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intro-pmcmc's Introduction

Introduction to Particle Markov chain Monte Carlo (PMCMC)

Supplementary materials related to Endo et al. "Introduction to particle Markov-chain Monte Carlo for disease dynamics modellers" (https://doi.org/10.1016/j.epidem.2019.100363).

Main files

  • rwmodel.Rmd/.html

    Rmarkdown to reproduce the random-walk model example described in Section 2.1 of the paper.

  • pmcmcTutorial.Rmd/.html

    Quick overview of PMCMC with a few examples, including the Read-Frost model example (Section 3.1) in the paper.

  • dureauLibbi.Rmd/.html

    Dureau model example (Section 3.2) in the paper.

Licence

MIT

Authors

Akira Endo, Edwin van Leeuwen, Marc Baguelin

intro-pmcmc's People

Contributors

akira-endo avatar blackedder avatar mjomaba avatar

Stargazers

LI YICHI avatar avatar Yasuo Kabe avatar avatar Hannah Waddel avatar Owain  gaunders avatar Fabienne Krauer avatar Michael DeWitt avatar Matthew Begun avatar Christophe Vuong avatar avatar Sean avatar Sam Abbott avatar

Watchers

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Forkers

abhisheksena w-mohammed baoyinyuan shakir507

intro-pmcmc's Issues

pmcmcTutorial.Rmd/.html

Maybe a silly question! I can run almost code in 'pmcmcTutorial.Rmd/.html', but when I run this:

inference_results<-RF_PMMH(simuRF$Y, PBar=F, p0=0.0001)

there is an error:

Error in if (lU < cumWj) { : missing value where TRUE/FALSE needed

Could you please give me some suggestion? Thank you!

README details

It would be really great to have some guidance in the readme as to what is where. It isn't that hard to work out which parts link to what in the paper but it would be nice not to have to think!

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