Light

Sam Abbott photo

seabbs Goto Github PK

followers: 224.0 following: 342.0 repos: 111.0 gists: 57.0

Name: Sam Abbott

Type: User

Company: @epiforecasts @cmmid

Bio: Real-time infectious disease modelling. Developing tools and methods for outbreak response, routine surveillance, and pandemic preparedness.

Twitter: seabbs

Location: Bristol

Blog: samabbott.co.uk

Hi there 👋

I'm an infectious disease researcher interested in real-time analysis, forecasting, semi-mechanistic modelling, and open-source tool development.

NOW

Mostly working @Epiforecasts (part of the London School of Hygiene and Tropical Medicine);
Also supporting @CDC Centre for Forecast and Outbreak Analytics;
⭐ Contributing to the epinowcast community developing tools and methods for current surveillance of infectious disease and preparing for future outbreaks;
🧻 Currently working on:
- If we want an estimate of the reproduction number do we need the renewal process? and associated Julia modelling toolkit.
- Developing a workbench for real-time and outbreak infectious disease modelling
- Course materials on nowcasting, forecasting, and evaluation
- 😴 🔌 🐑

BIO

🏢 2024-: Assistant professor in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
🏢 2023-: Contractor supporting the CDC Centre for Forecast and Outbreak Analytics
🏢 2020-2023: Postdoc in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
🏢 2017-2019: Data Scientist at Funding Circle
📜 2016-2019: PhD at the University of Bristol on modelling the use of the BCG vaccine in the UK
⚙️ I use daily: R, julia, stan
🏗️ I like to perform analysis using novel models on interesting data and generalise those approaches into software 📦s
🌍 I'm mostly active within the epinowcast community
🌱 Learning all about Julia and Turing.jl - currently wondering why in the world you would use callables.
📘 Reading: Probability and random processes
💬 Ping me about statistical modelling of infectious diseases, real-time analysis of infectious diseases, estimating transmission dynamics in real-time, and team science opportunities
📫 Reach me: [email protected] prob

Sam Abbott's Projects

cv

Sam Abbott's Curriculum Vitae

data2019ncov

Data on the 2019 Novel Coronavirus Outbreak (R Package)

directeffbcgpolicychange

Estimating the effect of the 2005 change in BCG policy in England: A retrospective cohort study

dockeratfc

Presentation outlining the use of Docker for data analysis

dotfiles

Personal dotfile and configuration

ecdc-weekly-growth-forecasts

COVID-19 cases forecasts for the ECDC Forecast Hub

epict

epiline

Bayesian Modelling in Epidemiology Case Line Lists

epinowcast-fixed-reporting-example

An example of how to modify epinowcast to work with fixed reporting schedules.

epinowcast-mlghw-2023

Abstract for MLGH workshop 2023

estzoonotictb

Explore, Visualise and Estimate the Global Zoonotic Tuberculosis Burden

etsmissing

Explore and evaluate the mechanisms for missing data in the Enhanced Tuberculosis Surveillance system.

explorebcgonoutcomes

Analysis to explore the association of BCG vaccination and TB outcomes.

exploreidmodels

A shiny app which allows the exploration of the dynamics of a range of simple infectious disease models

exploreringbp

Exploring the feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

fc-gam-talk

Slides for a Talk introducing Generalised Additive Models and providing signposting

fcdashboard

Shiny dashboard for exploratory data analysis of the funding circle loanbook

forecastingglobaltb

Using WHO Tuberculosis data to forecast future incidence rates

funding_circle

visualisations and analysis of https://www.fundingcircle.com/uk/ loanbook

gam-uob-course

Docker container, and notebooks from the GAM workshop at the University of Bristol 26/06/18

gettbinr

An R package for accessing and summarising the World Health Organisation Tuberculosis data.

h2o_tweets

R code and log data for the h2o tweets twitter bot

h2ohelper

An R package containing utility functions to help with using the h2o package in R

hhh4-workshop

Workshop on hhh4 and the endemic-epidemic framework

hospitalization-nowcast-hub

Collecting nowcasts of the 7-day hospitalization incidence in Germany.

householdcontacttracing

hpru-blog-post-gettbinr

A blog post on getTBinR for the HPRU Evaluation of Interventions blog

huisman.epinow2.evaluation

Code for the manuscript "Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2"

ici3d-pkg

R package for DAIDD and MMED clinics

ici3d.github.io

International Clinics on Infectious Disease Dynamics and Data (ICI3D) Program

1
2
3
4

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.