EpiModel

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Next read the lecture notes
Next read the lecture notes
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[https://drive.google.com/file/d/1lCrks24hCS-QJ2nzh6qCbcZRHRgbtqow/view?usp=sharing 202Clecture0 (Part 1)],
+
[https://drive.google.com/open?id=1G7Pf3S5hxnZeqrZb9ZKAxayfoEXPNZvD 202Clecture0 (Part 1)],
<i>Modeling the effects of public health interventions on COVID-19 transmission</i> which are adapted notes from
<i>Modeling the effects of public health interventions on COVID-19 transmission</i> which are adapted notes from
[https://timchurches.github.io/blog/posts/2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 work by Tim Churches].
[https://timchurches.github.io/blog/posts/2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 work by Tim Churches].
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Next, work through the tutorial [http://statnet.org/nme/d1-s2.pdf Deterministic Compartmental Models]. This is the <u>discrete time</u> version of the SIR model from the lecture notes [https://drive.google.com/file/d/1lCrks24hCS-QJ2nzh6qCbcZRHRgbtqow/view?usp=sharing 202Clecture0 (Part 1)].
+
Next, work through the tutorial [http://statnet.org/nme/d1-s2.pdf Deterministic Compartmental Models]. This is the <u>discrete time</u> version of the SIR model from the lecture notes [https://drive.google.com/open?id=1G7Pf3S5hxnZeqrZb9ZKAxayfoEXPNZvD 202Clecture0 (Part 1)].
Next, work through the tutorial [http://statnet.org/tut/BasicDCMs.html Basic DCMs with EpiModel]
Next, work through the tutorial [http://statnet.org/tut/BasicDCMs.html Basic DCMs with EpiModel]
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Next, work through the lecture notes
Next, work through the lecture notes
-
[https://drive.google.com/file/d/1Y7jb3_RDv2X4baFmRuRhuQ-brtqaD1Pi/view?usp=sharing 202Clecture0 (Part 2)],
+
[https://drive.google.com/open?id=1Y7jb3_RDv2X4baFmRuRhuQ-brtqaD1Pi 202Clecture0 (Part 2)],
which are also adapted notes from
which are also adapted notes from
[https://timchurches.github.io/blog/posts/2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 work by Tim Churches].
[https://timchurches.github.io/blog/posts/2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 work by Tim Churches].
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The  next lecture notes cover some possible interventions. To see these work through  
The  next lecture notes cover some possible interventions. To see these work through  
-
[https://drive.google.com/file/d/19Ju6J1bumUgtGRyMk0gRdJ6K7PJsY9N6/view?usp=sharing 202Clecture0 (Part 3)] and
+
[https://drive.google.com/open?id=19Ju6J1bumUgtGRyMk0gRdJ6K7PJsY9N6 202Clecture0 (Part 3)] and
-
[https://drive.google.com/file/d/1Q15tlE7h_rgdBPVHpTY-dSmlRczLDuYe/view?usp=sharing 202Clecture0 (Part 4)].
+
[https://drive.google.com/open?id=1Q15tlE7h_rgdBPVHpTY-dSmlRczLDuYe 202Clecture0 (Part 4)].
If you want to run the models yourself, use the Rmarkdown (Rmd) files at the end. They are best run in Rstudio.
If you want to run the models yourself, use the Rmarkdown (Rmd) files at the end. They are best run in Rstudio.
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<h2><strong> Lecture notes (PDF) </strong></h2>
<h2><strong> Lecture notes (PDF) </strong></h2>
{|
{|
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|[https://drive.google.com/file/d/1lCrks24hCS-QJ2nzh6qCbcZRHRgbtqow/view?usp=sharing Lecture 0 (Part 1) (PDF)]  
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|[https://drive.google.com/open?id=1G7Pf3S5hxnZeqrZb9ZKAxayfoEXPNZvD Lecture 0 (Part 1) (PDF)]  
|-
|-
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|[https://drive.google.com/file/d/1Y7jb3_RDv2X4baFmRuRhuQ-brtqaD1Pi/view?usp=sharing Lecture 0 (Part 2) (PDF)]  
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|[https://drive.google.com/open?id=1Y7jb3_RDv2X4baFmRuRhuQ-brtqaD1Pi Lecture 0 (Part 2) (PDF)]  
|-
|-
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|[https://drive.google.com/file/d/19Ju6J1bumUgtGRyMk0gRdJ6K7PJsY9N6/view?usp=sharing Lecture 0 (Part 3) (PDF)]
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|[https://drive.google.com/open?id=19Ju6J1bumUgtGRyMk0gRdJ6K7PJsY9N6 Lecture 0 (Part 3) (PDF)]
|-
|-
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|[https://drive.google.com/file/d/1Q15tlE7h_rgdBPVHpTY-dSmlRczLDuYe/view?usp=sharing Lecture 0 (Part 4) (PDF)]
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|[https://drive.google.com/open?id=1Q15tlE7h_rgdBPVHpTY-dSmlRczLDuYe Lecture 0 (Part 4) (PDF)]
|}
|}

Revision as of 06:50, 3 April 2020

Contents

Introduction to COVID-19 Epidemic modeling via EpiModel

These notes are a simple introduction to

In these notes we develop mathematical and stochastic models of the local epidemic spread of COVID- 19 infection. These stochastic compartmental models are implemented by the EpiModel software package. EpiModel is built on the R statistical language. In these notes we will examine the effect of various public health interventions on the epidemic spread.

Suggested course

I suggest you first view the first video.

These follow the tutorial Introduction to Network Modeling. It is a quite an introductory level and so you can work through it quickly, but it get some basic concepts across.

Next read the lecture notes 202Clecture0 (Part 1), Modeling the effects of public health interventions on COVID-19 transmission which are adapted notes from work by Tim Churches.

Next, work through the tutorial Deterministic Compartmental Models. This is the discrete time version of the SIR model from the lecture notes 202Clecture0 (Part 1).

Next, work through the tutorial Basic DCMs with EpiModel and through the tutorial Basic ICMs with EpiModel

Next, work through the lecture notes 202Clecture0 (Part 2), which are also adapted notes from work by Tim Churches.

The PDF are narrated in the video so you can view the videos after reading the PDF notes.

The next lecture notes cover some possible interventions. To see these work through 202Clecture0 (Part 3) and 202Clecture0 (Part 4).

If you want to run the models yourself, use the Rmarkdown (Rmd) files at the end. They are best run in Rstudio.

Lecture notes (PDF)

Lecture 0 (Part 1) (PDF)
Lecture 0 (Part 2) (PDF)
Lecture 0 (Part 3) (PDF)
Lecture 0 (Part 4) (PDF)

Videos of Lectures

Deterministic Compartmental Models (NME d1-s2) (Part 1) (mp4)
Lecture 0 (Part 1) (mp4)
Deterministic Compartmental Models (NME d1-s2) (Part 2) (mp4)
Deterministic Compartmental Models (NME d1-s2) (Part 43)(mp4)

Lecture notes (source code as Rmarkdown)

Lecture 0 (Part 1)(Rmd)
Lecture 0 (Part 2)(Rmd)
Lecture 0 (Part 3)(Rmd)
Lecture 0 (Part 4)(Rmd)
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