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Day2 L1

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8 views19 pages

Day2 L1

Uploaded by

Mado Saeed
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Day 2

Lecture 1:
Introduction to
infectious disease
modelling
Short course on modelling infectious disease dynamics in R
Ankara, Türkiye, June 2023

Dr Juan F Vesga

1
Aims of the session
• To Understand what do we mean by infectious disease models
• Introduced core concepts of infectious diseases dynamics
• Familiarize with existing types of ID models

2
[Widely repeated quote goes here ]

…and it is true!

3
What are models
• Some models intend to infer conclusions as we accrue
more data
• Most statistical models -> the model emerges from the data !

• Some models intend to describe a mechanism behind a


phenomenon
• Mathematical models
• Used for example in weather, physics, engineering, ecology,
and infectious diseases!

4
We need to understand the
phenomenon
• Weather: very predictable -> laws of physics

• Infectious diseases -> very complex!

• Biology of the pathogen


• Clinical characteristics
By definition a multidisciplinary field (all are welcome!)
• Host behaviour
• Population dynamics

5
So how does an ID model looks like?
For most people …

Danger!
complicated
stuff inside
Data of all shapes
Shiny model output
and colours !

Let’s unpack this black box (in three days!)

6
So how does an ID model looks like?
How it really looks…
A dynamic component!

Ia
𝜆𝛿
S
1−𝛿 Is
Carefully selected
A design of our A model projection
data to fuel
our mechanism phenomenon
described with maths

7
What type of data inputs?
Let’s imagine a cohort where
Given we understand the infected individuals become
mechanism we want to describe: symptomatic

Infected
𝜃 Symptomatic
• Model inputs are the
pieces of information
(facts) that bind together
our model design.
1
• We need statistics to 𝜃=
12 𝑑𝑎𝑦𝑠
interpret these binding
links.

8
What do we need to design a
mathematical model?
• Some maths
• For compartmental models we use ordinary differential
equations (ODEs)
• Some statistics : for summarising model inputs and for
processing model results

9
Ordinary differential equations
(ODEs)
• Mathematics used to describe change of a system, e.g:
speed (distance/time) :
Change in
distance

Change in
time
• At a steady speed of 70mph how far can we get in 2
hours? Solve :
•
• We will review this further applied to infectious diseases!
10
What about compartments?
• The previous example requires one single function
• We are interested in ODE systems with more than one state

𝑑𝐼
=− 𝐼 ( 𝑡 ) 𝜃
Infected
𝜃
Symptomatic
𝑑𝑡
𝑑𝑆
=𝐼 ( 𝑡 ) 𝜃
𝑑𝑡
• It is clear that this system describes the average behaviour
for such phenomenon

11
How we produce model output ?
• Back to our previous system

𝑑𝐼
=− 𝐼 ( 𝑡 ) 𝜃
𝑑𝑡 Numerical
integration using
𝑑𝑆 a software , R !
=𝐼 ( 𝑡 ) 𝜃
𝑑𝑡

12
What is the output?
• Is the integration of our
system over a time period
• We project the value of
our state variables (I and
Sy) over 60 days
• We don’t predict since
our results come from a
simplified systems and
assumptions
• Prediction is for statistics!
13
What about uncertainty in our
results?

Ia
𝜆𝛿
S
1−𝛿 Is
Uncertainty
Uncertainty Results in uncertainty
in the inputs
in the system around our projections

We can explore this range


If we introduce stochasticity
by calibrating our parameters

14
Types of mathematical models
• Deterministic • Stochastic
• A same set of model • A same set of model
parameters will always parameters can produce
produce the same results
different results
• The results are strictly
determined by the parameter • The results combine the
values given a system input and randomness in
• E.g., an infected individual the events of transition
will always develop symptoms • E.g., an infected individual
at an average rate . can or cannot develop
• We will focus on these !! symptoms out of chance.
15
Types of mathematical models
• Compartmental • Individual
• Describe the system of • Simulate individuals
interest at the population • Easier to code
level
• Harder to interpret
• Are good to understand
the average behaviour of • Computationally
a phenomenon expensive
• Easier to interpret • Require much more data
• Sometimes hard to code!

16
Focus in this short course
• We are interested in public health, not in maths!

• We want to apply mathematics and statistics to


understand infectious diseases

• These methods have a strong role in the current


landscape of public health and can help improve global
health!

17
Roles of transmission models in public
health

Supporting healthcare delivery

Info
rmi
n gd
ecis
ion
-m akin
g
Basic science: contributing
to evidence base for policy

18
What we should know by now
• What is a mathematical model
• What are the building blocks of models
• What are the basic maths for describing a model
• What types of mathematical models there are
• How can models contribute to public health

19

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