In the field of public health, there is a need to access health and healthcare-related data much faster than ever before. A pertinent example of this is the current coronavirus outbreak (COVID-19). In early February 2020, merely days after the first cases were confirmed in the UK, the Department of …

For the second year in a row, I was invited to speak at the annual Conference on Retroviruses and Opportunistic Infections (CROI). This year the conference was held in one of my favourite cities, Seattle. I spoke about my new web-based modelling tool that enables countries to enter data on their HIV …

Right from the start of my PhD, I was keen to avoid leaving the “writing up” stage until the last moment. After hearing stories from other students of 24-hour stints in the library and solid weekends spent slaving over their theses in the final months, I figured there must be another …

Thanks to Hadley’s ggplot2 package, we are no longer confined to base graphics plots in R. However, by default all fonts are generated using the ‘Helvetica’ family. Now this is a great sans serif font, as evidenced by the fact that it is use literally everywhere in everything. But …

As we progress toward the end of the fourth decade of the HIV epidemic, substantial progress has been made in reducing the morbidity and mortality of those living with HIV12, particularly due to the availability of antiretroviral therapy (ART)3. However, we must pause, and assess the current state …

Lately, I have been working on developing a friendly shiny app around a mathematical model to enable non-modellers to get to grips with the model, play around and perhaps learn something too. This has really been as much about teaching myself Shiny as it has been about enabling others to interact …

I was recently invited to speak at the annual Conference on Retroviruses and Opportunistic Infections (CROI), held this year in Boston. I spoke briefly about some of my work on home-based counselling and testing programmes in western Kenya, particularly with regard to the timing of testing rounds …

I have always been interested in how these automated personal assistants: Siri, Google Now, Cortana etc. actually function. Aside from the speech recognition algorithms, the meaning of the sentence spoken to these programs must be deciphered and then acted upon pretty quickly. ‘Trigger’ …

Overview Having owned an Apple Watch since early May, I have built up a substantial amount of data in Apple’s ‘HealthKit’, detailing my daily steps from in excess of a year prior to owning the watch to at least six months after. Therefore, a simple analysis of whether the watch has …

As part of a new work package I am part of, we needed to develop a dynamic transmission model of HIV care that has a relatively user-friendly interface and that can be run on almost any device. The initial choice was to go with an Excel spreadsheet, and have a tab hidden in the background with the …

Having just watched the latest Apple keynote, I have to admit at being quite impressed at the latest products. Even John Gruber got it wrong! After flat-out claiming there would be no iPadPro announcement, there we have it! But the internet seems rather pre-occupied by the smile issue, and the …

After spending several hours today trying to figure out how to call R from an instance of Python running on the departmental cluster, I figured that I better document this. Why bother? Some background on my problem. I have an individual-based model written in C++ that describes the HIV epidemic in …

I wanted to document some code for accessing documents (only spreadsheets at the moment) through GoogleDocs using the DIDE cluster and R. Getting started. The R code is fairly self explanatory but involves two little tricks to get it to work: (1) manipulating the GoogleDocs URL to export the …

Taking comfort in the fact that I am sure that nobody will read this site except me, I have decided to procrastinate by writing something about a problem, or perhaps I should say challange that I am currently facing. To add some background, I have written an individual-based time-to-event model that …