Instructor Notes

Instructor notes

Contact matrices

R

# Generate the contact matrix for Zambia only
contact_data_zambia <- socialmixr::contact_matrix(
  survey = zambia_sa_survey,
  countries = "Zambia", # key argument
  age.limits = c(0, 20),
  symmetric = TRUE
)

OUTPUT

Removing participants without age information. To change this behaviour, set the 'missing.participant.age' option

OUTPUT

Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option

R

# Print the contact matrix for Zambia only
contact_data_zambia

OUTPUT

$matrix
         contact.age.group
age.group   [0,20)      20+
   [0,20) 3.650000 1.451168
   20+    1.988136 2.461856

$demography
   age.group population proportion  year
      <char>      <num>      <num> <int>
1:    [0,20)    8006201  0.5780636  2010
2:       20+    5843835  0.4219364  2010

$participants
   age.group participants proportion
      <char>        <int>      <num>
1:    [0,20)          180 0.08490566
2:       20+         1940 0.91509434

R

# Print the vector of population size for {epidemics}
contact_data_zambia$demography$population

OUTPUT

[1] 8006201 5843835

Simulating transmission

Instructor Note

By the end of this tutorial, learners should be able to replicate the above image on their own computers.

Choosing an appropriate model

Instructor Note

The focus of this tutorial is understanding existing models to decide if they are appropriate for a defined question.

In this tutorial different types of intervention and how they can be modelled are introduced. Learners should be able to understand the underlying mechanism of these interventions (e.g. reduce contact rate) as well as how to implement the code to include such interventions.

Comparing public health outcomes of interventions

Instructor Note

In this tutorial we introduce the concept of the counter factual and how to compare scenarios (counter factual versus intervention) against each other.

Comparing vaccination strategies

Modelling disease burden

Instructor Note

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”.