seabbs
Real-time infectious disease modelling. Developing tools and methods for outbreak response, routine surveillance, and pandemic preparedness.
@epiforecasts @cmmidBristol
Pinned Repositories
covidregionaldata
An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisations, and tests. National level data is also supported using a range of data sources as well as linelist data and links to intervention data sets.
EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
forecast.vocs
Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluation of the use of sequence data for short-term forecasts in both real-world settings and in user generated scenarios.
scoringutils
Utilities for Scoring and Assessing Predictions
epinowcast
Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.
cv
Sam Abbott's Curriculum Vitae
getTBinR
An R package for accessing and summarising the World Health Organisation Tuberculosis data.
idmodelr
Infectious disease model library and utilities
thesis
PhD thesis submitted to the University of Bristol. Title: Modelling BCG vaccination in the UK: What is the impact of changing policy?
TweetRstudioCheatsheets
A Twitter bots which tweets a randomly selected Rstudio cheatsheet each day
seabbs's Repositories
seabbs/cv
Sam Abbott's Curriculum Vitae
seabbs/idmodelr
Infectious disease model library and utilities
seabbs/TweetRstudioCheatsheets
A Twitter bots which tweets a randomly selected Rstudio cheatsheet each day
seabbs/blogdown-site
Source code for my old personal website
seabbs/exploreidmodels
A shiny app which allows the exploration of the dynamics of a range of simple infectious disease models
seabbs/badtobetter
Better computational practice - Bad to better
seabbs/cste-forecasting-workshop
An approachable introduction to estimating the effective reproduction number. It's meant for any and all levels of comfort with writing code
seabbs/seabbs
Personal repository
seabbs/ecdc-weekly-growth-forecasts
COVID-19 cases forecasts for the ECDC Forecast Hub
seabbs/epinowcast-fixed-reporting-example
An example of how to modify epinowcast to work with fixed reporting schedules.
seabbs/epict
seabbs/presentations
A repository containing presentations that I have given or that I am in the process of writing
seabbs/regional-secondary
Prototype function for forecasting a secondary observation from a primary observation across multiple regions. An example application of this function can be found here: https://github.com/epiforecasts/covid-german-forecasts/blob/master/rt-forecast/update-death-from-cases.R. See the documentation of EpiNow2 for more details: https://epiforecasts.io/EpiNow2/dev/
seabbs/80-percent-good-enough
What is 80% good enough for real-time analyses during the COVID-19 pandemic
seabbs/covid19-forecast-hub-de
German and Polish COVID-19 Forecast Hub
seabbs/dotfiles
Personal dotfile and configuration
seabbs/EpiLine
Bayesian Modelling in Epidemiology Case Line Lists
seabbs/epinowcast-MLGHW-2023
Abstract for MLGH workshop 2023
seabbs/hhh4-workshop
Workshop on hhh4 and the endemic-epidemic framework
seabbs/hospitalization-nowcast-hub
Collecting nowcasts of the 7-day hospitalization incidence in Germany.
seabbs/ici3d-pkg
R package for DAIDD and MMED clinics
seabbs/ICI3D.github.io
International Clinics on Infectious Disease Dynamics and Data (ICI3D) Program
seabbs/ICRTC-methods
Methods for correcting the interval censoring and right truncation in time delays data
seabbs/post-processing-forecasts
seabbs/provoc
PROportions of Variants of Concern using counts, coverage, and a variant matrix.
seabbs/resources
seabbs/RPkg.jl
Julia Style Package Manager for RCall users
seabbs/seabbs.github.io
Personal website
seabbs/Term.jl
Julia library for stylized terminal output
seabbs/touchstone
Smart benchmarking of pull requests with statistical confidence