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@stan-dev @paul-buerkner

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seabbs/README.md

Hi there 👋

I'm an infectious disease researcher interested in real-time analysis, forecasting, and semi-mechanstic modelling

NOW
BIO
  • 🏢 I'm currently working at London School of Hygiene and Tropical Medicine
  • 📜 I did my PhD at the University of Bristol (2019)
  • ⚙️ I use daily: R, 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 R Community
  • 🌱 Learning all about Julia and INLA
  • 📘 Rereading Regression and other stories and the Lord of the Rings (not at the same time).
  • 💬 Ping me about statistical modelling of infectious diseases, real-time analysis of infectious diseases, and estimating the effective reproduction number
  • 📫 Reach me: sam.abbott@lshtm.ac.uk

Pinned

  1. thesis Public

    PhD thesis submitted to the University of Bristol. Title: Modelling BCG vaccination in the UK: What is the impact of changing policy?

    C++ 8 1

  2. epiforecasts/EpiNow2 Public

    Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

    HTML 55 18

  3. epiforecasts/idbrms Public

    Population-level infectious disease modelling as an extension of brms.

    R 2 1

  4. epiforecasts/covidregionaldata Public

    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, hospitalisa…

    R 31 17

  5. epiforecasts/covid-rt-estimates Public

    National and subnational estimates of the time-varying reproduction number for Covid-19

    R 29 11

  6. epiforecasts/forecast.vocs Public

    Forked from jbracher/branching_process_delta

    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 evaluatio…

    R 2 1

5,621 contributions in the last year

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Contribution activity

October 2021

Created 174 commits in 15 repositories
Created 3 repositories

Created a pull request in epiforecasts/covid19-forecast-hub-europe that received 5 comments

2021-10-04 - EpiForecast submission

This is an automated submission.

+6,145 −0 • 5 comments
Opened 36 other pull requests in 8 repositories
epiforecasts/forecast.vocs 22 merged
KITmetricslab/covid19-forecast-hub-de 3 merged
epiforecasts/evaluate-delta-for-forecasting 3 merged
epiforecasts/universe 2 merged
epiforecasts/covid19-forecast-hub-europe 2 merged
seabbs/grumpy_slack_bot 2 merged
seabbs/eval-germany-sm-nowcasting 1 merged
jbracher/branching_process_delta 1 closed
Reviewed 19 pull requests in 6 repositories
epiforecasts/forecast.vocs 10 pull requests
epiforecasts/EpiNow2 5 pull requests
seabbs/eval-germany-sm-nowcasting 1 pull request
epiforecasts/covid 1 pull request
epiforecasts/covid.german.forecasts 1 pull request
epiforecasts/evaluate-delta-for-forecasting 1 pull request

Created an issue in epiforecasts/forecast.vocs that received 1 comment

Add tests of forecast functions

Add tests of forecast functions. Likely sensible to use memoise to keep runtimes low.

1 comment
Opened 21 other issues in 2 repositories
epiforecasts/forecast.vocs 8 closed 11 open
seabbs/eval-germany-sm-nowcasting 2 open
Started 1 discussion in 1 repository
epiforecasts/forecast.vocs
33 contributions in private repositories Oct 5 – Oct 21

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