R Applied to Epidemiology and Infectious Disease in Glasgow

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Antonio Hegar, organizer of the R Glasgow user group (also on Twitter), shared with the R Consortium his efforts to build an R community in Glasgow. He discussed the widespread use of R in Glasgow across a broad range of fields and stressed the need to bring together R users for knowledge sharing. He also shared his work as an epidemiologist with the Ministry of Health in Belize for reporting COVID-19-related data for public policy and planning. 

Antonio Hegar, Epidemiologist | Health Data Scientist | Public Health Researcher

Please share about your background and involvement with the RUGS group.

I am a Ph.D. student at Glasgow Caledonian University here in Scotland. My Ph.D. is focused on Machine Learning applied to large health databases, in other words, big data. Before starting my Ph.D. I worked for over five years at the local Ministry of Health in Belize, which is where I am from. R has been my primary statistical tool because of all the functionalities it offers. I come from an epidemiology/public health background and use R for my analyses. 

I came over to the UK at the end of the pandemic in late 2021, and like many people, I was stuck at home due to all the restrictions. Nevertheless, I wanted to reach out and learn as much as possible about R from the respective experts across a broad range of fields and I knew that in Glasgow there is a very large R community. So I started looking around and found the R Glasgow group on Meetup and decided to give it a try. I joined, and luckily enough Andrew Baxter was organizing it at that time along with other members. I attended a few online meetings which were very productive and I have been following it up ever since. Since the beginning of this year, I have tried to be more active in the group by organizing events.

Please share about a project you are currently working on or have worked on in the past using the R language. Goal/reason, result, anything interesting, especially related to the industry you work in?

I have worked at the Ministry of Health in Belize using R and R Markdown to generate reports for COVID-19 outbreaks. So basically I applied mathematical modeling to infectious diseases which in this case was COVID-19, and made forecasts. My mathematical model took data from the local Ministry of Health and forecasted hospitalization rates, infection rates, and mortality rates. All this information was compiled into a report which was used by local officials and the Ministry of Health for planning. 

What resources/techniques do/did you use?

As I mentioned, I used R Markdown for generating reports. As you might be aware that at the height of the pandemic, every country had a dashboard. I used Shiny for creating private dashboards displaying public health data for the Ministry of Health. Besides that, I also used the tidyverse and dplyr a lot. 

I also did data imputation because whenever you are working with real-life data, especially public health data, there are a lot of gaps. So data imputation using mice and different R packages help you fill in the gaps in the data. 

ggplot is another tool I used a lot for this project. When you are dealing with a non-technical audience you need really easy-to-understand charts and graphs which will help them easily and quickly understand what you are trying to display. So I did a lot of data visualization with ggplot and was constantly trying to look at new techniques to make data as attractive as possible. 

Can you share what the R community is like in Glasgow and Scotland in general? 

To be very honest with you, my response would be that I cannot really speak about it. As much as I have tried engaging, and of course, I am a member of the local R group, it’s proven to be much more difficult than I anticipated to actually have a cohesive understanding of the wider R community. 

What I could say from what I have noticed from looking at university websites and looking at the profiles of different lecturers and researchers is that R is definitely used across the board in all of the major universities in Glasgow. I imagine it’s the same in many other major cities like Edinburgh in Scotland. So there are people using it for modeling, geospatial analysis, public health, epidemiology, finance, and economics. 

I have met online or seen the profiles of many people who claim to be using R. But in terms of community or the lack of community, it’s all very dispersed at the moment. Which is another point that I wanted to discuss. On the surface, it appears that there is a lot of support and a lot of enthusiasm for using R at the individual as well as research department levels. But in terms of forming a cohesive group where people will come together and share ideas, that hasn’t been as forthcoming as I would have wanted. It’s less of an R community, in my point of view, and more of a network of R users with different nodes around the place. But not necessarily a functioning complete organization. 

I would like to take this opportunity to reach out to R users living in Glasgow. R Glasgow can provide R users in Glasgow with a great opportunity to learn and grow together. I would also like to give a call for speakers. As we are hosting our events online, we would love to have speakers from around the globe join our events. 

How do I Join?

R Consortium’s R User Group and Small Conference Support Program (RUGS) provides grants to help R groups around the world organize, share information and support each other. We have given grants over the past four years, encompassing over 65,000 members in 35 countries. We would like to include you! Cash grants and meetup.com accounts are awarded based on the intended use of the funds and the amount of money available to distribute. We are now accepting applications!

The post R Applied to Epidemiology and Infectious Disease in Glasgow appeared first on R Consortium.

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