macpan-workshop

Video Resources

This document describes videos about macpan2 that could be useful for workshop participants.

• Videos to Watch Before the Workshop (with exercises)
  • Required to Watch Before the Workshop
  • Potentially Useful to Watch Before the Workshop
  • Useful Workshop Preparation Exercises (not required)
• Additional Videos

Videos to Watch Before the Workshop (with exercises)

I’ve described some videos and related pre-workshop resources below. If you have any questions about these or anything else before the workshop, please leave a comment here. Note that commenting will require that you have a GitHub account, so either feel free to get one or just email me directly.

Required to Watch Before the Workshop

Please watch the following videos to prepare for the workshop (links are to Google Drive).

1. 5:06 minutes – Background and motivation for macpan2
2. 8:46 minutes – Specifying simple models
3. 8:28 minutes – Simulating from models

Code that is discussed in the videos is here.

Potentially Useful to Watch Before the Workshop

If you are not familiar with R or the tidyverse suite of packages, please consider watching the following videos from this video series.

1. R Programming: How to get started
2. How to Install R Packages
3. Data Science with the Tidyverse in R
4. Introduction to the Pipe Operator

Useful Workshop Preparation Exercises (not required)

The above videos give you the background to do the following exercises. It would be great if you did some of these before the workshop, but it is not required.

Create a model specification of an SEIR model.

Create a model specification of an elaboration of an SEIR model that has been modified for measles (diagram immediately following this box). This modified SEIR model includes a box for vaccinated individuals, $V$, and isolated infectious individuals, $I_{\text{iso}}$. The force of infection, $\mathrm{\Lambda }$, is given by $\frac{\beta I}{N}$, where $N$ is the total number of individuals in the population. The vaccine efficacy is $ϵ$ and the proportion of exposed individuals who isolate is $\theta$.

Specify a model that you use or are interested in.

Simulate one or more of the state variables in one of the above models. A challenge here will be to choose good default numerical values for the parameters and initial conditions.

In doing these exercises you might find it helpful to use the macpan2 website as a reference. Pages that could be particularly useful are the quick start guide and documentation for the mp_tmb_model_spec, mp_per_capita_flow, mp_simulator, and mp_trajectory.

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