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toggle navigation home posts projects talks teaching contact tags cv phd student and data scientist bidd, university of bristol funding circle biography i am a mathematical modeller and data scientist interested in using data-driven approaches to develop models to help understand the world. i studied mathematics at the university of durham, completing an mmath degree in 2014. i then completed a masters in advanced mathematical biology at the university of york. as part of my thesis project, i spent a summer at the university of glasgow, studying the patterns of drug resistance in e-coli. across various species in tanzania. i am currently completing a phd in social medicine at the university of bristol, studying the deployment of the bcg vaccine in the uk. i also work as a data scientist at funding circle developing predictive models and conducting ad hoc analysis. interests mathematical modelling data science reproducible research r tuberculosis peer to peer lending education phd in social medicine, 2018 university of bristol msc in advanced mathematical biology, 2015 university of york mmath in mathematics, 2014 university of durham recent posts more posts fri, sep 28, 2018 6 min read r gettbinr 0.5.5 now on cran - 2017 data. gettbinr 0.5.5 is now on cran and should be available on a mirror near you shortly! this update is mainly about highlighting the availability of tb data for 2017, although some small behind the scenes changes were required to get the code set up going forward for yearly updates. a few more plotting options have been added, along with the corresponding tests (definitely the most exciting news). the full changelog is below along with a short example highlighting some of the changes in the 2017 data. continue reading wed, may 16, 2018 4 min read r gettbinr 0.5.4 now on cran - new data, map updates and a new summary function. gettbinr 0.5.4 is now on cran and should be available on a mirror near you shortly! this update includes an additional data set for 2016 containing variables related to drug resistant tuberculosis, some aesthetic updates to mapping functionality and a new summarise_tb_burden function for summarising tb metrics. behind the scenes there has been an extensive test overhaul, with vdiffr being used to test images, and several bugs fixes. see below for a full list of changes and some example code exploring the new functionality. continue reading wed, apr 11, 2018 25 min read r exploring tuberculosis monitoring indicators in england; using dimension reduction and clustering introduction i recently attended the public health research and science conference, run by public health england (phe), at the university of warwick. i was mainly there to present some work that i have been doing (along with my co-authors) estimating the direct effects of the 2005 change in bcg vaccination policy on tuberculosis (tb) incidence rates (slides) but it was also a great opportunity to see what research is being done within, and partnered with, phe. continue reading tue, feb 27, 2018 13 min read r exploring estimates of the tuberculosis case fatality ratio - with gettbinr this is a quick post exploring estimates of the case fatality ratio for tuberculosis (tb) from data published by the world health organisation (who). it makes use of gettbinr (which is now on cran), pacman for package management, hrbrthemes for plot themes, and pathwork for combining multiple plots into a storyboard. for an introduction to using gettbinr to explore the who tb data see this post. it is estimated that in 2016 there was more than 10 million cases of active tb, with 1. continue reading mon, jan 15, 2018 7 min read r exploring global trends in tuberculosis incidence rates - with gettbinr 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. continue reading projects * all r packages shiny apps tableau rstats phd courses p2p finance 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 . bidd modelling course the course practicals for the modelling infectious disease short course `run by bidd at the university of bristol. 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. since the original development of this dashboard funding circle has stopped publishing it’s full loanbook, this means that some functionality will no longer work as originally intended and that data will no longer be updated. 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 tuber

URL analysis for samabbott.co.uk

https://www.samabbott.co.uk/post/gettbinr-5-4/
https://www.samabbott.co.uk/./tags/tableau
https://www.samabbott.co.uk/talks/bidd_group_talk_18_03_06/presentation.html
https://www.samabbott.co.uk/./tags/course
https://www.samabbott.co.uk/./tags/clustering
https://www.samabbott.co.uk/./tags/outreach
https://www.samabbott.co.uk/./tags/personal-project
https://www.samabbott.co.uk/talks/phe-applied-epi-2018/presentation.pdf
https://www.samabbott.co.uk/./tags/deep-dive
https://www.samabbott.co.uk/./tags/gettbinr
https://www.samabbott.co.uk/talk/group_talk_17_08/
https://www.samabbott.co.uk/./#projects
https://www.samabbott.co.uk/./#contact
https://www.samabbott.co.uk/post/gettbinr-5-4/#disqus_thread
https://www.samabbott.co.uk/post/est-cfr-gettbinr/
bristol.ac.uk
seabbs.co.uk
phe-events.org.uk
bris.ac.uk

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