will

Perhaps you are trying to add your nice new object as data for an R package. But wait. It has [gasp] foreign letters in its dimnames, so ’R CMD check’ will certainly complain. What you need is something to turn R’s natural Unicode-processing goodness into a relic from the ... [Read more...]

R Markdown to other document formats

December 26, 2012 | Will

Perhaps you have a file written in Markdown with embedded R of the kind that RStudio makes so nice and easy but you’d like a range of output formats to keep your collaborators happy.  Say latex, pdf, html and MS Word.  Here’s what you might do I shall ... [Read more...]

Mapping SNPs to Genes for GWAS Enrichment Analysis

June 30, 2011 | Will

There are several tools available for conducting a post-hoc analysis of GWAS data looking for enrichment of significant SNPs using literature or pathway based resources. Examples include GRAIL, ALLIGATOR, and WebGestalt among others (see SNPath R Pac...
[Read more...]
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