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In November I attended Epidemics, which is a conference focused on modelling infectious diseases. There was a lot of great work and perhaps most excitingly a lot of work being offered as R packages. I’ve recently begun wrapping all my analytical work in R packages, as it makes producing reproducible research a breeze! Unfortunately all of this work is still making it’s way towards publication and for a variety of reasons can’t be shared until it has passed this hurdle.

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This interactive dashboard uses data on Tuberculosis incidence from 1913-1916 released by Public Health England and combines it with data on the interventions against Tuberculosis that have been discovered/implemented over the last century. The data was cleaned and imported into R using the tbinenglanddataclean R package, which also contains information on how to apply for additional data, scripts to clean data extracts and graphing functions to visualise them. The dashboard is a work in progress and additional interventions, new figures and increased interactivity will be added over time.

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Previously I have looked at visualising the Property Partner portfolio using tableau, and explored their resale date from July 2017. In this post I will be exploring the August Open House resale data focussing on property premiums over both initial and latest valuation. The code for this post is available here. Property Partner advertises returns by combining both projected capital and rental returns. Properties are held for 5 years at which point any capital gain can be realised.

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As peer to peer lending matures platforms have begun to have increasingly divergent stances on sharing their data, making it increasingly important that their is external pressure on them to improve their data sharing. This blog series will focus on platforms sharing their data, exploring what their data is saying and suggesting possible changes to their releases that would make it easier for investors to gain insights on their own.

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The Pebble Game is a shiny application that simulates a simple game which has been designed to reflect real world epidemics and the vaccination programmes used to control them. It involves repeatedly drawing pebbles from a bag, which contains two distinct pebble types (to represent vaccinated and unvaccinated individuals). The number of pebbles that are drawn each round is dependent on the number of infect-able (i.e unvaccinated) cases drawn in the previous round, and the infectiousness of the simulated disease.

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Projects

Explore Global Tuberculosis

A shiny app showcasing the functionality of getTBinR. It allows the exploration of the global burden of Tuberculosis. Any metric in the WHO data can be explored, with country selection using the built in map, and animation possible by year. Source code available here.

Explore Infectious Disease Models

This shiny app has been developed to allow the exploration of the parameter space of compartmental infectious disease models. It is designed to be used as a teaching aid when introducing people to the concepts behind infectious disease models without requiring them to interact with the underlying code. A number of infectious disease models are included, such as a Susceptible, Exposed, Infected, Recovered model. Source code available here.

Show Me Perseus

A shiny app to remove potential friction for new R users when using the R perseus package. Source code available here.

getTBinR

Quickly and easily import analysis ready TB burden data, from the World Health Orgnaisation (WHO), into R. The aim of the package is to speed up access to high quality TB burden data, using a simple R interface. Generic plotting functions are provided to allow for rapid graphical exploration of the WHO TB data. This package is inspired by a blog post, which looked at WHO TB incidence rates. See here for the WHO data permissions.

Introduction to TB Modelling

A shiny app reproducing the models used in the Introduction to Tuberculosis modelling course practicals, run by TB MAC at the 2017 Union conference. See the TB MAC website for course materials and further resources. The models used in this course, and reproduced in this shiny app, were based on one published by Lin et al.. The source code is available on here

Tuberculosis in England and Wales

A shiny dashboard providing interactive plots of Tuberuclosis Incidence in England and Wales using publicly available data. The source code is available on here

Property Partner Portfolio Visualisation

A series of Tableau dashboards visualising the Property Partner portfolio

FC Dashboard

FC dashboard is a simple tool for exploratory data analysis on the funding circle loanbook. The source code can be found here. This is an independant project and is in no way associated with funding circle.

idmodelr

R package that contains utility functions for infectious disease modelling. It’s main functionality is to facilitate the use of other available modelling packages such as pomp. Although, it does offer some basic modelling functionality itself. The source code is available on here

The Pebble Game

The Pebble Game is a shiny application that simulates the pebble game. This is a simple game that has been developed by BIDD at the University of Bristol, to help a general audience understand the role of vaccination in preventing the onward transmission of infectious disease. The source code can be found here.

Funding Circle Data Anaylsis

Visualisation and analysis of the Funding Circle loanbook.

PhD: Research Aims

Summary of the research aims for my PhD thesis

prettypublisher

R package to help in formatting R markdown documents into a publishable format. The source code is available on here

tbinenglanddataclean

R package containing the scripts required to clean data from the Enhanced Tuberculosis Surveillance system, and the Labour Force Survey, and to then calculate Tuberculosis incidence. The source code is available here

Teaching

I am helping to develop practicals for a short course at the School of Social and Community Medicine at the University of Bristol. As part of this I am developing a shiny app to allow exploration of a range of simple infectious disease models.

Contact

  • [email protected]
  • BF8, Oakfield House, School of Social and Community Medicine, University of Bristol